Topic: Putting Limits on the Diversity of Life
Member # 1201
posted 10. April 2004 18:30
Putting Limits on the Diversity of Life.
(Part Four. Continued... 3)
Philos Trans R Soc Lond B Biol Sci. 2002 Apr 29;357(1420):471-92. Host races in plant-feeding
insects and their importance in sympatric speciation. Dres M, Mallet J.
"We recognize host races as kinds of species that regularly exchange genes…" "Host races provide a convenient, although admittedly somewhat arbitrary intermediate stage along the speciation continuum." "We apply this criterion to 21 putative host race systems. Of these, only three are unambiguously classified as host races, but a further eight are strong candidates that merely lack accurate information on rates of hybridization or gene flow. Thus, over one-half of the cases that we review are probably or certainly host races, under our definition."
Nature. 2002 May 23;417(6887):440-3. Host-plant adaptation drives the parallel evolution of
reproductive isolation. Nosil P, Crespi BJ, Sandoval CP.
"The parallel evolution of reproductive isolation provides strong evidence for natural selection in the process of speciation, but only one… example from nature is known. Populations of the walking-stick insect Timema cristinae…" "…divergent selection for host adaptation, and not genetic drift…"
Genome Res. 2002 May;12(5):729-38. Structure and evolution of the Smith-Magenis syndrome repeat gene clusters, SMS-REPs. Park et al.
"The SMS-REP LCRs are highly homologous (>98%) and contain at least 14 genes/pseudogenes each. SMS-REPs are not present in mice [but in primates]"
Evolution Int J Org Evolution. 2002 Mar;56(3):597-616. Discovery and phylogenetic analysis of a riverine species flock of African electric fishes (Mormyridae: Teleostei). Sullivan et al.
"The evolution of species-specific mate recognition signals is of particular interest within speciose
monophyletic groups with restricted distributions (known as "species flocks"). However, the explosive nature of speciation in these clades makes difficult the reconstruction of their phylogenetic history" "…we recognize 38 forms that are distinct in their morphologies and electric organ discharge (EOD) characteristics. Of these 38, only four clearly correspond to described species" "…we infer an incongruence between the mitochondrial gene tree and the organismal phylogeny…"
Evolution Int J Org Evolution. 2002 Mar;56(3):527-45. Divergence of mitochondrial dna is not corroborated by nuclear dna, morphology, or behavior in Drosophila simulans. Ballard et al.
"Evidence presented in this study suggests that mtDNA is not a good indicator of organismal subdivision in D. simulans. Furthermore, there is no evidence to suggest that Wolbachia causes any reduction in nuclear gene flow in this species. The observed differentiation in mtDNA is not corroborated by data from NADH: ubiquinone reductase 75kD subunit precursor or the Alcohol dehydrogenase-related loci, from the shape or size of the male genital arch, or from assortative premating behavior." "We conclude with an iterated appeal to include phylogenetic and statistical tests of neutrality as a supplement to phylogenetic and population genetic analyses when using mtDNA…"
Mol Biol Evol. 2002 Jul;19(7):1100-13. Contrasting rates of mitochondrial molecular evolution in
parasitic Diptera and Hymenoptera. Castro LR, Austin AD, Dowton M.
"Relative rate tests indicated generally that the parasitic lifestyle was not associated with an
increased rate of genetic divergence in the Diptera but reaffirmed that it was in the Hymenoptera.
Similarly, a departure from compositional stationarity was not associated with parasitic Diptera but was in parasitic Hymenoptera. Finally, mitochondrial (mt) gene rearrangements were not observed in any of the dipteran species examined. The results indicate that these genetic phenomena are not accelerated in parasitic Diptera compared with nonparasitic Diptera."
Proc R Soc Lond B Biol Sci. 2002 Jun 22;269(1497):1301-5. The evolution of parasites from
their hosts: intra- and interspecific parasitism and Emery's rule. Lowe RM, Ward SA, Crozier RH.
"…either the rarer or the commoner species may become the parasite…"
Trends Genet. 2002 May;18(5):259-64. The rise and fall of SRY. Marshall Graves JA.
"…it is dispensable, having been lost at least twice independently in different rodent lineages."
Philos Trans R Soc Lond B Biol Sci. 2002 Apr 29;357(1420):493-503. Bird song, ecology and
speciation. Slabbekoorn H, Smith TB.
"The study of bird song dialects was once considered the most promising approach for investigating the role of behaviour in reproductive divergence and speciation. However, after a series of studies yielding conflicting results, research in the field slowed significantly. Recent findings, on how ecological factors may lead to divergence in both song and morphology, necessitate a re-examination. We focus primarily on species with learned song, examine
conflicting results in the literature and propose some potential new directions for future studies." "In analysing the role of song learning in reproductive divergence, we focus on post-dispersal plasticity in a conceptual framework."
Syst Biol. 2000 Sep;49(3):383-99. Seabird and louse coevolution: complex histories revealed by 12S rRNA sequences and reconciliation analyses. Paterson AM, Wallis GP, Wallis LJ, Gray RD.
"The number of cospeciation events was significantly more than would be expected from chance alone (P < 0.01)"
To be Continued....
[ 12. April 2004, 17:40: Message edited by: Fernando Castro-Chavez ]
Member # 1201
posted 10. April 2004 18:35
Putting Limits on the Diversity of Life.
(Part Four. Continued... 4)
Trends Parasitol. 2002 Mar;18(3):121-4. When is a parasite species a species? Kunz W. [Comment in: Trends Parasitol. 2002 Oct;18(10):439-40; author reply 440.]
“Regrettably, 140 years after the publication of Darwin's Origin of Species, we face the grotesque situation that we still do not know what is a species whose origin Darwin wanted to explain.”
Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6714-9. A locus for female discrimination behavior causing sexual isolation in Drosophila. Doi et al.
“The genetic basis of sexual isolation that contributes to speciation is one of the unsolved questions in evolutionary biology.”
Science. 2001 Mar 2;291(5509):1742-8. Genetic clues to dispersal in human populations: retracing the past from the present. Cann RL
“Because of automated technologies and linkage analysis, we are poised to harvest a wealth of information about our past, if we are successful in moving beyond a current polarization regarding models of human evolution. Rather than just suggesting that true resolution will only come by considering fossil or archaeological evidence, the realistic and appropriate application of genetic models for analysis of population structure is also necessary.”
Nature. 2001 Feb 8;409(6821):707-10. Wolbachia-induced incompatibility precedes other hybrid incompatibilities in Nasonia. Bordenstein SR, O'Hara FP, Werren JH. [Comment in: Nature. 2001 Feb 8;409(6821):675-7.]
“Wolbachia are cytoplasmically inherited bacteria that cause a number of reproductive alterations in insects, including cytoplasmic incompatibility, an incompatibility between sperm and egg that results in loss of sperm chromosomes following fertilization. Wolbachia are estimated to infect 15-20% of all insect species, and also are common in arachnids, isopods and nematodes. Therefore, Wolbachia-induced cytoplasmic incompatibility could be an important factor promoting rapid speciation in invertebrates, although this contention is controversial.” “The presence of Wolbachia severely reduces the frequency of hybrid offspring in interspecies crosses. However, antibiotic curing of the insects results in production of hybrids. Furthermore, F1 and F2 hybrids are completely viable and fertile, indicating the absence of F1 and F2 hybrid breakdown [between the parasitic wasps Nasonia giraulti and Nasonia longicornis].”
Evolution Int J Org Evolution. 2001 Jun;55(6):1077-84. Perspective: From mutants to mechanisms? Assessing the candidate gene paradigm in evolutionary biology. Haag ES, True JR.
“Examples come from both plants and animals, and range from intraspecific to interordinal taxonomic ranges. The use of mutationally defined candidate genes to predict evolutionary mechanisms has so far been most fruitful in explaining intraspecific variants, where it has been effective in both plants and animals. In several cases these efforts were facilitated or supported by parallel results from quantitative trait loci studies, in which natural alleles controlling continuous variation in developmental model organisms were mapped to mutationally defined genes. However, despite these successes the approach's utility seems to rapidly decay as a function of phylogenetic distance. This suggests that the divergence of developmental genetic systems is great even in closely related organisms and may become intractable at larger distances. We discuss this result in the context of what it teaches us about development, the future prospects of the candidate gene approach…”
Trends Genet. 2002 Feb;18(2):74-82. Genome architecture, rearrangements and genomic disorders. Stankiewicz P, Lupski JR.
“An increasing number of human diseases are recognized to result from recurrent DNA rearrangements involving unstable genomic regions. These are termed genomic disorders, in which the clinical phenotype is a consequence of abnormal dosage of gene(s) located within the rearranged genomic fragments. Both inter- and intrachromosomal rearrangements are facilitated by the presence of region-specific low-copy repeats (LCRs) and result from nonallelic homologous recombination (NAHR) between paralogous genomic segments. LCRs usually span approximately 10-400 kb of genomic DNA, share >or= 97% sequence identity, and provide the substrates for homologous recombination, thus predisposing the region to rearrangements.”
Heredity. 2001 Nov;87(Pt 5):522-9. Multiplicity of infection and the evolution of hybrid incompatibility in segmented viruses. Frank SA.
“Some viral genomes are divided into segments. When multiple viruses infect a single cell, progeny form by reassorted mixtures of genomic segments. Hybrid incompatibilities arise when a progeny virus has incompatible segments from different parental viruses. Hybrid incompatibility has been observed in influenza and in the multiparticle plant virus Dianthovirus.” “This paper presents mathematical and computer simulation models to study hybrid incompatibility between diverging strains. The models identify multiplicity of infection as a key factor. When many viral particles infect each host cell, the effective ploidy of the genetic system is high. High ploidy dilutes the contribution of each locus to the phenotype, weakening the selective intensity on each locus. Weaker selection on variant alleles allows the population to maintain greater genetic diversity and to be more easily perturbed by stochastic fluctuations. Greater diversity and stochastic fluctuations explore more widely the space of epistatic interactions, causing more frequent shifts among favoured combinations of alleles. Variable ploidy of viral genetics differs from standard Mendelian genetics.”
Proc R Soc Lond B Biol Sci. 2001 Dec 22;268(1485):2515-23. Ancient mitochondrial DNA and morphology elucidate an extinct island radiation of Indian Ocean giant tortoises (Cylindraspis). Austin JJ, Arnold EN.
“…extinct vertebrates, the endemic tortoises (Cylindraspis) of the Mascarene Islands in the Indian Ocean. Mitochondrial DNA corroborates morphological evidence that there were five species of tortoise…” “The history of Mascarene tortoises contrasts with that of the Galapagos, where only a single species is present and surviving populations are genetically much more similar. However, they too show some reduction in anti-predator mechanisms and multiple development of populations with saddlebacked shells.”
Toxicon. 2001 Dec;39(12):1899-916. Venomous cone snails: molecular phylogeny and the generation of toxin diversity. Espiritu DJ, Watkins M, Dia-Monje V, Cartier GE, Cruz LJ, Olivera BM.
“'Focal hypermutation': This sudden, almost saltatory change in sequence is always restricted to the mature toxin region… is a remarkable, mechanistically unexplained and specialized feature of Conus peptide diversification”
Heredity. 2001 Apr;86(Pt 4):439-50. Is the decline of desert bighorn sheep from infectious disease the result of low MHC variation? Gutierrez-Espeleta et al.
“Bighorn sheep populations have greatly declined in numbers and distribution since European settlement, primarily because of high susceptibility to infectious diseases transmitted to them from domestic livestock. It has been suggested that low variation at major histocompatibility complex (MHC) genes, the most important genetic aspect of the vertebrate immune system, may result in high susceptibility to infectious disease. Therefore, we examined genetic polymorphism at a MHC gene (Ovca-DRB) in a large sample, both numerically and geographically, of bighorn sheep. Strikingly, there were 21 different alleles that showed extensive nucleotide and amino acid sequence divergence. In other words, low MHC variation does not appear to be the basis of the high disease susceptibility and decline in bighorn sheep.”
Genome Res. 2001 Jun;11(6):1018-33. The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes. Inoue et al.
“CMT1A and HNPP exemplify a paradigm for genomic disorders wherein unique genome architectural features result in susceptibility to DNA rearrangements that cause disease” “…low recombination frequency in males may enable a chromosomal misalignment at proximal and distal CMT1A-REPs and promote unequal crossing over, which occurs 10 times more frequently in male meiosis.”
Appl Environ Microbiol. 2001 Aug;67(8):3501-13. Rapid evolution of a sexual reproduction gene in centric diatoms of the genus Thalassiosira. Armbrust EV, Galindo HM.
“Sexual reproduction is commonly assumed to occur in the vast majority of diatoms due to the intimate association of this process with cell size control. Surprisingly, however, little is known about the impact of sexual events on diatom population dynamics.” “The Sig1 genes of the four closely related Thalassiosira species also displayed high levels of sequence divergence compared to the levels observed with a second gene, Fcp, probably explaining why Sig1 could not be amplified from more distantly related species.”
Heredity. 2001 Feb;86(Pt 2):195-205. Roles of lineage sorting and phylogenetic relationship in the genetic diversity at the self-incompatibility locus of Solanaceae. Lu Y.
“Using the mean terminal branch lengths of trans-specific alleles on the allelic genealogy to infer phylogenetic relationship among species, P. longifolia was found to be more closely related to P. cinerascens than to P. crassifolia. Nonetheless, the distribution of terminal branch lengths of P. longifolia was more similar to that of P. crassifolia than to that of P. cinerascens, suggesting phylogenetic relationship may have little effect on species-specific polymorphism. Similar habitat and growth characters, yet contrasting S-polymorphism, between P. longifolia and P. cinerascens also reject previous hypotheses that habitat and growth characters are the major factors responsible for interspecific differences in S-polymorphism. A likely scenario is that species-specific S-polymorphism is based on lineage sorting whose effect is further modified by species age and historical changes in population parameters.”
Proc Natl Acad Sci U S A. 2001 May 22;98(11):6233-40. Evolution of genome-phenome diversity under environmental stress. Nevo E.
“The genomic era revolutionized evolutionary biology. The enigma of genotypic-phenotypic diversity… was central in the research program of the Institute of Evolution, University of Haifa, since 1975.” “We advanced ecological genetics into ecological genomics and analyzed globally ecological, demographic, and life history variables in 1,200 diverse species across life, thousands of populations, and tens of thousands of individuals tested mostly for allozyme and partly for DNA diversity.” “The organization and evolution of molecular and organismal diversity in nature at global, regional, and local scales are nonrandom and structured; display regularities across life; and are positively correlated with, and partly predictable by, abiotic and biotic environmental heterogeneity and stress… overriding, the effects of mutation, migration, and stochasticity.”
Mol Biol Evol. 2001 Jun;18(6):975-81. Host-associated speciation in a coral-inhabiting barnacle. Mokady O, Brickner I.
“Little morphological variability was revealed between barnacles collected from two morphs of the hydrocoral Millepora dichotoma (encrusting or branching) or from its congener Millepora platyphylla, but a molecular analysis revealed an unexpected pattern of DNA sequence divergence.”
Proc R Soc Lond B Biol Sci. 2001 Jun 22;268(1473):1297-306. Evolutionary history and speciation modes in the cyprinid genus Barbus. Machordom A, Doadrio I.
“…the relationships between the proposed lineages also show that genome duplication may be considered as a homoplasic character since it must have occurred over at least three independent periods and/or in three independent areas. In relation to the possible saltational evolutionary model for the polyploid species examined here, it was found that, although feasible at the nuclear level, the mitochondrial markers looked at do not appear to have undergone this type of evolution. Rather, they seem to have experienced more or less constant change through time.”
Mol Biol Evol. 2001 Sep;18(9):1789-99. Ongoing evolution of strand composition in bacterial genomes. Rocha EP, Danchin A.
“We tried to identify the substitutions involved in the establishment of replication strand bias, which has been recognized as an important evolutionary factor in the evolution of bacterial genomes. First, we analyzed the composition asymmetry of 28 complete bacterial genomes and used it to test the possibility that asymmetric deamination of cytosine might be at the origin of the bias. The model showed significant correlation to the data but left unexplained a significant portion of the variance and indicated a systematic underestimation of GC skews in comparison with TA skews. Second, we analyzed the substitutions acting on the genes from five fully sequenced Chlamydia genomes that had not suffered strand switch…”
J Bacteriol. 2002 May;184(10):2626-33. The evolving genome of Salmonella enterica serovar Pullorum. Liu GR, Rahn A, Liu WQ, Sanderson KE, Johnston RN, Liu SL.
“…the genome of S. enterica serovar Pullorum RKS5078 is organized very differently from the majority of salmonellas, with three major inversions and one translocation. This extraordinary genome structure was seen in most S. enterica serovar Pullorum strains examined, with different structures in a minority of S. enterica serovar Pullorum strains. We describe the coexistence of different genome structures among the same bacteria as genomic plasticity.”
Syst Biol. 1997 Dec;46(4):622-53. Molecular systematics of the Canidae. Wayne RK, Geffen E, Girman DJ, Koepfli KP, Lau LM, Marshall CR.
“Despite numerous systematic studies, the relationships among many species within the dog family, Canidae, remain unresolved.” “…the taxonomically rich canidae fauna of South America and the development in three species of the trenchant heel, a unique meat-cutting blade on the lower first molar” “…the fossil record provides little evidence for the origins of divergent South American species such as the maned wolf and the bush dog” “We attempted to resolve these two issues and five other specific taxonomic controversies by phylogenetic analysis of 2,001 base pairs of mitochondrial DNA (mtDNA) sequence data from 23 canidae species” “…an important chapter… remains to be discovered in the fossil record…” “The origin of the trenchant heel is not well resolved by our data, although the maximum parsimony tree is weakly consistent with a single origin followed by multiple losses of the character in several extant species.”
Proc R Soc Lond B Biol Sci. 2002 Apr 22;269(1493):793-9. Bantu language trees reflect the spread of farming across sub-Saharan Africa: a maximum-parsimony analysis. Holden CJ.
“The Bantu language tree reflects the spread of farming across this part of sub-Saharan Africa between ca. 3000 BC and AD 500. Modern Bantu subgroups, defined by clades on parsimony trees, mirror the earliest farming traditions both geographically and temporally. This suggests that the major subgroups of modern Bantu stem from the Neolithic and Early Iron Age, with little subsequent movement by speech communities.”
J Biosci. 2002 Feb;27(1 Suppl 1):27-33. Horizontal gene transfer and bacterial diversity. Dutta C, Pan A.
“Bacterial genomes are extremely dynamic and mosaic in nature. A substantial amount of genetic information is inserted into or deleted from such genomes through the process of horizontal transfer. Through the introduction of novel physiological traits from distantly related organisms, horizontal gene transfer often causes drastic changes in the ecological and pathogenic character of bacterial species…”
Evolution Int J Org Evolution. 2002 Feb;56(2):322-9. A test of ecologically dependent postmating isolation between sympatric sticklebacks. Rundle HD.
“I tested a prediction of the ecological model concerning the fitness of hybrids between two young, sympatric species of threespine sticklebacks (Benthics and Limnetics). The two species are ecologically and morphologically divergent: the Benthic is adapted to feeding on invertebrates in the littoral zone of the lake whereas the Limnetic is adapted to feeding on zooplankton in the open water. The growth rate of two types of hybrids, the Benthic backcross and the Limnetic backcross, as well as both parent species, was evaluated in enclosures in both parental habitats in the lake. The use of backcrosses is ideal because a comparison of their growth rates in the two habitats estimates an ecologically dependent component of their fitness while controlling for any intrinsic genetic incompatibilities that may exist between the Benthic and Limnetic genomes. The backcross results revealed a striking pattern of ecological dependence: in the littoral zone, Benthic backcrosses grew at approximately twice the rate of Limnetic backcrosses, while in the open water, Limnetic backcrosses grew at approximately twice the rate of Benthic backcrosses.” “Although the rank order of growth rates of all cross-types in the littoral zone was Benthic > Benthic backcross > Limnetic backcross > Limnetic, neither backcross differed significantly from the parent from which it was mainly derived.” “Results in the open water were less clear and were not fully consistent with the ecological model of speciation…”
EXS. 2002;(92):237-45. The use of physiological data to corroborate cospeciation events in symbiosis. Nishiguchi MK.
“Both host and symbiont can be cultured separately, providing a new avenue to test phylogenetic congruence through molecular and physiological techniques.”
Mol Ecol. 2002 Mar;11(3):619-25. Speciation via introgressive hybridization in East African cichlids? Salzburger W, Baric S, Sturmbauer C.
“…a mosaic of alleles derived from both parental lineages…” “…increase of genetic and phenotypic diversity due to hybridization…”
Mol Ecol. 2002 Mar;11(3):387-405. The discovery of three genetic races of the dwarf mistletoe Arceuthobium americanum (Viscaceae) provides insight into the evolution of parasitic angiosperms. Jerome CA, Ford BA.
“…host identity, geographical isolation and environmental factors have contributed to race formation in A. americanum.” “Given sufficient time, it is possible that these races will become reproductively isolated…”
Evolution Int J Org Evolution. 2002 Jan;56(1):58-69. Episodic chromosomal evolution in Planipapillus (Onychophora: Peripatopsidae): a phylogenetic approach to evolutionary dynamics and speciation. Rockman MV, Rowell DM.
“Planipapillus, a clade of onychophorans from southeastern Australia, exhibits substantial chromosomal variation. In the context of a robust phylogeny based on nuclear and mitochondrial sequence data, we evaluate models… that differ in the roles assigned to selection, mutation, and drift.” “A likelihood-ratio test approach, which is independent of our point estimates of ancestral states, rejects an evolutionary model in which the mutation rate is constant and centric fusions are effectively neutral.”
Evolution Int J Org Evolution. 2002 Jan;56(1):191-8. Molecular correlates of reproductive isolation. Fitzpatrick BM.
“Evolution of reproductive isolation as a byproduct of genetic divergence in isolated populations is the dominant (albeit not exclusive) mode of speciation in sexual animals. But little is known about the factors linking speciation to general divergence. Several authors have argued that allopatric speciation should proceed more rapidly if isolated populations also experience divergent selection. Reproductive isolation between allopatric populations is not subject to direct selection; it can accumulate only by random drift or as a fortuitous byproduct of selection on other traits.”
Evolution Int J Org Evolution. 2002 Jan;56(1):111-20. Patterns of divergence in the effects of mating on female reproductive performance in flour beetles. Nilsson T, Fricke C, Arnqvist G.
“We performed an experiment designed to assess genetic divergence in the effects of mating on female reproductive performance in flour beetles, Tribolium castaneum. Females were mated to males of three different wild-type genotypes at two different frequencies, in all possible reciprocal combinations. Male genotype affected all aspects of female reproduction, through its effects on female longevity, total offspring production, reproductive rate, mating rate, and fertility. Moreover, male and female genotype interacted in their effects on offspring production and reproductive rate.”
Biochem Genet. 2001 Dec;39(11-12):395-406. Phylogenetics of freshwater black basses (Centrarchidae: Micropterus) inferred from restriction endonuclease analysis of mitochondrial DNA. Johnson RL, Magee JB, Hodge TA.
“Members of the genus Micropterus form a close natural unit with little morphologic and meristic variation.” “The phylogeny inferred from Dollo parsimony cladistic analysis… was inconsistent with published meristic analyses.”
Genetica. 2001;112-113:515-34. Adaptive divergence and the evolution of reproductive isolation in the wild: an empirical demonstration using introduced sockeye salmon. Hendry AP.
“Populations exposed to different ecological environments should diverge for phenotypic traits that influence survival and reproduction” “…immigrants become less fit than residents and… hybrids perform poorly in either environment…” “…sockeye salmon (Oncorhynchus nerka) introduced from a common ancestral source into a new lake system (Lake Washington, Washington). The introduced fish founded several new populations, two of which experience very different environments during breeding and early development (Cedar River v.s. Pleasure Point beach). Over 13 generations, the two populations diverged for adult traits (female body size, male body depth; measured in the wild) and embryo traits (survival to hatching, development rate, size at emergence; measured in a common environment).”
Genetica. 2001;112-113:445-61. Lateral plate evolution in the threespine stickleback: getting nowhere fast. Bell MA.
“Gasterosteus aculeatus is a small Holarctic fish with marine, anadromous, and freshwater populations. Marine and anadromous populations apparently have changed little… and exhibit limited geographical variation.” “Although highly divergent freshwater isolates of G. aculeatus have existed… they have rarely experienced sustained evolutionary divergence leading to formation of widespread, phenotypically distinct species.”
Genetica. 2001;112-113:223-43. Ring species as bridges between microevolution and speciation. Irwin DE, Irwin JH, Price TD.
“Theoretical models… ring species are ideal systems for research into the role of both ecological and geographical differentiation in speciation, but few examples have been studied in detail.”
Evolution Int J Org Evolution. 2001 Dec;55(12):2550-67. A single ancient origin of brood parasitism in African finches: implications for host-parasite coevolution. Sorenson MD, Payne RB.
“…the parasitic finches (Viduidae) are not recently derived from either weavers (Ploceidae) or grassfinches (Estrildidae), but represent a third distinct lineage.” “Our study reduces by one the tally of avian lineages…”
Mol Phylogenet Evol. 2002 Feb;22(2):303-14. Molecular phylogeny of hybridizing species from the genus Spartina Schreb. (Poaceae). Baumel A, Ainouche ML, Bayer RJ, Ainouche AK, Misset MT.
“Interspecific hybridization events have been reported in the genus Spartina Schreb. (Poaceae), involving the east American species Spartina alterniflora…” “…belonging to the same lineage…” “Significant incongruence has been encountered between the waxy based tree and both the ITS and trnT-trnL trees concerning the position of S. densiflora…”
Mol Phylogenet Evol. 2002 Feb;22(2):258-68. Speciation in the globeflower fly Chiastocheta spp. (Diptera: Anthomyiidae) in relation to host plant species, biogeography, and morphology. Despres L, Pettex E, Plaisance V, Pompanon F.
“The species relationship indicated by egg morphology is only partly supported by molecular data. Moreover, a strong discrepancy between nucleotide variation and male genitalia morphology variation was found, particularly within and among European species coexisting on a single host plant.” “We discuss alternative evolutionary scenarios…”
Immunogenetics. 2001 Oct;53(8):695-708. Mhc class I genes of swordtail fishes, Xiphophorus: variation in the number of loci and existence of ancient gene families. Figueroa F, Mayer WE, Sato A, Zaleska-Rutczynska Z, Hess B, Tichy H, Klein J.
“The analysis revealed the existence of multiple loci (at least seven in some individuals) whose numbers vary among the different species and probably also among individuals of the same species. The variation does not seem to bear any relationship to the taxonomy of the genus.”
Nature. 2001 Dec 20-27;414(6866):901-5. The genetic architecture of divergence between threespine stickleback species. Peichel et al.
“The genetic and molecular basis of morphological evolution is poorly understood, particularly in vertebrates. Genetic studies of the differences between naturally occurring vertebrate species have been limited by the expense and difficulty of raising large numbers of animals and the absence of molecular linkage maps for all but a handful of laboratory and domesticated animals.” “Substantial alterations in spine length, armour plate number, and gill raker number are controlled by genetic factors that map to independent chromosome regions. Further study of these regions will help to define the number and type of genetic changes that underlie morphological diversification…”
Evolution Int J Org Evolution. 2001 Oct;55(10):1932-42. Evidence for Dobzhansky-Muller incompatibilites contributing to the sterility of hybrids between Mimulus guttatus and M. nasutus. Fishman L, Willis JH.
“Both chromosomal rearrangements and negative interactions among loci (Dobzhansky-Muller incompatibilities) have been advanced as the genetic mechanism underlying the sterility of interspecific hybrids” “…we investigated the quantitative genetics of hybrid sterility in a line cross between two members of the Mimulus guttatus species complex (M. guttatus and M. nasutus). Hybrids showed partial male and female sterility, and the patterns of infertility were not consistent with the action of chromosomal rearrangements alone.” “Dobzhansky-Muller interactions also resulted in the breakdown of several nonreproductive characters and appear to contribute to correlations between male and female fertility in the F2 generation. These results parallel and contrast with the genetics of postzygotic isolation in model animal systems and are a first step toward understanding…”
Environ Mol Mutagen. 2001;38(2-3):248-60. Three R's of bacterial evolution: how replication, repair, and recombination frame the origin of species. Brown EW, LeClerc JE, Kotewicz ML, Cebula TA.
“The genetic diversity of bacteria results not only from errors in DNA replication and repair but from horizontal exchange and recombination of DNA sequences from similar and disparate species as well. New individuals carrying adaptive changes are thus being spawned constantly among the population at large. When new selection pressures appear, these are the individuals that survive, at the expense of the general population, to forge new populations.” “We present novel phylogenetic evidence for horizontal transfer of three genes involved in DNA replication and repair (mutS, uvrD, and polA).” “Our data underscore that recombination plays both a diversifying and a homogenizing role in defining the structure of the E. coli genome.”
Mol Ecol. 2001 Oct;10(10):2541-54. Phenotypic evolution and hidden speciation in Candidula unifasciata ssp. (Helicellinae, Gastropoda) inferred by 16S variation and quantitative shell traits. Pfenninger M, Magnin F.
“In C. unifasciata, no significant association between population pairwise FST estimates and corresponding morphological fixation indices could be detected, indicating independent evolution of the two character sets.”
Genetics. 2001 Nov;159(3):1179-89. Female meiosis drives karyotypic evolution in mammals. Pardo-Manuel de Villena F, Sapienza C. [Erratum in: Genetics 2002 Mar;160(3):1263.]
“Speciation is often accompanied by changes in chromosomal number or form even though such changes significantly reduce the fertility of hybrid intermediates. We have addressed this evolutionary paradox by expanding the principle that nonrandom segregation of chromosomes takes place whenever human or mouse females are heterozygous carriers of Robertsonian translocations, a common form of chromosome rearrangement in mammals.”
Annu Rev Phytopathol. 1999;37:197-246. THE EVOLUTION OF ASEXUAL FUNGI: Reproduction, Speciation and Classification. Taylor J, Jacobson D, Fisher M.
“…asexual or sexual reproductive morphology does not necessarily correlate with clonal or recombining reproductive behavior…” “Although approximately one fifth of described fungi have been thought to be asexual and clonal, recent studies have shown that they are also recombining. Whether a particular pathogen reproduces clonally or by recombination depends on factors relating to its biology and its distribution in space and time. Knowing the identity of species and populations and their reproductive modes, while taking a broad view of pathogen behavior in space and time, should enhance the ability of pathologists to control pathogens and even predict their behavior.”
Protein Sci. 2001 Nov;10(11):2207-18. Characterization of ostrich (Struthio camelus) beta-microseminoprotein (MSP): identification of homologous sequences in EST databases and analysis of their evolution during speciation. Lazure C, Villemure M, Gauthier D, Naude RJ, Mbikay M.
“Noticeably, no beta-microseminoprotein-related gene could be found in the recently completed fruit fly genome…”
Mol Phylogenet Evol. 2001 Oct;21(1):55-71. Molecular phylogenies of fig wasps: partial cocladogenesis of pollinators and parasites. Lopez-Vaamonde et al.
“…there is not perfect congruence of pollinator and parasite phylogenies (for any substantial clade)…
Evolution Int J Org Evolution. 2001 Aug;55(8):1706-9. Mimicry on the QT(L): genetics of speciation in Mimulus. Bleiweiss R.
“Ecological studies suggest that hummingbird-pollinated plants in North America mimic each other to increase visitation by birds. Published quantitative trait locus (QTL) data for two Mimulus species indicate that floral traits associated with hummingbird versus bee pollination results from a few loci with major effects on morphology…”
EMBO J. 2001 Sep 3;20(17):4874-83. Heterologous, splicing-dependent RNA editing in chloroplasts: allotetraploidy provides trans-factors. Schmitz-Linneweber C, Tillich M, Herrmann RG, Maier RM.
“RNA editing is unique among post-transcriptional processes in plastids, as it exhibits extraordinary phylogenetic dynamics leading to species-specific editing site patterns.” “Surprisingly, it turned out that the spinach site is edited in the heterologous nuclear background”
Evolution Int J Org Evolution. 2001 Jun;55(6):1085-94. The evolution of postzygotic isolation: accumulating Dobzhansky-Muller incompatibilities. Orr HA, Turelli M.
“These results let us estimate. albeit crudely, the probability, p, that two diverged sites from different species will contribute to hybrid sterility or inviability.”
Hereditas. 2000;133(3):255-61. Chromosomal rearrangement in autotetraploid plants of Arabidopsis thaliana. Weiss H, Maluszynska J.
“Arabidopsis is believed to be a true diploid (x = 5) with numerous ecotypes (accessions) and only a very few natural polyploid populations reported. Few studies were undertaken to induce polyploidy in Arabidopsis, however none of those gave the cytogenetic characteristics of polyploid plants. Our analysis of chromosome pairing of colchicine-induced autotetraploid Arabidopsis (Wilna ecotype) revealed preferential bivalent pairing in PMCs (pollen mother cells). In order to attempt to explain this phenomenon, first of all more detailed cytogenetic studies of autopolyploid plants have been undertaken…” “…chromosome behaviour in relation to diploidization of autopolyploids and to evaluate the degree of chromosomal rearrangements during this process.”
Evolution Int J Org Evolution. 2001 Apr;55(4):677-83. Evolutionary rates and species diversity in flowering plants. Barraclough TG, Savolainen V.
“Genetic change is a necessary component of speciation, but the relationship between rates of speciation and molecular evolution remains unclear.” “Rates of protein and morphological evolution… correlate… not with species numbers.”
Mol Phylogenet Evol. 2001 May;19(2):187-201. Evolution of the mitochondrial DNA control region and cytochrome b genes and the inference of phylogenetic relationships in the avian genus Lophura (Galliformes). Randi et al.
“Presence of conserved functional motifs in the inferred amino acid sequences, conserved secondary structures of the flanking tRNA(Pro) and tRNA(Thr), and Southern hybridization concordantly suggest that these cyt b represent functional mitochondrial genes and not nuclear transpositions…” “…cyclic changes in late Pleistocene climate and landscape might not have increased rates of speciation in genus Lophura in Sundaland.”
Trends Genet. 2001 May;17(5):237-9. Birth and death of duplicated genes in completely sequenced eukaryotes. Wagner A.
“Gene and genome duplications are commonly regarded as being of major evolutionary significance. But how often does gene duplication occur? And, once duplicated, what are the fates of duplicated genes? How do they contribute to evolution? In a recent article, Lynch and Conery analyze divergence between duplicate genes from six eukaryotic genomes. They estimate the rate of gene duplication, the rate of gene loss after duplication and the strength of selection experienced by duplicate genes. They conclude that although the rate of gene duplications is high, so is the rate of gene loss…”
Evolution Int J Org Evolution. 2001 Mar;55(3):587-97. Cladogenesis and loss of the marine life-history phase in freshwater galaxiid fishes (Osmeriformes: Galaxiidae). Waters JM, Wallis GP.
“Switches from migratory (diadromous) to nonmigratory (freshwater) life histories are known to have occurred repeatedly in some aquatic taxa. However, the significance of the loss of diadromy as an initiator for speciation remains poorly understood.” “Sympatric taxa are not monophyletic, suggesting that their coexistence reflects secondary contact rather than sympatric speciation.” “The divergence (maximum 11.5%) between Tasmanian and New Zealand G. brevipinnis, although large, supports marine dispersal rather than vicariance as the principle biogeographic mechanism on an intercontinental scale.”
Chromosome Res. 2001;9(2):107-20. Comparative chromosome and mitochondrial DNA analyses and phylogenetic relationships within common voles (Microtus, Arvicolidae). Mazurok et al.
“The four species of common voles within the genus Microtus--M. kirgisorum, M. transcaspicus, M. arvalis, and M. rossiaemeridionalis--are so closely related that neither morphological features nor paleontological evidence allow clarification of their phylogeny.” “A comparison of high resolution GTG-banding patterns allows us to ascertain the similarity between the karyotypes of these species, revealing that they are composed of rearrangements of the same chromosomal elements” “…FITCH and KITSCH computer programs were used …”
Mol Biol Evol. 2001 May;18(5):801-11. Molecular evolution of the ocnus and janus genes in the Drosophila melanogaster species subgroup. Parsch et al.
“Genes involved in male fertility are potential targets for sexual selection, and their evolution may play a role in reproductive isolation and speciation. Here we describe a new Drosophila melanogaster gene, ocnus (ocn), that encodes a protein abundant in testes nuclear extracts. RT-PCR indicates that ocn transcription is limited to males and is specific to testes. ocn shares homology with another testis-specific gene, janusB (janB), and is located just distal to janB on chromosome 3. The two genes also share homology with the adjacent janusA (janA) gene…”
Biometrics. 1999 Jun;55(2):355-65. A multiplicative-epistatic model for analyzing interspecific differences in outcrossing species. Wu R, Li B.
“Epistasis may play an important role in evolution and speciation. Under multiplicative interactions between different loci, an analytical model is proposed to estimate genetic parameters at the individual locus level that contribute to interspecific differences in outcrossing species.” “Use of clones offers a tremendous power to test the adequacy of the model. However, the utilization of the model with species that cannot be cloned is also discussed. An example with interspecific hybrids of two forest tree species is used to demonstrate the model.”
Mol Ecol. 2001 Mar;10(3):721-35. The effect of habitat type on speciation rates and range movements in aquatic beetles: inferences from species-level phylogenies. Ribera I, Barraclough TG, Vogler AP.
“The expectation that species turnover is higher in lotic lineages due to their lower dispersal propensity compared to lentic species was not strongly supported.” “We discuss two explanations for our failure to detect differences between the two clades. First, current methods for analysing species-level phylogenies may be sensitive to taxonomic and sampling artefacts.”
Mol Ecol. 2001 Mar;10(3):551-68. The role of hybridization in evolution. Barton NH.
“'Hybrid speciation', in which fit combinations of alleles are established, is more problematic…” “heterosis arises only when traits are additive, whereas the latter two patterns require dominance. Moreover, because adaptation is via substitutions of small effect, Fisher's model does not generate the strong effects of single chromosome regions often observed in species crosses.”
Nature. 2001 Mar 22;410(6827):463-6. Intraspecific competition favours niche width expansion in Drosophila melanogaster. Bolnick DI.
“The relationship between intraspecific competition and diversification is known from theory, and has been used as the foundation for some models of speciation. However, there has been little empirical proof that niches evolve in response to intraspecific competition” “…competition in a population can drive niche expansion…”
Evol Dev. 2000 Mar-Apr;2(2):78-84. Macroevolution is more than repeated rounds of microevolution. Erwin DH. [Comment in: Evol Dev. 2000 Mar-Apr;2(2):61-2.]
“Initially, paleontologists and other evolutionary biologists advanced a variety of non-Darwinian evolutionary processes as explanations for patterns found in the fossil record, emphasizing macroevolution as a source of morphologic novelty. Later, paleontologists, from Simpson to Gould, Stanley, and others, accepted the primacy of natural selection but argued that rapid speciation produced a discontinuity between micro- and macroevolution. This second phase emphasizes the sorting of innovations between species. Other discontinuities appear in the persistence of trends…” “These discontinuities impose a hierarchical structure to evolution and discredit any smooth extrapolation from allelic substitution to large-scale evolutionary patterns…” “…macroevolution… unexplained by microevolution…”
J Gen Virol. 2001 Apr;82(Pt 4):713-22. Evolutionarily conserved RNA secondary structures in coding and non-coding sequences at the 3' end of the hepatitis G virus/GB-virus C genome. Cuceanu NM, Tuplin A, Simmonds P.
“Using a combination of covariance scanning and analysis of variability at synonymous sites, we previously demonstrated that the coding regions of HGV/GBV-C may contain extensive secondary structure of undefined function (Simmonds & Smith, Journal of Virology 73, 5787-5794, 1999 ). In this study we have carried out a detailed comparison of the structure of the 3'untranslated region (3'UTR) of HGV/GBV-C with that of the upstream NS5B coding sequence.” “The prediction of similar structures in the same region of hepatitis C virus may allow the functions of these structures to be determined with a more tractable experimental model.”
Proc R Soc Lond B Biol Sci. 2000 Dec 22;267(1461):2517-21. Intraspecific phylogenetic congruence among multiple symbiont genomes. Funk et al.
“Eukaryotes often form intimate endosymbioses with prokaryotic organisms. Cases in which these symbionts are transmitted cytoplasmically to host progeny…” “This study thus provides the first evidence for strictly vertical transmission…” “These results may reflect the obligate nature of this intimate mutualism…”
Nature. 2001 Jan 11;409(6817):185-8. Correlated evolution of morphology and vocal signal structure in Darwin's finches. Podos J. [Comment in:
Nature. 2001 Jan 11;409(6817):139-40.]
“According to classical theories of speciation, mating signals diversify, in part, as an incidental byproduct of adaptation by natural selection to divergent ecologies, although empirical evidence in support of this hypothesis has been limited…” “…diversification of beak morphology and body size has… patterns of vocal signal… birds with large beaks and body sizes have… songs with comparatively low rates of syllable repetition and narrow frequency bandwidths. The converse is true for small birds.”
Proc Natl Acad Sci U S A. 2001 May 8;98(10):5389-92. The biotic crisis and the future of evolution. Myers N, Knoll AH.
“Not so well known but probably more significant in the long term is that the crisis will surely disrupt and deplete certain basic processes of evolution, with consequences likely to persist for millions of years. Distinctive features of future evolution could include…end to the speciation of large vertebrates…” “Despite this likelihood, we have only a rudimentary understanding of how we are altering the evolutionary future. As a result of our ignorance, conservation policies fail to reflect long-term evolutionary aspects of biodiversity loss.”
Proc Natl Acad Sci U S A. 2001 May 8;98(10):5471-6. Declines of biomes and biotas and the future of evolution. Woodruff DS.
“In response to the on-going rapid decline of biomes and homogenization of biotas, the panelists predicted changes in species geographic ranges, genetic risks of extinction, genetic assimilation, natural selection, mutation rates, the shortening of food chains, the increase in nutrient-enriched niches permitting the ascendancy of microbes, and the differential survival of ecological generalists. Rates of evolutionary processes will change in different groups, and speciation in the larger vertebrates is essentially over” “…interventionist genetic…” “…to better equip us for stewardship of the processes of evolution, and one suggesting that such stewardship is now our responsibility. The ultimate test of evolutionary biology as a science is not whether it solves the riddles of the past but rather whether it enables us to manage the future of the biosphere. Our inability to make clearer predictions about the future of evolution has serious consequences for both biodiversity and humanity.”
Mol Biol Evol. 2001 Mar;18(3):376-83. Polymorphism in abalone fertilization proteins is consistent with the neutral evolution of the egg's receptor for lysin (VERL) and positive darwinian selection of sperm lysin. Swanson WJ, Aquadro CF, Vacquier VD.
“…there was a subdivision in the VERL sequences in the pink abalone and a lack of heterozygous individuals between groups, suggesting that the evolution of assortative mating may be in progress…”
Riv Biol. 2000 Sep-Dec;93(3):513-24. Ontogeny, phylogeny and the origin of biological information. Davison JA.
“Accepting the evidence that evolution is largely finished and that sexual reproduction is incapable of supporting macroevolution… Acceptance of these possibilities…”
Regarding radioactive ‘speciation’:
Water. 2002 Jan-Feb;40(1):5-13. Natural attenuation reactions at a uranium mill tailings site, western U.S.A. Zhu C, Anderson GM, Burden DS.
“This paper presents a modeling analysis of the geochemical evolution of a contaminated sandy aquifer at a uranium mill tailings site in the western United States.” “For the flushing stage, it is predicted that reactions with surface-bound species will dominate the reaction paths, and more pore volumes are required to neutralize the plume than predicted by models that do not consider surface reactions. Direct mineralogical and surface analysis is needed to substantiate this assertion.”
To be Continued....
[ 12. April 2004, 17:39: Message edited by: Fernando Castro-Chavez ]
Member # 1201
posted 13. April 2004 17:19
Putting Limits on the Diversity of Life.
(Part Four. Continued... 5)
‘Speciation’ does not occurred in the present or in the past, neither ‘evolution’.
"You can never solve a problem on the level on which it was created." "A man should look for what is, and not for what he thinks should be." Albert Einstein.
Fragment from: “The Galapagos Islands: Evolution's Sacred Ground, by Ray Bohlin, Ph.D.”
“Most of these six ground finches will interbreed, and the hybrids are fertile, meaning they can also breed among themselves. This information is quite startling because it means that these six species may actually be one species. And the actual degree of change is quite miniscule. The average beak size may change by only a half a millimeter from dry to wet season. These six finches are also indistinguishable in their mtDNA. As an icon of evolution, the finches are far less than hoped for.”
“The marine iguana's cousin, the land iguana eats cactus pads and leafy vegetation and never ventures toward the sea... Evolutionists suggest that these two species derived from a common ancestor over ten to twenty million years ago (although the oldest island is only 3 million years old!). But we learned that these two species would interbreed on occasion. The hybrids live for only seven to eight of the usual forty years, and their eating habits are strangely intermediate. The hybrids will eat cactus but not leafy vegetation, and will eat seaweed and algae but only at low tide when they can scramble over the rocks to get it. They won't enter the water. This level of hybridization makes it unlikely they are as old as evolutionists suggest.”
[Jonathan Wells, Icons of Evolution (Washington, DC: Regnery Publishing 2000), p. 159-175;
The fact that evolution is not true can be seen also in Darwin’s finches, they are the same species or kind: “fertile parents = fertile offspring.” Nothing is 'evolving' beyond the natural limits established within the species:
Darwin's Avian Muses Continue To Evolve
Carl Zimmer. Science 26 April 2002; 296: 633-635.
"The two species on Daphne Major can and sometimes do interbreed, and their hybrids--far from being mulelike reproductive dead ends--are a source of fresh genetic variability." "Interbreeding may be one of the secrets... hybrids may be an unrecognized factor..." "...five male cactus finches for every female. A few desperate males mated with female ground finches, which then produced perfectly healthy and fertile hybrids." "As a result, ground finch genes are flowing into the cactus finch gene pool--a process called introgression--making their beaks blunter." "Other biologists are surprised that two distantly related species can produce healthy hybrids..." "This new source of genetic diversity makes it easier for a species with donated genes to adapt to a changing environment, the Grants claim."
In the words of the researchers themselves:
Grant PR, Grant BR.
Genetics and the origin of bird species.
Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7768-75. http://www.pnas.org/cgi/content/full/94/15/7768
"...the populations are only partly reproductively isolated, interbreeding occurs, and some of the hybrids survive to breed" "...species hybridize, rarely, and are capable of producing fertile hybrids that backcross to the parental species" "...interbreeding of species and the breeding of hybrids ..."
[Refs: Grant, P. R. & Grant, B. R. (1992) Science 256, 193-197; Grant, P. R. & Grant, B. R. (1997) Biol. J. Linn. Soc. 60, 317-343; Grant, B. R. & Grant, P. R. (1997) in Endless Forms: Species and Speciation, eds. Howard, D. J. & Berlocher, S. H. (Oxford Univ. Press, Oxford)]
"...field observations of natural hybridization have been made on the islands of Daphne Major…”
[Grant, P. R. (1993) Philos. Trans. R. Soc. London Ser. B 340, 127-139, Grant, P. R. & Price, T. D. (1981) Am. Zool. 21, 795-811, Boag, P. T. & Grant, P. R. (1984) Biol. J. Linn. Soc. 22, 243-287]
“…and [the island] Genovesa”
[Grant, B. R. & Grant, P. R. (1989) Evolutionary Dynamics of a Natural Population: The Large Cactus Finch of the Galápagos (Univ. Chicago Press, Chicago)].
“These show that all six species of Darwin's ground finches (genus Geospiza) hybridize (rarely) with at least one other congeneric species. In addition some intergeneric crosses are known among the tree finches and warbler finch, and breeding hybrids have been produced”
[Grant, P. R. (1986) Ecology and Evolution of Darwin's Finches (Princeton Univ. Press, Princeton, N. J.), Bowman, R. I. (1983) in Patterns of Evolution in Galápagos Organisms, eds. Bowman, R. I., Berson, M. & Leviton, A. E. (American Association for the Advancement of Science, San Francisco), pp. 237-537].
On Daphne Major Geospiza fortis (medium ground finch) hybridizes with G. scandens (cactus finch), another resident species, and G. fuliginosa (small ground finch), an uncommon immigrant. Contrary to expectation from the reinforcement hypothesis, hybrids formed by Geospiza fortis breeding with G. scandens and G. fuliginosa are both viable and fertile to a degree similar to that of the contemporary offspring of conspecific matings; so are the first two generations of backcrosses" "Backcrossing negates the hypothesis of speciation occurring entirely in allopatry." "In tests of several species the discrimination was often weak, implying that song difference, by itself, would not be sufficient to prevent interbreeding."
"At the point of ring closure or overlap where two populations establish secondary contact they do not interbreed, or do so extremely rarely; e.g., herring gull and lesser black-backed gull. A crossfostering experiment with these gulls showed that, as in Darwin's finches, misimprinted birds are capable of producing viable hybrids, i.e., once the premating isolating mechanism is broken”
[Harris, M. P. (1970) Ibis 112, 488-498; Harris, M. P., Morley, C. & Green, G. H. (1978) Bird Study 25, 161-166]
Some of the Grant’s’s recent works:
Grant PR, Grant BR, Keller LF, Markert JA, Petren K.
Inbreeding and interbreeding in Darwin's finches.
Evolution Int J Org Evolution. 2003 Dec;57(12):2911-6.
Markert JA, Grant PR, Grant BR, Keller LF, Coombs JL, Petren K.
Neutral locus heterozygosity, inbreeding, and survival in Darwin's ground finches (Geospiza fortis and G. scandens).
Heredity. 2004 Apr;92(4):306-15.
Keller LF, Grant PR, Grant BR, Petren K.
Environmental conditions affect the magnitude of inbreeding depression in survival of Darwin's finches.
Evolution Int J Org Evolution. 2002 Jun;56(6):1229-39.
More references from the Pubmed search ‘speciation’ and ‘evolution’:
Annu Rev Genet. 2000;34:401-437. Polyploid incidence and evolution. Otto SP, Whitton J.
“…whether polyploidization itself has a significant effect on patterns and rates of diversification remains an open question.” “Theoretical models support the potential for increased adaptability in polyploid lineages” “…yet conclusive evidence that polyploidy has changed rates and patterns of diversification remains elusive.”
Bioessays. 2000 Dec;22(12):1134-41. Dualism and conflicts in understanding speciation. Schilthuizen M.
“Speciation is a central but elusive issue in evolutionary biology. Over the past sixty years, the subject has been studied within a framework conceived by Ernst Mayr and Theodosius Dobzhansky and subsequently developed further by numerous other workers. In this "isolation" theory, the evolution of reproductive isolation is a key element of speciation; natural selection is given only secondary importance while gene flow is considered prohibitive to the process. In this paper, I argue that certain elements in this approach have produced confusion and irreconcilability among students of speciation. The more prominent debates in speciation (i.e., the species definition, sympatry/allopatry, and the role of reinforcement) all derive from an inherent conflict between the "isolation" theory and Darwin's "selection" view on species and speciation (in which disruptive selection is crucial). New data, mainly from field ecology, molecular population genetics, laboratory studies with Drosophila and computer analysis, all suggest that the isolation theory may no longer be the most desirable vantage point from which to explore speciation.” “The traditional preoccupation with reproductive isolation has created gaps in our knowledge of several crucial issues, mainly regarding the role of environmental selection and its connection with mate selection” “…the method [proposed by Schilthuizen M.] under the pure drift model is verified via Monte Carlo simulations.”
Mol Biol Evol. 2000 Apr;17(4):601-15. Evolution of nucleotide substitutions and gene regulation in the amylase multigenes in Drosophila kikkawai and its sibling species. Inomata N, Yamazaki T.
“…we do not know whether there was any evolutionary relationship between the two.”
Proc R Soc Lond B Biol Sci. 2000 Mar 7;267(1442):497-503. The shifting roles of dispersal and vicariance in biogeography. Zink RM, Blackwell-Rago RC, Ronquist F.
“…no cladogram was obtained for which all lineages were congruent.” “An expanded database is now needed to estimate the relative roles of each process” “…much older than typically presumed.”
Cytogenet Cell Genet. 2000;88(3-4):296-304. Comparative cytogenetics of hamsters of the genus Calomyscus. Graphodatsky et al.
“Natural hybrids between individuals with different karyotypes were recorded, and regular chromosome pairing in meiosis was observed in laboratory hybrids.” “There is no unequivocal evidence suggesting the role of chromosomal change in the speciation of the populations of Calomyscus examined.”
Mol Biol Evol. 2000 Jun;17(6):897-907. Phylogenetic analysis under reticulate evolution. Xu S.
“The usual assumption that species have evolved from a common ancestor by a simple branching process--where each branch is genetically isolated--has been challenged by the observation of frequent hybridization between species in natural populations. In fact, most plant species are thought to have hybrid origins. This reticulate pattern of species evolution has posed problems in the definition of speciation and in phylogenetic reconstruction, especially when molecular data are used. As a result, hybridization has been largely treated as an evolutionary accident or statistical error in phylogenetic analysis.”
Proc R Soc Lond B Biol Sci. 2000 Feb 22;267(1441):327-32. The inheritance of female preference functions in a mate recognition system. Ritchie MG.
“Mate recognition systems (MRSs) play a major role in sexual selection and speciation, yet few studies have analysed both male and female components in detail” “…the inheritance of male song and female preference functions followed in crosses between subspecies” “…there is no evidence for a role of maternally derived sex-linked genes in female preference or of maternal effects.”
Plant Cell. 1999 Aug;11(8):1433-44. Molecular analysis of the anthocyanin2 gene of petunia and its role in the evolution of flower color. Quattrocchio et al.
“Analysis of P. axillaris subspecies with white flowers showed that they contain an2(-) alleles with two alternative frameshifts at one site [an2, anthocyanin2 locus, the main determinant of color differences, a regulator of the anthocyanin biosynthetic pathway that encodes a transcription factor, a MYB domain protein], apparently caused by the insertion and subsequent excision of a transposon. A third an2(-) allele has a nonsense mutation elsewhere, indicating that it arose independently.”
Proc R Soc Lond B Biol Sci. 2000 Dec 7;267(1460):2375-84. Historical contingency and ecological determinism interact to prime speciation in sticklebacks, Gasterosteus. Taylor EB, McPhail JD.
“Historical contingency and determinism are often cast as opposing paradigms under which evolutionary diversification operates. It may be, however, that both factors act together to promote evolutionary divergence, although there are few examples of such interaction in nature.” “Sympatric sticklebacks, therefore, provide an example of adaptive radiation by determinism contingent upon historical conditions promoting unique ecological interactions, and illustrate how contingency and determinism may interact to generate geographical variation in species diversity.”
Heredity. 2000 Jan;84 ( Pt 1):97-102. Are the same genes responsible for intra- and interspecific variability for sex comb tooth number in Drosophila? Nuzhdin SV, Reiwitch SG.
“One of the most interesting unresolved puzzles is the relationship between intraspecific variability in morphological traits and their interspecific divergence” “…the vast majority of intraspecific variants could be deleterious mutations … In this case intraspecific variation would not ultimately generate interspecific trait differences.” “Whether or not these effects result from the same genes requires further examination.”
Bioessays. 1999 Dec;21(12):1052-8; discussion 1059. Molecular evidence for the early divergence of placental mammals. Easteal S.
“Paleontological and molecular data suggest quite different patterns…” “Resolving this discrepancy requires a consideration of the assumptions that underlie both approaches. It is argued here that the pattern indicated by the molecular approach is the most likely to be correct.”
Bioessays. 2000 Dec;22(12):1085-94. Speciation by postzygotic isolation: forces, genes and molecules. Orr HA, Presgraves DC.
“…molecular genetic data are limited…”
Mol Phylogenet Evol. 2000 Nov;17(2):244-55. Molecular phylogenetics of the holly leafminers (Diptera: Agromyzidae: Phytomyza): species limits, speciation, and dietary specialization. Scheffer SJ, Wiegmann BM.
“Species boundaries of previously known and of undescribed holly leafmining species were confirmed with the molecular data, with one exception…” “…these traits are evolutionarily labile…”
Curr Opin Chem Biol. 2001 Feb;5(1):86-9. Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms. Ball CA, Cherry JM.
“…duplicate gene pairs in Saccharomyces, Arabidopsis, Caenorhabditis and Drosophila are high: 30%, 60%, 48% and 40%, respectively…”
J Theor Biol. 2001 Jan 7;208(1):91-107. The influence of predator--prey population dynamics on the long-term evolution of food web structure. Drossel B, Higgs PG, McKane AJ.
“Predator-prey interactions are nonlinear…” “…we find no evidence for self-organized criticality.”
Mol Biol Evol. 2001 Feb;18(2):112-9. Three divergent rDNA clusters predate the species divergence in Quercus petraea (Matt.) Liebl. and Quercus robur L. Muir G, Fleming CC, Schlotterer C. “Quercus petraea and Quercus robur are two closely related oak species that frequently hybridize. We sequenced 70 clones containing the 5.8S and ITS2 regions of ribosomal DNA (rDNA) from these two species and did not detect a species-specific difference.” “Despite a large between-rDNA-families divergence, rDNA sequences were very similar within families…”
Am J Bot. 2000 Dec;87(12):1857-1870. Molecular phylogeny and biogeography of Linanthus (Polemoniaceae). Bell CD, Patterson RW.
“Our data suggest two separate and well-supported lineages of LINANTHUS: in close association with two other genera-LEPTODACTYLON: and PHLOX: These results… do not support the traditional classification of the genus as a natural group, nor do they support the sectional classification within the genus.”
Genome Res. 2000 Nov;10(11):1719-25. Horizontal gene transfer in bacterial and archaeal complete genomes. Garcia-Vallve S, Romeu A, Palau J.
“There is growing evidence that horizontal gene transfer is a potent evolutionary force in prokaryotes, although exactly how potent is not known” “…informational genes were less likely to be transferred than operational genes.”
Behav Processes. 2000 Oct 5;51(1-3):111-134. The role of mating preferences in shaping interspecific divergence in mating signals in vertebrates. Ptacek MB.
“Pheromonal signals serve as the primary basis for species-specific mating cues in many salamander species, most mammals and even some fishes” “…the link between intraspecific preferences and interspecific divergence and speciation remains to be more fully tested.”
Science. 2000 Oct 20;290(5491):516-9. Rapid evolution of reproductive isolation in the wild: evidence from introduced salmon. Hendry et al. [Comment in: Science. 2000 Oct 20;290(5491):462-3; Science. 2001 Jan 12;291(5502):251-2; Science. 2001 Mar 9;291(5510):1853]
“…nothing is known about how quickly reproductive isolation actually evolves when new environments are first colonized.”
Mem Inst Oswaldo Cruz. 2000;95 Suppl 1:193-200. Viral diseases and human evolution. Leal Ede S, Zanotto PM.
“…all viral agents cause disease and some may in fact be considered beneficial…”
[The authors go as far as to propose the oddity that virus are a ‘driving force’ in ‘human evolution’]
Annu Rev Microbiol. 1999;53:71-102. Wolbachia pipientis: microbial manipulator of arthropod reproduction. Stouthamer R, Breeuwer JA, Hurst GD.
“W. pipientis's most common effect is a crossing incompatibility between infected males and uninfected females. Little is known about the genetics and biochemistry of these symbionts because of their fastidious requirements. The affinity of W. pipientis for the microtubules associated with the early divisions in eggs may explain some of their effects.” “W. pipientis isolates are also of interest as vectors for the modification of wild insect populations, in the improvement of parasitoid wasps in biological pest control, and as a new method for interfering with diseases caused by filarial nematodes.”
[Similarly to the previous article, the authors here go as far as to indicate that other authors have also ‘agreed’ in the oddity that Wolbachia is a ‘driving force’ in insect, crustacean, mite, and filarial nematodes ‘speciation’]
Evolution Int J Org Evolution. 2000 Aug;54(4):1337-48. Tests of pleistocene speciation in montane grasshoppers (genus Melanoplus) from the sky islands of western North America. Knowles LL.
“…relationships among some taxa remain unresolved…”
Evolution Int J Org Evolution. 2000 Aug;54(4):1303-12. Interspecific genetics of mate recognition: inheritance of female acoustic preference in Hawaiian crickets. Shaw KL.
“Female mating behavior plays a fundamental role in the divergent evolution of mate recognition systems that may lead to speciation. Despite this important role, the phenotypic and genetic bases of female mating behavior remain poorly understood.” “I examine how preference differences are inherited in hybrid crosses between these species [two species of Hawaiian crickets, Laupala kohalensis and L. paranigra]. Females expressed unimodal preference functions and were generally more attracted to pulse rates characterizing their own species. Unimodal preference functions also characterized F1 and backcross generations, with hybrid females expressing preferences for intermediate pulse rates. Pulse rate preferences segregated in the backcross generation. Mean pulse rate preference matched mean pulse rate in both parental and hybrid generations. Based on F1 hybrids and segregation patterns in backcross females…” “…changes in acoustic communication signals occurred through shifts in mean pulse rates and pulse rate preferences among populations”
Genes Genet Syst. 2000 Jun;75(3):119-30. Sex gene pool evolution and speciation: a new paradigm. Singh RS, Kulathinal RJ.
“…a paradigm shift to the study of SRR [sex and reproduction related ] genes can provide new approaches to solving some of the old problems in evolutionary biology” “…genes affecting viability versus fertility is the key…”
Bioessays. 2000 Oct;22(10):938-46. Reproductive mode and speciation: the viviparity-driven conflict hypothesis. Zeh DW, Zeh JA.
“In birds and frogs, species pairs retain the capacity to produce viable hybrids…” “We propose that reproductive mode is a critically important but previously overlooked factor in the speciation process.” “The viviparity-driven conflict hypothesis provides a parsimonious explanation…”
Heredity. 2000 Jul;85 ( Pt 1):20-9. Are flightless Galapaganus weevils older than the Galapagos Islands they inhabit? Sequeira AS, Lanteri AA, Scataglini MA, Confalonieri VA, Farrell BD.
“This estimate exceeds geological ages of the extant emerged islands, although it agrees well with molecular dating of endemic Galapagos iguanas, geckos and lizards. An apparent explanation for the disagreement between geological and molecular time-frames is… submarine seamounts (sunken islands)…”
Chromosoma. 2000 Jul;109(4):245-58. Molecular cytogenetic analyses and phylogenetic studies in the Nicotiana section Tomentosae. Lim KY, Matyasek R, Lichtenstein CP, Leitch AR.
“Here we present another approach to phylogeny, using fluorescent in situ hybridisation [GISH]” “…interesting in the context of the debate on genetically modified organisms and the escape of genes into the wild.” “It is known for N. tabacum that gene conversion has converted most 18S-5.8S-26S rDNA units of N. sylvestris origin into units of an N. tomentosiformis type. Clearly if such a phenomenon were widespread across the genome, genomic in situ hybridisation (GISH) to distinguish the S and T genomes would probably not work since conversion would tend to homogenise the genomes. The fact that GISH does work suggests a limited role for gene conversion…”
J Theor Biol. 2000 Aug 21;205(4):527-42. Rapid speciation via parallel, directional selection on regulatory genetic pathways. Johnson NA, Porter AH.
“When the phenotype is subject to parallel selection in a pair of independent populations, we find that the fitnesses of F(1)and F(2)hybrids often drop to very low values as the populations respond in genetically different and incompatible ways. The simulations support the predictions of the analytical models. Hybrid fitness reduction occurs more often as the number of loci in the pathway increases, and as the binding site interactions become more complex. Less hybrid fitness reduction is seen when the populations start with imperfect binding in the pathway. In contrast, when we constructed the phenotype without gene regulation using multiplicative rules, isomorphic to the additive phenotype commonly assumed in evolutionary models, we found no appreciable F(1)fitness reduction and only slight F(2)fitness reduction. The interaction of genetic drift and mutation, even at very high rates, did not reduce hybrid fitness at all on the time-scales we considered” “…much more empirical information is needed on the effect of allelic variability in regulatory site interactions before this role is fully understood.”
Immunogenetics. 2000 Jun;51(7):556-75. Mhc class II B gene evolution in East African cichlid fishes. Figueroa et al.
“The analysis revealed point mutations to be the most important mechanism…” “The phylogeny of the exon was incongruent with that of the flanking introns…”
Mem Inst Oswaldo Cruz. 2000 Jul-Aug;95(4):545-51. Analysis of genetic diversity of Trypanosoma cruzi: an application of riboprinting and gradient gel electrophoresis methods. Stothard et al.
“Phenetic analysis of PCR-RFLP profiles indicated that, with one or two exceptions, stocks of T. cruzi could be broadly partitioned into two groups that formally corresponded to T. cruzi I and T. cruzi II respectively.” “Whether or not these divergent types are equally transcriptionally active throughout the life cycle, remain to be assessed.”
Med Vet Entomol. 2000 Jun;14(2):149-64. Cytogenetics of the Anopheles gambiae complex in Sudan, with special reference to An. arabiensis: relationships with East and West African populations. Petrarca et al.
“In the great majority of the samples all polymorphic inversions were found to be in Hardy-Weinberg equilibrium.”
Mol Phylogenet Evol. 2000 Jun;15(3):369-80. Evolution in the high Andes: the phylogenetics of Muscisaxicola ground-tyrants. Chesser RT.
“Relationships among Muscisaxicola species were found to differ substantially from those of previous views, suggesting convergence in traditional avian taxonomic characters within the genus.”
Am J Bot. 2000 Jun;87(6):793-810. Intersectional gene flow between insular endemics of Ilex (Aquifoliaceae) on the Bonin Islands and the Ryukyu Islands. Setoguchi H, Watanabe I I.
“Intersectional hybridization and nuclear gene flow were independently observed in insular endemics of ILEX: on both sets of islands…”
Heredity. 2000 May;84 ( Pt 5):587-98. Quantitative trait loci and gene interaction: the quantitative genetics of metapopulations. Goodnight CJ.
“…when there is only additive gene action, populations can differentiate for population means, but not for residual local average effects.”
Nature. 2000 May 25;405(6785):451-4. Chromosomal evolution in Saccharomyces. Fischer et al.
“The chromosomal speciation model invokes chromosomal rearrangements as the primary cause of reproductive isolation.” “Reproductive isolation in yeast is due to post-zygotic barriers, as many species mate successfully but the hybrids are sterile” “…rearrangements have occurred between closely related species, whereas more distant ones have colinear genomes. Thus, chromosomal rearrangements are not a prerequisite for speciation in yeast and the rate of formation of translocations is not constant. These rearrangements appear to result from ectopic recombination between Ty elements or other repeated sequences.”
Proc Natl Acad Sci U S A. 2000 May 9;97(10):5313-6. The phylogeny of closely related species as revealed by the genealogy of a speciation gene, Odysseus. Ting CT, Tsaur SC, Wu CI.
“Molecular differentiation between races or closely related species is often incongruent with the reproductive divergence of the taxa of interest” “…we analyzed DNA polymorphism at the Odysseus (OdsH) locus of hybrid sterility between Drosophila mauritiana and Drosophila simulans…” “This locus thus may represent a test case…”
Genetics. 2000 Mar;154(3):1053-68. Trinucleotide repeats are clustered in regulatory genes in Saccharomyces cerevisiae. Young ET, Sloan JS, Van Riper K.
“DNA trinucleotide repeats (TNRs) are found at a higher-than-expected frequency within ORFs, and the amino acids encoded by the TNRs represent a biased set. TNRs are rarely conserved between genes with related sequences, suggesting high instability or a recent origin.” “TNRs could serve as hot spots for recombination…”
Proc R Soc Lond B Biol Sci. 2000 Feb 7;267(1440):217-23. Constraints on polyploid evolution: a test of the minority cytotype exclusion principle. Husband BC.
“Polyploid evolution is often considered a mechanism of instant speciation; yet the establishment of rare tetraploids within diploid populations may be constrained by a frequency-dependent mating disadvantage (minority cytotype exclusion principle). I tested this hypothesis…” “Seed set in tetraploids was independent of cytotype frequency. The frequency-independent effect in tetraploids reflects higher assortative mating, partly because of non-random patterns of bee visitation. Bees visited a disproportionately high number of diploid inflorescences; however, the proportion of successive flights between tetraploids increased above random expectations as the frequency of tetraploids decreased. These results provide the first experimental test of frequency-dependent fitness in diploid-polyploid mixtures…”
Nature. 2000 Feb 24;403(6772):886-9. Rapid evolution of reproductive barriers driven by sexual conflict. Gavrilets S. [Comment in: Nature. 2000 Sep 14;407(6801):149-50.]
“The positive selection for evolutionary novelty that appears to be acting on fertilization systems seems paradoxical because successful reproduction requires the close matching of female and male traits.” “Here I develop a simple mathematical model…”
Plant Mol Biol. 2000 Jan;42(1):205-24. Hybridization, introgression, and linkage evolution. Rieseberg LH, Baird SJ, Gardner KA.
“We recommend that future studies of hybrid genomes focus on natural hybrids, not only because of the paucity of data in this area, but also because of the availability of highly recombinant hybrid genotypes in hybrid zones. Of particular value will be studies of long-lived or difficult-to-propagate organisms, which previously have not been amenable to genetic study.”
Mol Phylogenet Evol. 2000 Feb;14(2):232-49. Study of the evolutionary relationships among Limonium species (Plumbaginaceae) using nuclear and cytoplasmic molecular markers. Palacios et al.
“…the remaining subsections into which section Limonium is currently divided seem to be artificial.”
TRENDS IN ECOLOGY AND EVOLUTION. 2000 Mar;15(3):104-109. Colonization and diversification: towards a phylogeographic synthesis for the Canary Islands. Juan I I, Emerson BC, Orom I I, Hewitt GM.
“Some authors have considered Canarian endemisms as relicts of Tertiary origin, but new molecular data suggest a general pattern of continental dispersion…” “Recent phylogeographic studies are revealing variants of the simple stepping-stone colonization model that seems to hold for many Hawaiian groups. Many factors can generate deviations from such a pattern.” “An understanding of island colonization and diversification can best be developed from an ecosystem level synthesis as more data for the Canarian archipelago come to hand.”
Tissue Antigens. 1999 Dec;54(6):560-4. Trans-speciation maintenance in the MHC region of a polymorphism which includes a polymorphic dinucleotide locus, and the de novo arisal of a polymorphic tetranucleotide microsatellite. Crouau-Roy B.
“Alleles and the surrounding regions of DQCAR, a dinucleotide repeat tightly linked to HLA-DQB1, were sequenced in a range of primate species including man.” “The 5' sequence displayed six alleles in the individuals studied. One of these alleles was invariably associated with substitutions in the GT repeat and absence of the CTGT repeat…” “Those carrying allele 1 were only found in man…” “…alleles in the 5' region, but from different species, are… often more similar than alleles from the same species, a phenomenon already shown for some HLA genes.” “This study provides information… of the trans-speciation maintenance of polymorphism of its surrounding sequences.”
Genome. 1999 Dec;42(6):1033-41. Broad-sense sexual selection, sex gene pool evolution, and speciation. Civetta A, Singh RS.
“This article focuses on the need for an extension of sexual selection… as an alternative to models that limit speciation to strict demographic conditions or treat it simply as an epiphenomenon…”
Anim Behav. 1999 Jul;58(1):181-184. Mate choice in divergent morphs of the gastropod mollusc Littorina saxatilis (Olivi): speciation in action? Pickles AR, Grahame J.
“We investigated mate choice in the gastropod Littorina saxatilis (Olivi) in the laboratory, using snails taken from two shores, 20 km apart.”
Gene. 1999 Sep 30;238(1):115-34. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Brosius J.
“While the significance of middle repetitive elements had been neglected for a long time, there are again tendencies to ascribe most members of a given middle repetitive sequence family a functional role--as if the discussion of SINE (short interspersed repetitive elements) function only can occupy extreme positions” “…differences between the various classes of retrosequences concern mainly their copy numbers. Consequently, the function of SINEs should be viewed as pragmatic such as, for example, mRNA-derived retrosequences, without underestimating the impact of retroposition for generation of novel protein coding genes or parts thereof (exon shuffling by retroposition) and in particular of SINEs (and retroelements) in modulating genes and their expression.” “In addition to providing mobile regulatory elements, small RNA-derived retrosequences including SINEs can, in analogy to mRNA-derived retrosequences, also give rise to novel small RNA genes. Perhaps not representative for all SINE/master gene relationships, we gained significant knowledge by studying the small neuronal non-messenger RNAs, namely BC1 RNA in rodents and BC200 RNA in primates. BC1 is the first identified master gene generating a subclass of ID repetitive elements, and BC200 is the only known Alu element (monomeric) that was exapted as a novel small RNA encoding gene.”
Proc Natl Acad Sci U S A. 1999 Oct 12;96(21):11910-5. Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus) Schemske DW, Bradshaw HD Jr.
“A paradigm of evolutionary biology is that adaptation and reproductive isolation are caused by a nearly infinite number of mutations of individually small effect.” “Observations of F(2) hybrids produced by crossing bee-pollinated Mimulus lewisii with hummingbird-pollinated Mimulus cardinalis revealed that bees preferred large flowers low in anthocyanin and carotenoid pigments, whereas hummingbirds favored nectar-rich flowers high in anthocyanins. An allele that increases petal carotenoid concentration reduced bee visitation by 80%, whereas an allele that increases nectar production doubled hummingbird visitation.”
Curr Opin Microbiol. 1999 Oct;2(5):519-23. Gene transfer, speciation, and the evolution of bacterial genomes. Lawrence JG.
“Studies in microbial evolution have focused on the origin and vertical transmission of genetic variation within populations experiencing limited recombination. Genomic analyses have highlighted the importance of horizontal genetic transfer in shaping the composition of microbial genomes, providing novel metabolic capabilities, and catalyzing the diversification of bacterial lineages.”
J Theor Biol. 1999 Sep 7;200(1):19-37. Epigenetic inheritance, genetic assimilation and speciation. Pal C, Miklos I.
“Epigenetic inheritance systems enable the environmentally induced phenotypes to be transmitted between generations.” “…we discuss the "exploratory" behaviour of an epigenetic inheritance system on a one peak adaptive landscape. If a quantitative trait is far from the optimum, then it is advantageous to induce heritable phenotypic variation. Conversely, if the genotypes get closer to the peak, it is more favorable to canalize the phenotypic expression of the character. This process would lead to genetic assimilation. Next we show that the divergence of heritable epigenetic marks acts to reduce or to eliminate the genetic barrier between two adaptive peaks. Therefore, an epigenetic inheritance system can increase the probability of transition from one adaptive state to another.” “Remarkably, drift-induced transition is facilitated even if phenotypic variation is not heritable.”
Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10272-7. Developmental shifts and species selection in gastropods. Duda TF Jr, Palumbi SR.
“All eight species without planktonic life history phases recently and independently evolved this characteristic from ancestors with planktonic larval phases, showing that transitions in developmental mode are common in this group.” “Such results challenge the conclusion that increases in the number of nonplanktonic species relative to species with planktonic larvae over geologic time is necessarily a result of higher rates of speciation of nonplanktonic lineages…”
Science. 1999 Aug 20;285(5431):1265-7. Conservatism of ecological niches in evolutionary time. Peterson AT, Soberon J, Sanchez-Cordero V V.
“Theory predicts low niche differentiation between species over evolutionary time scales, but little empirical evidence is available.” “Reciprocal geographic predictions based on ecological niche models of sister taxon pairs of birds, mammals, and butterflies in southern Mexico indicate niche conservatism…”
Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9172-7. The signature of balancing selection: fungal mating compatibility gene evolution. May G, Shaw F, Badrane H, Vekemans X.
“A key problem in evolutionary biology has been distinguishing the contributions of current and historical processes to the maintenance of genetic variation.” “However, evidence for balancing selection and extended residence times has almost exclusively depended on identification of transspecific polymorphisms…” “The widespread geographic distribution of identical b1 alleles suggests that their association with differing A mating types is the result of recent recombination events.”
Nature. 1999 Jul 22;400(6742):354-7. On the origin of species by sympatric speciation. Dieckmann U, Doebeli M. [Comment in: Nature. 1999 Jul 22;400(6742):311-2.]
“Understanding speciation is a fundamental biological problem” “…sympatric speciation [lack of geographical isolation] has often been dismissed, partly because of theoretical difficulties. Most previous models analysing sympatric speciation concentrated on particular aspects of the problem while neglecting others. Here we present a model that integrates a novel combination of different features… [such as] assortative mating (where individuals mate preferentially with like individuals)…”
Nature. 1999 Jul 22;400(6742):351-4. Interactions among quantitative traits in the course of sympatric speciation. Kondrashov AS, Kondrashov FA. [Comment in: Nature. 1999 Jul 22;400(6742):311-2.]
“Here we use the hypergeometric phenotypic model to show that sympatric speciation is possible…”
Ann N Y Acad Sci. 1999 May 18;870:301-13. Evolution of DNA organization in hypotrichous ciliates. Prescott DM.
“…multiple, short, unique, noncoding sequences, called IESs, have been inserted into micronuclear genes. IESs are spliced out of each gene, and the gene segments, called MDSs, are ligated during conversion of the micronuclear genome to a macronuclear genome after cell mating.” “The origin of nonrandom scrambling patterns can be explained by a model of simultaneous insertion of multiple IESs into a germline gene…” “The significance of this fluidity for the life and evolution of these organisms is still obscure.”
Ann N Y Acad Sci. 1999 May 18;870:223-37. Speciation of cone snails and interspecific hyperdivergence of their venom peptides. Potential evolutionary significance of introns. Olivera et al.
“All 500 species of cone snails (Conus) are venomous predators. From a biochemical/genetic perspective, differences among Conus species may be based on the 50-200 different peptides in the venom of each species. Venom is used for prey capture as well as for interactions with predators and competitors. The venom of every species has its own distinct complement of peptides. Some of the interspecific divergence observed in venom peptides can be explained by differential expression of venom peptide superfamilies in different species and of peptide superfamily branching in various Conus lineages into pharmacologic groups with different targeting specificity. However, the striking interspecific divergence of peptide sequences is the dominant factor in the differences observed between venoms. The small venom peptides (typically 10-35 amino acids in length) are processed from larger prepropeptide precursors (ca. 100 amino acids).”
Mol Phylogenet Evol. 1999 Aug;12(3):360-85. Polyphyly and convergent morphological evolution in Commelinales and Commelinidae: evidence from rbcL sequence data. Givnish et al.
“Phylogenetic relationships of the five families of the order Commelinales remain an area of deep uncertainty in higher-level monocot systematics, despite intensive morphological and anatomical study.” “Species diversity is unrelated to the rate/amount of rbcL sequence evolution.”
Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7348-51. Mutation, recombination, and incipient speciation of bacteria in the laboratory. Vulic M, Lenski RE, Radman M.
“Mutations in the DNA mismatch repair system increase mutation and recombination. They may thereby promote the genetic divergence that underlies speciation...” “We knocked out the repair system in lines that had retained this function, and we restored function to those lines that had become defective. We then estimated recombination rates in various crosses between these repair-deficient and -proficient strains.”
Arch Virol. 1999;144(4):637-56. Evolution of herpes simplex virus type 1 under herpesviral evolutionary processes. Umene K, Sakaoka H.
“Relationships between HSV-1 genotypes and human ethnic groups can be traced by analyses of DNA polymorphisms of HSV-1 strains present in populations of various countries. A close association of an HSV-1 genotype with a particular historical human population seems probable. Such being the case, the host-linked mode is likely to be linked to diversification of HSV-1 in human populations.”
Anat Rec. 1999 Feb 15;257(1):15-31. Homeobox genes, fossils, and the origin of species. Schwartz JH.
“Ever since Darwin there has been a history of debate on the tempo and mode of evolution.” “I present a model of evolutionary change that is based on the Mendelian inheritance of mutations in regulatory genes and the fact that most nonlethal mutations arise in the recessive state. Since the new recessive allele will spread through many generations without expression until there is a critical mass of heterozygotes capable of producing homozygotes for the mutation, the novel feature thus produced will appear abruptly in the population and in more than one individual. This picture of punctuation is consistent with the fossil record, which typically fails to provide evidence of smoothly transitional states of morphological change.” “…this process does not depend on either reproductive isolation or genetic incompatibility... the species barrier between individuals is probably a matter of mate recognition.”
To be continued…
Member # 1201
posted 14. April 2004 16:42
Putting Limits on the Diversity of Life.
(Part Four. Continued... 6)
Rev Biol Trop. 1997 Jun;45(2):753-71. In search of a bacterial species definition. Moreno E.
“The bacterial species concept was examined within the framework of plant and animal associated alpha-2 proteobacteria, taking into consideration the phylogenetic, taxonomic and biological approaches as well as the microbiologists' perception. The virtue of the phylogenetic approach is that it gives an evolutionary perspective of the bacterial lineage; however the methods used possess low resolution for defining species located at the terminal branches of the phylogenetic trees. The merit of the taxonomic approach is that species are defined on the basis of multiple characteristics allowing high resolution at the terminal branches of dendograms; its disadvantage is the inaccuracy in the earlier nodes. On an individual level, the qualitative biological characteristics used for the definition of species frequently reveal shortcomings…” “…when considered together with the phylogenetic and taxonomic approaches, important uncertainties are discovered: these must be weighed if a practical definition of bacterial species is conceived. The microbiologists' perception is the criterion expressed by a group of sponsors who, based on scientific and practical grounds, propose a new bacterial species. The success of this new proposal is measured by its widespread acceptance and its permanence” “…the inherence is vertically transmitted as a result of binary fission and clonal expansion. This may be the case of some animal cell associated bacteria in which recombination appears to be precluded or exceptional. In the second case adaptive changes occurring within an individual can be horizontally transferred to many or all group members. This seems to be the condition of many intestinal and plant associated bacteria.” “…in clonal bacteria will depend almost exclusively on mutation and internal genetic rearrangement processes…” “…in reticulate bacteria will depend not only on these processes but in their genetic interactions with other bacterial strains. This uncertainty… is at the same time one of the key factors in defining a bacterial species.”
Antonie Van Leeuwenhoek. 1997 Jul;72(1):63-76. Eukaryotic molecular biodiversity: systematic approaches for the assessment of symbiotic associations. Hackstein JH.
“ 'Biodiversity' addresses the wealth of species that constitute the biosphere. Notwithstanding that they have been regarded as mental constructs in the past, species are really existing entities that form and disappear…” “Molecular techniques allow…” “…incredible diversity of protists: their importance for the global conversion of biomass and energy had been greatly underestimated until recently.” “Therefore, new concepts are required to calculate global biodiversity. Systematic approaches that evaluate small, complex biotopes exhaustively, or that calculate the number of symbionts or parasites on the basis of their potential hosts have already led to a substantial revision of earlier estimations. Here, an evaluation of potential animal hosts for methanogenic archaea and intestinal protists is described that reveals the importance of host taxonomy for the assessments. If molecular techniques can confirm the presumed specificity of symbiotic and parasitic associations a substantial revision of the current assumptions about the biodiversity of such organisms will be necessary.”
Antonie Van Leeuwenhoek. 1998 Jan;73(1):25-33. Santa Rosalia revisited: why are there so many species of bacteria? Dykhuizen DE.
“The diversity of bacteria in the world is very poorly known. Usually less than one percent of the bacteria from natural communities can be grown in the laboratory. This has caused us to underestimate bacterial diversity and biased our view of bacterial communities. The tools are now available to estimate the number of bacterial species in a community and to estimate the difference between communities. Using what data are available, I have estimated that thirty grams of forest soil contains over half a million species. The species difference between related communities suggests that the number of species of bacteria may be more than a thousand million.”
[Sub-speciation is the real variation within species. Sub-speciation is confounded with ‘speciation’, which is the evolutionist speculation of the fictitious ‘jumping’ of one species to be transformed into another species. The best test is the original definition of kind, that can be applied to the word ‘Species’: “Fertile parents producing fertile offspring”, that implies the need of the reproductive ‘fertility test’ also for the offspring. ‘Evolution’ tries to confound the unlearned with tricky and weak definitions of ‘species’ to walk around and aside from the simple and original truth present in the word ‘kind’]
Proc R Soc Lond B Biol Sci. 1998 Jan 7;265(1390):25-32. Spatially induced speciation prevents extinction: the evolution of dispersal distance in oscillatory predator-prey models. Savill NJ, Hogeweg P.
“…if the populations reproduce sexually, local gene flow can inhibit the evolution of increasing dispersal distances, and hence the spatial patterns are not lost. Speciation and coexistence can also occur in the sexually reproducing species.”
[Same comment as in the previous Abstract]
Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7768-75. Genetics and the origin of bird species. Grant PR, Grant BR.
“Ideas about the genetics of speciation in general trace back to Dobzhansky who worked with Drosophila. These ideas are an insufficient guide for reconstructing speciation in birds…” “…the genetic basis to the origin of bird species is to be sought in the inheritance of adult traits…” “The genetic basis of the origin of postmating isolating factors affecting the early development of embryos (viability) and reproductive physiology (sterility) is almost completely unknown. Bird speciation is facilitated by small population size, involves few genetic changes, and occurs relatively rapidly.”
[Same comment as in the earlier Abstract. Here ‘sub-speciation’ is been sold as ‘speciation’ in order to keep the ‘double-talk’, the ‘weak and confusing terminologies’, and the illusory concepts of ‘evolution’, but the full text, as demonstrated before, presents a different picture in which different ‘species’ of Galapagos finches interbreed and produce fertile offspring, being then, not different ‘species’ but the same ‘species’. The error being in the easy and superficial morphological classification done by Darwin and by others, instead of being based on the ancient definition of ‘kind’ previously discussed (“fertile progenitors yielding fertile little ones that in its time will breed producing fertile offspring”). ‘Species’ cannot only be defined morphologically, as dogs, cows and humans demonstrate]
Mol Phylogenet Evol. 1997 Apr;7(2):158-72. Evolutionary age of the Galapagos iguanas predates the age of the present Galapagos islands. Rassmann K.
“The results strengthen the hypothesis that extended speciation times in the Galapagos are possible and provide an estimate of the minimum time inhabited islands of the archipelago may have existed.”
[Those iguanas also interbreed, being then the same species; so, the ‘dating’ here and in every other ‘evolutionary estimate’ is totally useless]
Proc R Soc Lond B Biol Sci. 1997 Mar 22;264(1380):355-60. Genetic distinctiveness of a village population of house mice: relevance to speciation and chromosomal evolution. Fraguedakis-Tsolis S, Hauffe HC, Searle JB.
“It has frequently been proposed that genetic drift/founder events are of importance in the fixation of chromosomal rearrangements; this study provides the first direct evidence for their occurrence in alpine mouse populations.”
[Did they did fertility experiments to see if both kinds of mice interbreed and have fertile offspring? No]
J Theor Biol. 1995 Dec 7;177(3):237-45. A genetical theory of species selection. Rice SH.
“So long as we are careful in defining "species", the logic of species selection is sound. This does not mean, however, that this process can influence evolutionary dynamics under realistic conditions. The principal challenge to the efficacy of species selection as an evolutionary mechanism is the idea that selection between individuals within species will be so much more efficient as to swamp out any effects of selection between species.” “Quantitative characters, such as body size, generally change too readily for species selection to be relevant….” “Complex characters, however, may be good candidates to be influenced by species selection. The interaction of selection within and between species can be subtle, with individual selection looking, from the standpoint of a species, very much like development of an individual.”
[‘Species’ defined as a Kind, as previously declared]
Philos Trans R Soc Lond B Biol Sci. 1996 Jun 29;351(1341):753-64. Small mammal differentiation on islands. Berry RJ.
“The reason for the distinctiveness of small mammals on islands has traditionally attracted some imaginative story-telling, usually invoking isolation (as a relict) followed by adaptation and/or random genetic changes.” “Probably most post-colonization change is adaptive, although possibly limited in extent both by the initial paucity of variation and by the conservative effect of intragenomic interactions” “…the 'founder effect' or principle commonly invoked in discussions about evolution on islands involves a founder 'event', followed by founder 'selection'. Island differentiation is not necessarily a precursor to speciation…” “Notwithstanding, island forms provide a valuable 'laboratory' for testing new genetic combinations, a small proportion of which may prove evolutionarily exciting. Only more empirical studies will uncover their evolutionary importance.”
J Mol Evol. 1997;44 Suppl 1:S57-64. Genome plasticity as a paradigm of eubacteria evolution. Watanabe H, Mori H, Itoh T, Gojobori T.
“…We found that dynamic rearrangements have so frequently occurred in eubacterial genomes as to break operon structures…” “Interestingly, in such eubacterial genomes of high plasticity, we could find several highly conservative regions with the longest conserved region comprising the S10, spc, and alpha operons.”
Development. 1999 Feb;126(5):851-9. Fossils, molecules and embryos: new perspectives on the Cambrian explosion. Valentine JW, Jablonski D, Erwin DH.
“Various attempts to date those branchings by using molecular clocks have disagreed widely” “…timing of the evolution of the developmental systems of living metazoan body plans is still uncertain…”
J Biochem (Tokyo). 1999 Apr;125(4):649-57. Halobacterial rhodopsins. Mukohata et al.
“The four kinds of rhodopsin in each strain are assumed, on the basis of their genera-specific distributions…” “The original rhodopsin ancestor is speculated to be closest to the proton pump (bacteriorhodopsin).”
Mol Biol Evol. 1996 Feb;13(2):397-406. Positive selection and sequence rearrangements generate extensive polymorphism in the gamete recognition protein bindin. Metz EC, Palumbi SR.
“Bindin is a gamete recognition protein of sea urchins that mediates species-specific attachment of sperm to an egg-surface receptor during fertilization. Sequences of bindin from closely related urchins show fixed species-specific differences. Within species, highly polymorphic bindin alleles result from point substitution, insertion/deletion, and recombination.” “These results show that polymorphism in mate recognition loci… can arise within natural populations.”
J Mol Biol. 1999 Jan 8;285(1):163-74. Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation. Ihara et al.
“By calculating the branch lengths between the gene duplication point and each halophilic archaea speciation point, we could speculate…”
Proc R Soc Lond B Biol Sci. 1999 Apr 7;266(1420):677-85. Molecular phylogenetic evidence for the evolution of specialization in anemonefishes. Elliott JK, Lougheed SC, Bateman B, McPhee LK, Boag PT.
“The molecular phylogeny differs from the tree based on morphological data…” “Further phylogenetic studies of additional anemonefish species are required to substantiate this hypothesis.”
Immunogenetics. 1998;47(2):115-23. Characterization of chimpanzee TCRV gene polymorphism: how old are human TCRV alleles? Jaeger EE, Bontrop RE, Parham P, Wickings EJ, Kadwell M, Lanchbury JS.
“The functional relevance of the majority of human T-cell receptor A and B [TCRA and B] variable region gene polymorphisms is controversial.” “We investigated at the DNA level whether 15 human TCRA and B polymorphisms exist in contemporary chimpanzee populations. Polymorphisms consisted of variable region replacements, a recombination signal sequence base change, and silent mutations. With one exception, none of these human TCR polymorphisms were observed in contemporary chimpanzees.” “Chimpanzee TCRAV and BV regions were however polymorphic for variation so far not observed in human groups” “…TCRA and B polymorphisms have not been maintained by selection to the same degree as postulated for MHC polymorphisms.”
J Hum Evol. 1999 Jun;36(6):687-703. Evolution of a HOXB6 intergenic region within the great apes and humans. Deinard A, Kidd K.
“Data accumulated over the past decade from several loci suggest that nonhuman primates have a greater amount of intraspecific genetic variation relative to humans” “…these HOXB6 data continue to support earlier findings that Homo sapiens sapiens has less genetic variation than any great ape species (Ruano et al., 1992; Deinard & Kidd, 1995)”
Genetics. 1998 Oct;150(2):863-72. Speciation and domestication in maize and its wild relatives: evidence from the globulin-1 gene. Hilton H, Gaut BS.
“…the domestication of maize was a recent event that could have been based on a very small number of founding individuals. Maize retained a substantial proportion of the genetic variation of its progenitor through this founder event, but diverged rapidly in morphology.”
Front Biosci. 1998 Jul 27;3:D739-45. Evolution of the human HLA-DR region. Andersson G.
“…in the contemporary human population… species-specific DRB gene organizations are found. The plasticity of DR gene organization as well as the extensive allelic polymorphism of expressed DR-beta molecules are features which suggest that DR molecules are under distinct selective pressure compared to HLA-DQ and HLA-DP class II molecules. The extensive allelic polymorphism of HLA-DR transplantation antigens is exclusively provided by the beta-chain of these heterodimeric antigen presenting molecules. Most of this polymorphism appears to have been generated recently.”
Proc Natl Acad Sci U S A. 1997 Aug 5;94(16):8634-9. Rapid evolution of sex-related genes in Chlamydomonas. Ferris PJ, Pavlovic C, Fabry S, Goodenough UW.
“Biological speciation ultimately results in prezygotic isolation-the inability of incipient species to mate with one another-but little is understood about the selection pressures and genetic changes that generate this outcome.” “Low stringency Southern analyses failed to detect any fus1 homologs in other Chlamydomonas species and detected only one mid homolog… found in C. incerta, the species in culture that is most closely related to C. reinhardtii. Its mid gene carries numerous nonsynonymous and synonymous codon changes compared with the C. reinhardtii mid gene. In contrast, very high sequence conservation of both the mid and fus1 sequences is found in natural isolates of C. reinhardtii, indicating that the genes are not free to drift within a species but do diverge dramatically between species. Striking divergence of sex determination and mate recognition genes also has been encountered in a number of other eukaryotic phyla, suggesting that unique, and as yet unidentified, selection pressures act on these classes of genes…”
Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14628-31. The shape of female mating preferences. Ritchie MG.
“The shape of preferences is important in many models of sexual selection, mate recognition, communication, and speciation, yet it has rarely been measured precisely. Here I examine preference shape for male calling song in a bushcricket (katydid). Preferences change dramatically between races of a species, from strongly directional to broadly stabilizing (but with a net directional effect). Preference shape generally matches the distribution of the male trait. This is compatible with a coevolutionary model of signal-preference evolution, although it does not rule out an alternative model, sensory exploitation. Preference shapes are shown to be genetic in origin.”
Mol Phylogenet Evol. 1996 Jun;5(3):495-510. Phylogenetics and evolution of the Daphnia longispina group (Crustacea) based on 12S rDNA sequence and allozyme variation. Taylor et al.
“Although members of the crustacean genus Daphnia have been the target of much research, there is little understanding of the group's evolutionary history. We addressed this gap by inferring…” “This discordance was consistent with…” “…the estimated times of these divisions were inconsistent with vicariance events suggesting recent dispersal among continents.”
Philos Trans R Soc Lond B Biol Sci. 1996 Mar 29;351(1337):349-60. The systematics of North American Daphnia (Crustacea: Anomopoda): a molecular phylogenetic approach. Colbourne JK, Hebert PD.
“Despite extensive studies on the ecology and evolution of the freshwater microcrustacean Daphnia, there is little understanding of the evolutionary history of the genus. Past attempts at reconstructing phylogenetic relationships among Daphnia species have been highly controversial, mainly because of the poor taxonomy of the genus. However, following a revised taxonomy of the daphniid fauna of North America, we conducted a comprehensive appraisal of systematic relationships within the genus…” “…cladogenesis in the genus has been constrained. Our study also reveals that interspecific hybridization occurs between taxa which show very large sequence divergence (up to 14%)…”
Biosystems. 1997;43(2):137-44. Reinforcement of genetic coherence: a single-locus model. Steiner W, Gregorius HR.
“While mechanisms of speciation have received considerable attention in biology, their counterpart, mechanisms of genetic coherence, are addressed only implicitly, if at all.” “Mating systems thus serve the preservation of adaptability.”
Chromosome Res. 1998 Aug;6(5):351-60. Repetitive DNA sequences in the common vole: cloning, characterization and chromosome localization of two novel complex repeats MS3 and MS4 from the genome of the East European vole Microtus rossiaemeridionalis. Elisaphenko et al.
“Comparative analysis revealed no significant stretches of homology in the nucleotide sequences between the two repeats, suggesting that the repeats originated independently…” “The localization pattern of the repeats on the vole chromosomes confirms the independent origin of the two repeats…”
Heredity. 1999 Apr;82 Pt 4:347-54. Sexual imprinting, learning and speciation. Irwin DE, Price T.
“Learned mate preferences may play an important role in speciation. Sexual imprinting is a process whereby mate preferences are affected by learning at a very young age, usually using a parent as the model.” “If different species are hybridizing, both sexual imprinting and learning to avoid heterospecifics during adulthood promote assortative mating…” “The role of behaviour and learning in completing the speciation process is relatively overlooked.”
Immunol Rev. 1999 Feb;167:119-32. Toward an evolutionary genomics of the avian Mhc. Edwards SV, Hess CM, Gasper J, Garrigan D.
“These and other results suggest that the evolution of class II B genes in birds conforms to a mixture of several models…” “Large-scale sequencing studies in these and other species, though still in their infancy, will prove invaluable for studying the comparative structures of avian Mhcs, as well as patterns of selection, mutation and linkage disequilibrium at several scales.”
Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):5107-10. Phylogeny of a rapidly evolving clade: the cichlid fishes of Lake Malawi, East Africa. Albertson RC, Markert JA, Danley PD, Kocher TD.
“Lake Malawi contains a flock of >500 species of cichlid fish that have evolved from a common ancestor within the last million years. The rapid diversification of this group has been attributed to morphological adaptation and to sexual selection, but the relative timing and importance of these mechanisms is not known.” “Previous attempts to reconstruct the relationships among these taxa using molecular methods have been frustrated by the persistence of ancestral polymorphisms within species. Here we describe results from a DNA fingerprinting technique that overcomes this problem by examining thousands of polymorphisms distributed across the genome.” “We demonstrate that adaptive divergence in trophic morphology played an important role during the early history of the lake. Subsequent species diversity has arisen with little change in trophic morphology, which suggests that other forces are responsible for the continued speciation of these fishes.”
Mol Phylogenet Evol. 1999 Apr;11(3):426-40. Evolution of a mitochondrial cytochrome b gene sequence in the species-rich genus sebastes (Teleostei, Scorpaenidae) and its utility in testing the monophyly of the subgenus Sebastomus. Rocha-Olivares A, Kimbrell CA, Eitner BJ, Vetter RD.
“The monophyly of the genus [rockfishes (Sebastes)] is generally accepted, as is the validity of most of the numerous species found along the West Coast of North America. However, the subgeneric groupings that would help in the proposal and interpretation of various speciation schemes are poorly supported based on widely overlapping morphological characters. The use of genetic characters provides an alternative approach.” “The monophyly of Sebastomus was supported in extensive phylogenetic analyses using distance, cladistic, and likelihood methods. Further corroboration was obtained from permutation- and simulation-based statistical tests.”
J Mol Evol. 1998 Dec;47(6):772-83. Phylogenetic relationships within the genus Equus and the evolution of alpha and theta globin genes. Oakenfull EA, Clegg JB.
“These results from the alpha genes are corroborated by theta gene data and are in contrast to mitochondrial DNA studies of the phylogeny of this genus.”
Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2864-8. Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. de Vargas et al.
“Our results, together with previous studies, suggest that a considerable part of the diversity among planktonic foraminifers has been overlooked in morphological taxonomies.”
Nucleic Acids Res. 1999 Mar 1;27(5):1243-50. The evolutionary scrambling and developmental unscrambling of germline genes in hypotrichous ciliates. Prescott DM.
“Genes in the germline (micronuclear) genome of hypotrichous ciliates are interrupted by multiple, short, non-coding, AT-rich sequences called internal eliminated segments, or IESs. During conversion of a micronucleus to a somatic nucleus (macronucleus) after cell mating, all IESs are excised from the germline genes and the gene segments, called macronuclear-destined segments, or MDSs, are spliced. Excision of the approximately 150 000 IESs from a haploid germline genome in Oxytricha nova requires approximately 150 000 recombinant events. In three of 10 genes the MDSs are scrambled. During macronuclear development the MDSs are unscrambled, possibly by folding of the DNA to allow MDSs to ligate in the correct order. The nine MDSs in the actin I gene of O.nova are scrambled in the random order, 3-4-6-5-7-9-2-1-8, and MDS 2 is inverted. The 14 MDSs in the alphaTP gene of O.nova and Stylonychia mytilus are scrambled in the non-random order, 1-3-5-7-9-11-2-4-6-8-10-12-13-14. The 45 MDSs in the DNA pol alpha gene are non-randomly scrambled into an odd/even series, with an inversion of one-third of the gene.” “The non-random scrambled patterns in the alphaTP and DNA pol alpha genes are explained by multiple, simultaneous IES insertions.” “Shifting of IESs has the effect of 'transferring' nucleotides from one MDS to another, but does not change the overall sequence of nucleotides in the combined MDSs.”
Curr Opin Genet Dev. 1997 Dec;7(6):807-13. Origin, evolution, and excision of internal elimination segments in germline genes of ciliates. Prescott DM.
“Recently initiated molecular/genetic studies may eventually clarify the role of the parental macronucleus in IES excision and gene unscrambling as well as the molecular mechanisms of these events.”
Nat Genet. 1998 Dec;20(4):362-5. Genomic imprinting is disrupted in interspecific Peromyscus hybrids. Vrana PB, Guan XJ, Ingram RS, Tilghman SM. [Comment in: Nat Genet. 1998 Dec;20(4):315-6; Nat Genet. 1999 Jun;22(2):130-1] [Erratum in: Nat Genet 1999 Feb;21(2):241]
“Genomic imprinting, the unequal expression of gene alleles on the basis of parent of origin, is a major exception to mendelian laws of inheritance. By maintaining one allele of a gene in a silent state, imprinted genes discard the advantages of diploidy, and for this reason the rationale for the evolution of imprinting has been debated” “…theory predicts that there should be no selection for imprinting in a monogamous species. Crosses between the monogamous rodent species Peromyscus polionotus and the polyandrous Peromyscus maniculatus yield progeny with parent-of-origin growth defects that could be explained if imprinting was absent in the monogamous species. We find, however, that imprinting is maintained in P. polionotus, but there is widespread disruption of imprinting in the hybrids.”
FEMS Microbiol Lett. 1998 Nov 15;168(2):303-11. Multiple copies of ammonia monooxygenase (amo) operons have evolved under biased AT/GC mutational pressure in ammonia-oxidizing autotrophic bacteria. Klotz MG, Norton JM.
“While the near identity of the multiple operon copies makes it impossible to determine…” “We propose that the elimination of third basepair degeneracy between copies within one organism is implemented by a rectification mechanism…”
Mol Microbiol. 1998 Nov;30(3):647-56. A gonococcal porA pseudogene: implications for understanding the evolution and pathogenicity of Neisseria gonorrhoeae. Feavers IM, Maiden MC.
“Unexpectedly, a porA gene was identified in the gonococcal genome.” “Lack of PorA expression in the gonococcus resulted from mutations in the promoter region, which prevented transcription, and frameshift mutations in the coding region of the porA gene.” “This implies that, while advantageous during colonization of the upper respiratory tract, this protein has no function in, or hinders, colonization of the urogenital tract.”
Electrophoresis. 1998 Oct;19(14):2391-5. Analysis of sequence homogenisation in rDNA arrays of Haemonchus contortus by denaturing gradient gel electrophoresis. Gasser et al.
“Testing different theories of concerted evolution experimentally has been hampered mainly due to the lack of appropriate model systems and technical limitations.” “The results showed that individuals of interbreeding populations of H. contortus can have rDNA arrays that are partially or fully homogenised for different sequence variants (despite interindividual variation), suggesting that the homogenisation process is driven mainly by intrachromosomal exchange. The findings also demonstrated the capacity of the DGGE-sequencing strategy to quantify the frequency of ITS-2 sequence types within individual nematodes from different populations without the need for cloning or Southern blot procedures. This has important implications for studying the mechanisms of sequence homogenisation in rDNA and pre-rRNA processing…”
J Theor Biol. 1998 Jun 21;192(4):545-559. Information Theory, Scaling Laws and the Thermodynamics of Evolution. Wallace R, Wallace RG.
“Renormalization symmetry and the Legendre transformation are imposed on a parametized form of ergodic source uncertainty, a widely-applied model for "languages" ranging from the spoken word to genetic codes. Using the Shannon-McMillan theorem to identify a duality between source uncertainty and free energy density, this procedure:” “…gives a power law for that phase change near transition…” “…gives "equations of state" relating ensemble averages which should be observable within coalesced systems…” “…and comparison made with the work of Eigen and his associates.”
Cytobios. 1998;93(374):141-6. Amplification of telomeric DNA and the extent of karyotypic evolution. Pathak S, Dolhonde JA, Multani AS.
“…not all C-banded regions in rodent species are telomeric DNA.”
Science. 1998 Oct 16;282(5388):471-2. Host-race formation in the common cuckoo. Marchetti et al.
“…gene flow through the male line prevents completion of the speciation process.”
Genetica. 1998;102-103(1-6):569-80. Genetic measurement of theory of epistatic effects. Wagner GP, Laubichler MD, Bagheri-Chaichian H.
“Epistasis is defined as the influence of the genotype at one locus on the effect of a mutation at another locus. As such it plays a crucial role…” “In mathematical population genetics, however, epistasis is often represented as a mere noise term in an additive model of gene effects.” “A review of general measurement theory shows that the scaling of a quantitative concept has to reflect the empirical relationships among the objects.” “The Kacser Burns model of metabolic flux is analyzed for the presence of epistatic effects on flux. It is shown that the non-linearity of the Kacser Burns model is not sufficient to cause A x A epistasis among the genes coding for enzymes. It is concluded that non-linearity of the genotype-phenotype map is not sufficient to cause epistasis. Finally, it is shown that there exist correlations among the additive and epistatic effects among pairs of loci, caused by the inherent symmetries of Mendelian genetic systems. For instance, it is shown that a mutation that has a larger than average additive effect will tend to decrease the additive effect of a second mutation, i.e., it will tend to have a negative (canalizing) interaction with a subsequent gene substitution. This is confirmed in a preliminary analysis of QTL-data for adult body weight in mice.”
Mol Phylogenet Evol. 1998 Aug;10(1):104-17. A molecular perspective on the systematics and evolution of the genus Arvicanthis (Rodentia, Muridae): inferences from complete cytochrome b gene sequences. Ducroz JF, Volobouev V, Granjon L.
“Systematics of the genus Arvicanthis, the African unstriped grass rat, are somewhat controversial. Most recent taxonomic revisions list five to six species but the definition of some of these (Arvicanthis dembeensis, Arvicanthis nairobae, and Arvicanthis niloticus) is uncertain.” “We also suggest referring to A. dembeensis as A. niloticus, as our cytochrome b data do not support its recognition as a distinct species.” “Confrontation of our molecular results with chromosomal data shows a high degree of congruence between the two datasets.”
Mol Phylogenet Evol. 1998 Aug;10(1):37-48. Rapid speciation, morphological evolution, and adaptation to extreme environments in South African sand lizards (Meroles) as revealed by mitochondrial gene sequences. Harris DJ, Arnold EN, Thomas RH.
“The DNA data provide some corroboration for the relationships within Meroles based on morphology and consequently for the model as well. The disparity in internal branch lengths between the maximum parsimony morphological and maximum likelihood DNA trees may well indicate that the multiple adaptations to desert conditions arising on the main lineage of Meroles evolved quite rapidly.”
Mol Phylogenet Evol. 1998 Aug;10(1):11-22. Molecular phylogeny and evolution of the deep-sea fish genus Sternoptyx. Miya M, Nishida M.
“…associated structures strongly supported the former as the preferred hypothesis.” “There has been no discernible speciation event in the southern population…”
J Mol Evol. 1998 Aug;47(2):211-21. Shaping of Drosophila alcohol dehydrogenase through evolution: relationship with enzyme functionality. Atrian S, Sanchez-Pulido L, Gonzalez-Duarte R, Valencia A.
“Drosophilidae is a large, widely distributed family of Diptera including 61 genera, of which Drosophila is the most representative.” “Drosophila alcohol dehydrogenase (ADH), a member of the short-chain dehydrogenase/reductase family (SDR), is responsible for the oxidation of alcohols, but its direct involvement in fitness, including alcohol tolerance and utilization, gives rise to much controversy.” “To build a hypothesis which could shed light on this dilemma, we analyzed the amino acid variability found in the 57 protein ADH sequences reported up to now, identified the taxon-specific residues, and localized them in a three-dimensional ADH model. Our results define three regions whose shaping has been crucial for ADH differentiation…”
Mol Biol Evol. 1998 Jul;15(7):901-9. Sex-related genes, directional sexual selection, and speciation. Civetta A, Singh RS.
“Recent studies of speciation have been dominated by a molecular approach to dissect the genetic basis of hybrid male sterility, a specific form of postmating reproductive isolation. However, relatively little attention has been paid to the evolution of genes involved in premating isolation and genes generally involved in other sex-related functions (e.g., mating behavior, fertilization, spermatogenesis, sex determination)” “…a saturation in the number of nucleotide substitutions… may mask any sign of directional selection between more distantly related species.”
Int J Parasitol. 1998 May;28(5):727-37. Parasite extinction and colonisation and the evolution of parasite communities: a simulation study. Vickery WL, Poulin R.
“…because the composition of parasite communities tends to reflect their ancestry, the effect of host ecology will often be very difficult to detect.”
Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):5112-5. Diploid hybrid speciation in Penstemon (Scrophulariaceae). Wolfe AD, Xiang QY, Kephart SR.
“Hybrid speciation has played a significant role in the evolution of angiosperms at the polyploid level. However, relatively little is known about the importance of hybrid speciation at the diploid level.” “Previous studies were inconclusive regarding the purported hybrid nature of these species because of a lack of molecular markers sufficient to differentiate the parental taxa in the hybrid complex. We developed hypervariable nuclear markers using inter-simple sequence repeat banding patterns to test these classic hypotheses of diploid hybrid speciation in Penstemon. Each species in the hybrid complex was genetically distinct, separated by 10-42 species-specific inter-simple sequence repeat markers. Our data do not support the hybrid origin of P. spectabilis but clearly support the diploid hybrid origin of P. clevelandii. Our results further suggest that the primary reason diploid hybrid speciation is so difficult to detect is the lack of molecular markers able to differentiate parental taxa from one another…”
J Mol Evol. 1998 May;46(5):589-601. Molecular evolution of the globin gene cluster E in two distantly related midges, Chironomus pallidivittatus and C. thummi thummi. Hankeln et al.
“Surprisingly, globin gene E, for which up to now no corresponding protein has been detected in the larval hemolymph of C. t. thummi, shows the highest degree of interspecies sequence conservation. This points to an essential, as yet unknown function of this globin.”
Folia Primatol (Basel). 1998;69 Suppl 1:250-85. Evolutionary history of lorisiform primates. Rasmussen DT, Nekaris KA.
“Several Eocene prosimians of the northern continents, including both omomyids and adapoids, have been suggested as possible lorisoid ancestors, but these cannot be substantiated as true strepsirhines.” “Another unnamed Fayum primate resembles modern cheirogaleids in dental structure and body size” “…the debate about whether these represent lorisines or galagines is reviewed. Neontological data are used to address the controversial branching sequences among extent lorisid clades.” “The hypothesis of an African clade containing both pottos and galagos to the exclusion of Asian lorisines is less tenable. True galagines are found in the fossil record of Namibia, while true lorisines are known from the Miocene of Asia.”
Mol Phylogenet Evol. 1998 Apr;9(2):204-19. Molecular evolution of the internal transcribed spacers (ITS1 and ITS2) and phylogenetic relationships among species of the family Cucurbitaceae. Jobst et al.
“…deviations to the taxonomic classification were also observed.” “A polyphyletic origin of the New World species must be considered. In the genus Cucurbita different "types" of ITS sequences within one species exist, possibly due to the high frequency of introgression during domestication or due to polyploidization events…”
Philos Trans R Soc Lond B Biol Sci. 1998 Feb 28;353(1366):261-74. Sexual conflict and speciation. Parker GA, Partridge L.
“We review theoretical models relevant to resolution of this conflict.”
Philos Trans R Soc Lond B Biol Sci. 1998 Feb 28;353(1366):177-86. Factors affecting levels of genetic diversity in natural populations. Amos W, Harwood J.
“[In] the northern elephant seal and the cheetah… genetic polymorphism is virtually absent” “…we suggest that the low levels of variability observed in endangered populations are more likely to result from a combination of publication biases, which tend to inflate the level of variability which is considered 'normal', and inbreeding effects, which may hasten loss of variability due to drift” “…evidence that heterozygous sites mutate more frequently than equivalent homozygous sites, plausibly because mismatch repair between homologous chromosomes during meiosis…” “Our model, based on meiotic drive in mammals, but easily extended to other systems, would tend to facilitate population isolation by generating molecular incompatabilities.”
Mol Biol Evol. 1998 Jan;15(1):17-27. The evolutionary relationships between the two bacteria Escherichia coli and Haemophilus influenzae and their putative last common ancestor. de Rosa R, Labedan B.
“…the memory of the gene order present in the last common ancestor has been blurred, but a few short conserved chromosomal fragments can still be detected in present-day E. coli and H. influenzae.”
Genetics. 1997 Nov;147(3):1381-7. Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Feldman et al.
“…genomic changes may provide the physical basis for the diploid-like meiotic behavior of polyploid wheat.”
Proc Natl Acad Sci U S A. 1998 Jan 20;95(2):612-6. Slow rate of molecular evolution in high-elevation hummingbirds. Bleiweiss R.
“Estimates of relative rates of molecular evolution from a DNA-hybridization phylogeny for 26 hummingbird species provide evidence for a negative association between elevation and rate of single-copy genome evolution. This effect of elevation on rate remains significant even after taking into account a significant negative association between body mass and molecular rate. Population-level processes do not appear to account for these patterns because (i) all hummingbirds breed within their first year and (ii) the more extensive subdivision and speciation of bird populations living at high elevations predicts a positive association between elevation and rate. The negative association between body mass and molecular rate in other organisms has been attributed to higher mutation rates in forms with higher oxidative metabolism. As ambient oxygen tensions and temperature decrease with elevation, the slow rate of molecular evolution in high-elevation hummingbirds also may have a metabolic basis.”
Int J Parasitol. 1997 Nov;27(11):1289-97. Parasite speciation within or between host species?--phylogenetic evidence from site-specific polystome monogeneans. Littlewood DT, Rohde K, Clough KA.
“…speciation has not occurred in one host. Morphological evolution of polystomes has been very slow: few differences between species and even genera… and this is matched by low substitution rates of nucleotides, and the ambiguous position of species of different genera, depending on whether COI or 28S rDNA sequences are used.”
Schizophr Bull. 1997;23(3):521-3. Temporolimbic or transcallosal connections: where is the primary lesion in schizophrenia and what is its nature? Crow TJ. [Comment on: Schizophr Bull. 1997;23(3):423-35.]
“A critique of the article by Bogerts on the temporolimbic system theory is presented.” “The anatomical changes can be considered as a boundary component of the anatomical variation that is characteristic of the species.”
[This author concluded oddly saying, "Language and psychosis have a common evolutionary origin"!]
J Mol Evol. 1997 Nov;45(5):499-508. Evolution of orthologous intronless and intron-bearing globin genes in two insect species. Gruhl M, Kao WY, Bergtrom G.
“While globin genes ctt-2beta and ctt-9.1 in Chironomus thummi thummi each have a single intron, all of the other insect globin genes reported so far are intronless.” “Maintenance of a large family of globin genes not only ensured high levels of hemoglobin production, but may have facilitated the extensive divergence of chironomids into as many as 5000 species.”
Proc Natl Acad Sci U S A. 1997 Sep 2;94(18):9740-5. Character displacement in some Cnemidophorus lizards revisited: a phylogenetic analysis. Radtkey RR, Fallon SM, Case TJ.
“Ecological studies have demonstrated the role of competition in structuring communities; however, the importance of competition as a vehicle for evolution by natural selection and speciation remains unresolved” “…the phylogenetic analysis reveals potential cryptic species within mainland populations of C. tigris.”
Mol Biol Evol. 1997 Jul;14(7):769-77. Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae). Gaut BS, Clark LG, Wendel JF, Muse SV.
“At nonsynonymous sites, the pattern of rate heterogeneity is not correlated between loci, primarily due to an aberrant pattern of rate heterogeneity at nonsynonymous sites of rbcL. We compare patterns of synonymous rate heterogeneity to predictors based on the generation time effect and the speciation rate hypotheses. Although there is some evidence for generation time effects, neither generation time effects nor speciation rates appear to be sufficient to explain patterns of rate heterogeneity in the grass plastid sequences.”
Genetica. 1997;100(1-3):197-204. The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution. Heslop-Harrison et al.
“Retrotransposons make up a major fraction--sometimes more than 40%--of all plant genomes investigated so far.” “Unlike the pAL1 sequence, however, the Ty1-copia signal is also detectable as weaker, diffuse hybridization along the lengths of the chromosomes.”
J Theor Biol. 1997 Jun 21;186(4):441-7. Escape from evolutionary stasis by transposon-mediated deleterious mutations. McFadden J, Knowles G.
“It is presently unclear how founder populations escape from an adaptive peak to found a new species. Insertion sequences, transposons and other mobile DNA elements are found in all species of eukaryotes, bacteria and archaebacteria, where they have been sought and are usually considered to be genomic parasites or selfish genes. However, many transposons and other mobile repetitive DNA are remarkably species or phyla-specific…” “We have constructed a genetic algorithm designed to model both spontaneous and transposon-mediated mutations in populations of asexual digital organisms… as they compete for resources within an artificial adaptive landscape” “…may be… initiated by irreversible deleterious mutations induced by transposition.”
Cell Mol Life Sci. 1997 Jun;53(6):508-15. Annexin gene structures and molecular evolutionary genetics. Morgan RO, Fernandez MP.
“Computational and cladistic sequence analyses have permitted the determination of original gene duplication dates and mutation rates for the ten known vertebrate annexins. Molecular genetic and evolutionary studies of annexins can help to define their structure-function relationships elucidate their individual physiological roles and ultimately link them to hereditary phenotypes.”
Proc Natl Acad Sci U S A. 1997 May 27;94(11):5722-7. Molecular evolution of angiosperm mitochondrial introns and exons. Laroche J, Li P, Maggia L, Bousquet J.
“Gene-to-gene differences in numbers of substitutions per site were found to be higher for nonsynonymous than synonymous sites, and this could be due to differential selection if mutation rate is assumed constant for the genome. Some mitochondrial genes have evolved as fast as chloroplast genes, thus faster than previously thought.”
J Mol Biol. 1997 May 23;268(5):857-68. Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module. Riley M, Labedan B.
“…we have defined two main classes of paralogous proteins. One class is formed of proteins which contain a unique structural segment homologous to a single set of related proteins. The other class corresponds to proteins which contain more than one structural segment of homology, each segment homologous to unrelated sets of proteins. We define such an independent structural segment of homology as a module. This modular structure (mean length equivalent to 209 amino acids) corresponds often to entire proteins, but there are also proteins that appear to be assembled from two or three independent modules having independent origins.” “Examining 1404 independent structural segments of homology, composed of both modules and entire proteins, we found that the segments of homology fell into 352 sequence-related groups or families. The majority of these families (ranging from 2 to 62 members) are functionally homogeneous” “…each one being already of the same size and having a function similar to all members of its progeny.”
Mol Phylogenet Evol. 1997 Apr;7(2):252-60. Phylogeny and evolution of the Sulidae (Aves:Pelecaniformes): a test of alternative modes of speciation. Friesen VL, Anderson DJ.
“Although the allopatric model of speciation is widely accepted, it does not provide a satisfactory explanation for many evolutionary phenomena. Several alternative models exist, but they remain largely untested for vertebrate animals. In the present paper, a molecular phylogeny was used to test competing models of speciation in a seabird family, the Sulidae.” “Lineage divergence events for which the mode of speciation could be deduced did not fit the predictions of either allopatric or sympatric models, but apparently involved either peripatric or parapatric processes.”
Virology. 1997 Feb 17;228(2):394-9. A full-length and replication-competent proviral clone of SIVAGM from tantalus monkeys. Soares MA, Robertson DL, Hui H, Allan JS, Shaw GM, Hahn BH.
“African green monkeys (AGM) are classified into four distinct species (commonly termed vervet, grivet, sabaeus, and tantalus monkeys), all of which are known to be infected with simian immunodeficiency virus (SIVAGM) in the wild. Sequence analysis of partial gag and env regions has indicated that each of the four species harbors a phylogenetically distinct SIVAGM subtype. This species-specific diversity suggests that African green monkeys have been infected with SIVAGM for an extended period of time…” “However, our understanding of the evolutionary history of this group of viruses is still incomplete, in part because sequence information for most isolates is limited to small subgenomic regions. There are only six SIVAGM proviruses which have been sequenced in their entirety, and these represent only three of the four SIVAGM lineages (i.e., SIVAGMgri, SIVAGMver, and SIVAGMsab). In this paper, we have generated the first full-length proviral clone for SIVAGM infecting tantalus monkeys (SIVAGMtan). Lambda phage techniques were employed…” “The proviral clone was also biologically active since transfection yielded replication-competent virions. Amino acid sequence comparisons of all major viral proteins indicated that TAN was roughly equidistant from previously characterized sabaeus, grivet, and vervet strains, thus confirming that it represents a fourth independent SIVAGM lineage.”
J Hum Evol. 1997 Feb-Mar;32(2-3):289-322. Early hominid evolution and ecological change through the African Plio-Pleistocene. Reed KE.
“This study uses the morphological adaptations of mammalian assemblages found with early hominids to reconstruct the habitat based on each species' ecological adaptations, thus minimizing problems introduced by taxonomy and taphonomy. Research presented here compares east and south African Plio-Pleistocene mammalian fossil assemblages with 31 extant mammalian communities from eight different habitat types. All communities are analyzed through ecological diversity methods, that is, each species trophic and locomotor adaptations are used to reconstruct an ecological community and derive its vegetative habitat. Reconstructed habitats show that Australopithecus species existed in fairly wooded, well-watered regions. Paranthropus species lived in similar environs and also in more open regions, but always in habitats that include wetlands. Homo is the first hominid to exist in areas of fairly open, arid grassland.” “Therefore, the appearance of open savannas do not appear to have influenced the origination or adaptations of the earliest hominids, but could have contributed to their demise. As Stanley (1992) hypothesized, Homo species appear the first to be adapted to open, arid environments.”
J Theor Biol. 1997 Jan 7;184(1):51-64. Percolation on the fitness hypercube and the evolution of reproductive isolation. Gavrilets S, Gravner J.
“…genotype fitness can only be 0 (inviable genotype) or 1 (viable genotype).” “We have considered the most probable (within the present framework) scenario of biological evolution on holey landscapes [a (multidimensional) flat surface with many holes] assuming that it starts on a genotype from the largest connected component and proceeds along it by mutation and genetic drift.”
Am J Primatol. 1997;42(3):167-78. Radiation and speciation of spider monkeys, genus Ateles, from the cytogenetic viewpoint. Medeiros et al.
“These findings indicate the necessity of a more coherent taxonomic arrangement for the taxa of Ateles.”
Integr Physiol Behav Sci. 1997 Jan-Mar;32(1):86-100. Consciousness and biological order: toward a quantum theory of life and its evolution. Goswami A. [Comment in: Integr Physiol Behav Sci. 1997 Apr-Jun;32(2):132-42.]
“Biological order is discussed within the context of the idealist interpretation of quantum mechanics. A quantum mechanism is proposed for quantum speciation and for quantum evolution, in general. It is shown that an extension of neo-Darwinism to include quantum evolution via a quantum mechanism can resolve some of the recent controversies that have rattled evolution theory. It is pointed out that the quantum approach has the further benefit of giving a straightforward insight into the nature of life itself. Experimental support for some aspects of the theory is discussed.”
Naturwissenschaften. 1997 Jan;84(1):17-21. Evolution of the freshwater eels. Aoyama J, Tsukamoto K.
“The freshwater anguillid eels have an unusual life history and world-wide distribution. Questions about the phylogenetic relationships of this group and how their long spawning migrations and larval phase may contribute to their global distribution have not been addressed. This paper is first presentation of molecular phylogeny of Anguilla species, and based on this phylogenetic tree we suggest…”
Mol Phylogenet Evol. 1996 Oct;6(2):270-86. Molecular phylogenetic study of a myrmecophyte symbiosis: did Leonardoxa/ ant associations diversify via cospeciation? Chenuil A, McKey DB.
“…dates of speciation events appear to differ between ants and corresponding plants. An estimate of at least 4 million years was obtained for the separation of Aphomomyrmex and Petalomyrmex, whereas biological, biogeographic, and molecular-genetic data suggest a much more recent divergence for the plants. Thus, we reject the hypothesis of cospeciation and conclude that Aphomomyrmex and Petalomyrmex independently colonized different taxa of Leonardoxa.” “We discuss alternative evolutionary scenarios that are consistent with molecular data.”
Mol Phylogenet Evol. 1996 Oct;6(2):214-27. A mitochondrial cytochrome B phylogeny of the Alectoris partridges. Randi E.
“Recent speciation events originated A. chukar, A magna, and A. philbyi. A tentative calibration of rates of nucleotide evolution suggests that Alectoris speciated between ca. 6 and 2 million years ago. Consistent resolution of relationships among recent species of Alectoris may require the addition of sequences from genes evolving faster than cytochrome b.”
Genetics. 1996 Oct;144(2):689-703. Selection on X-linked genes during speciation in the Drosophila athabasca complex. Ford MJ, Aquadro CF.
“Using a modification of the HKA test, which uses fixed differences between the semispecies and a test based on differences in Fst among loci, we show that the greater differentiation of the X-linked loci compared with the autosomal loci is inconsistent with a neutral model of molecular evolution. We explore several evolutionary scenarios by computer simulation…” “…another X-linked trait, mating song differences among the semispecies, may have been the target of selection.”
Mol Ecol. 1996 Jun;5(3):341-50. Widespread geographical distribution of mitochondrial haplotypes in rock-dwelling cichlid fishes from Lake Tanganyika. Meyer A, Knowles LL, Verheyen E.
“Patterns of mtDNA differentiation in Simochromis were compared to those of other rock-dwelling cichlids to distinguish between competing hypotheses concerning the processes underlying their evolution. In striking contrast to previous findings, populations of Simochromis, even those separated by up to 300 km, were found to share mitochondrial DNA haplotypes. There is no correspondence between mtDNA genealogies and the geographical distribution of populations” “…abiotic and biotic factors shaping population genetic structure may differ substantially even among closely related species of rock-dwelling cichlids. Physical events and barriers to gene flow that are believed to have had a major impact on the geographical distribution and intralacustrine speciation of Tropheus do not seem to have equally strongly affected its close relative Simochromis. These findings emphasize that no single mechanism can be responsible for the formation of population structure…”
Philos Trans R Soc Lond B Biol Sci. 1996 Jun 29;351(1341):797-805. Mitochondrial phylogeography of rock-dwelling cichlid fishes reveals evolutionary influence of historical lake level fluctuations of Lake Tanganyika, Africa. Verheyen E, Ruber L, Snoeks J, Meyer A.
“…closely related populations occur on opposite shores of the lake…” “The phylogeographic pattern of eretmodine cichlids suggests that major fluctuations in the level of the lake have been important in shaping their adaptive radiation…” “The mitochondrially defined clades are in conflict with the current taxonomy of the group…”
Science. 1996 Aug 23;273(5278):1091-3. Late Pleistocene Desiccation of Lake Victoria and Rapid Evolution of Cichlid Fishes. Johnson et al.
“…the rate of speciation of cichlid fish in this tropical lake has been extremely rapid.”
Philos Trans R Soc Lond B Biol Sci. 1996 Jul 29;351(1342):877-95. DNA, morphology and fossils: phylogeny and evolutionary rates of the gastropod genus Littorina. Reid DG, Rumbak E, Thomas RH.
“The fossil record is sparse, but likewise consistent. A consensus tree is presented, showing clear resolution of basal and terminal branches, and a central unresolved polychotomy” “The central polychotomy may be explained by a burst of rapid speciation …”
Genetica. 1996 May;97(3):331-8. Chromosomal and molecular divergence in the Indian pygmy field mice Mus booduga-terricolor lineage of the subgenus Mus. Sharma T.
“…the terricolor chromosome types have diverged recently.”
Philos Trans R Soc Lond B Biol Sci. 1996 Jun 29;351(1341):785-94; discussion 795. Natural selection and random genetic drift as causes of evolution on islands. Barton NH.
“Theoretical obstacles to "founder effect speciation' are discussed, together with recent proposals for avoiding them. It is argued that although certain kinds of epistasis can facilitate the evolution of strong reproductive isolation, this favours divergence by selection as much as by random drift.”
Mol Phylogenet Evol. 1996 Jun;5(3):548-56. The presence/absence polymorphism and evolution of the p53 pseudogene in the genus Mus. Ohtsuka et al.
“Distribution of the p53 pseudogene within the house mouse species (genus Mus) was studied with polymerase chain reaction for 37 individuals that were caught at different localities. Pseudogene-specific fragments were detected in some, but not all, individuals of Mus musculus subspecies regardless of locality and type of subspecies. In addition, 3 of 7 individuals belonging to different Mus species carried the pseudogene in their genomes. These results show the existence of an interspecific presence/absence polymorphism of the p53 pseudogene in mice.”
J Mol Evol. 1996 Jun;42(6):685-705. Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. Cronn et al.
“5S RNA genes and their nontranscribed spacers are tandemly repeated in plant genomes at one or more chromosomal loci.” “Copy number varies over twentyfold in the genus, from approximately 1,000 to 20,000 copies/2C genome.” “Evidence presented also shows that duplicated 5S rDNA arrays in allopolyploids have retained their subgenomic identity since polyploid formation, thereby indicating that interlocus concerted evolution has not been an important factor in the evolution of these arrays. A descriptive model, one which incorporates the opposing forces of mutation and homogenization within a selective framework, is outlined to account for the empirical data presented.” “This result explains the apparent paradox that despite similar levels of gene and spacer diversity, phylogenetic analysis of spacer sequences yields highly resolved trees, whereas analyses based on 5S gene sequences do not.”
Mol Gen Genet. 1996 Mar 20;250(5):547-57. Self-incompatibility (S) alleles of the Rosaceae encode members of a distinct class of the T2/S ribonuclease superfamily. Sassa H, Nishio T, Kowyama Y, Hirano H, Koba T, Ikehashi H. [Erratum in: Mol Gen Genet. 1996 Aug 27;252(1-2):222.]
“Interestingly, some interspecific sequence similarities were higher than those within a species, possibly indicating that… self-incompatibility mechanisms in Rosaceae and Solanaceae are similar but arose independently…”
Mol Phylogenet Evol. 1996 Feb;5(1):188-201. The evolution of human populations: a molecular perspective. Ayala FJ, Escalante AA.
“Theories of founder-event speciation propose that speciation often occurs as a consequence of population bottlenecks, down to one or very few individual pairs. Proponents of punctuated equilibrium claim in addition that founder-event speciation results in rapid morphological change.” “Many human alleles are more closely related to pongid and cercopithecoid alleles than to other human alleles.” “This conclusion is confirmed by computer simulations showing the rate of decay of the polymorphisms over time. Computer simulations indicate, in addition…”
Annu Rev Microbiol. 1996;50:401-29. Towards a unified evolutionary genetics of microorganisms. Tibayrenc M.
“…better definition and sharper delimitation of presently described taxa, research of hidden genetic subdivisions…” “…species that are not subdivided into discrete phylogenetic lineages (panmictic species or basically sexual species with occasional bouts of short-term clonality fall into this category)…” “Improvements in available statistical methods are required to refine these distinctions and to better quantify the actual impact of gene exchange in natural microbial populations.” “The problems raised by natural genetic diversity are very similar for all microbial species, in terms of both basic and applied science. Despite this fact, a regrettable compartmentalization among specialists has hampered progress in this field.”
Genetika. 1996 Jan;32(1):14-22. [The problem of systemic mutation] [Article in Russian] Stegnii VN.
“The history of the problem of the role of systemic mutations in evolution is analyzed. The author's own phenomenological data on the spatial rearrangement of the chromosomal apparatus of germline tissue (that is regarded as systemic mutations) during the phylogeny of a number of dipterous insects are systematized.”
Genomics. 1995 Dec 10;30(3):583-93. Concerted evolution of the tandemly repeated genes encoding primate U2 small nuclear RNA (the RNU2 locus) does not prevent rapid diversification of the (CT)n.(GA)n microsatellite embedded within the U2 repeat unit. Liao D, Weiner AM.
“The persistence of the CT microsatellite, despite polymorphism and rapid evolution, suggests that it might play a functional role in concerted evolution of the RNU2 loci, perhaps as an initiation site for recombination and/or gene conversion.”
To be continued…
Member # 276
posted 17. April 2004 11:03
"Antonie Van Leeuwenhoek. 1998 Jan;73(1):25-33. Santa Rosalia revisited: why are there so many species of bacteria? Dykhuizen DE.
“The diversity of bacteria in the world is very poorly known. Usually less than one percent of the bacteria from natural communities can be grown in the laboratory. This has caused us to underestimate bacterial diversity and biased our view of bacterial communities. The tools are now available to estimate the number of bacterial species in a community and to estimate the difference between communities. Using what data are available, I have estimated that thirty grams of forest soil contains over half a million species. The species difference between related communities suggests that the number of species of bacteria may be more than a thousand million.”
[Sub-speciation is the real variation within species. Sub-speciation is confounded with ‘speciation’, which is the evolutionist speculation of the fictitious ‘jumping’ of one species to be transformed into another species. The best test is the original definition of kind, that can be applied to the word ‘Species’: “Fertile parents producing fertile offspring”, that implies the need of the reproductive ‘fertility test’ also for the offspring. ‘Evolution’ tries to confound the unlearned with tricky and weak definitions of ‘species’ to walk around and aside from the simple and original truth present in the word ‘kind’]"
Fernando, are you aware that the definition of 'species' among bacteria is somewhat different from the definitions of species among vertebrates? The nature of genetic exchange is quite different for those groups. For example, the reproductive 'fertility test' really doesn't work well for bacteria, where 'sex' is more like a controlled infection (or sometimes, uncontrolled) than an equal mixing and repartitioning of DNA to generate offspring.
And if 'kind' is so simple (which for Fernando, appears to be equivalent to the Biological Species Concept), why can't creationists agree on what constitutes the various, proposed 'kinds'? And what criteria would one use to assign the various bacteria to different 'kinds'?
[ 17. April 2004, 11:05: Message edited by: Argon ]
Member # 1201
posted 20. April 2004 13:22
Putting Limits on the Diversity of Life.
(Part Four. Number 8. Continued... 7)
Genetics. 1995 May;140(1):325-43. Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives. Kellogg EA, Appels R.
“5S RNAs form part of the ribosome in most organisms. In some, e.g., prokaryotes and some fungi, the genes are part of the ribosomal operon, but in most eukaryotes they are in tandem arrays of hundreds to thousands of copies separate from the main ribosomal array.” “We were therefore surprised to find that, for 28 diploid species of the wheat tribe (Triticeae), nucleotide diversity within an array is up to 6.2% in the genes, not significantly different from that of the nontranscribed spacers. Rates of concerted evolution must therefore be insufficient to homogenize the entire array. Between species, there are significantly fewer fixed differences in the gene than would be expected, given the high within-species variation. In contrast, the amount of variation between species in the spacer is the same as or greater than that within individuals. This leads to a paradox. High variation within an individual suggests that there is little selection on any particular gene within an array. But conservation of the gene across species implies that polymorphisms are periodically eliminated at a rate approximately equal to or greater than that of speciation. Levels of intraspecific polymorphism and interspecific divergence are thus decoupled. This implies that selective mechanisms exist to eliminate mutations in the gene without also affecting the spacer.”
J Hered. 1994 Nov-Dec;85(6):455-65. Evolution of number and morphology of mammalian chromosomes.
"Numerous hypotheses have been advanced to explain how selection might operate on the level of the chromosomal complement (chromosome selection) and how this process could be related to morphological divergence and speciation. Hypotheses emphasizing a general trend of increasing or decreasing diploid numbers in mammalian evolution are contradicted by documented studies from diverse families of mammals." "However, certain selective forces were identified... under limited conditions."
Heredity. 1994 Oct;73 ( Pt 4):339-45. Recombination suppressors and the evolution of new species. Trickett AJ, Butlin RK.
"Chromosomal rearrangements are often the only apparent difference between closely related species, although it is not clear whether they are a cause or a by-product of speciation."
Proc Natl Acad Sci U S A. 1995 Apr 25;92(9):3983-6. Founder-effect speciation theory: failure of experimental corroboration. Moya A, Galiana A, Ayala FJ.
“The theory of founder-effect speciation proposes that colonization by very few individuals of an empty habitat favors rapid genetic changes and the evolution of a new species. We report here the results obtained in a 10-year-long and large-scale experiment with Drosophila pseudoobscura designed to test the theory.” “Our results provide no support for the theories proposing that new species are very likely to appear as by-products of founder events.”
J Theor Biol. 1995 Dec 7;177(3):237-45. A genetical theory of species selection. Rice SH.
“So long as we are careful in defining "species", the logic of species selection is sound. This does not mean, however, that this process can influence evolutionary dynamics under realistic conditions.”
Proc Natl Acad Sci U S A. 1994 Aug 16;91(17):8160-4. Chromosomal speciation and adaptive radiation of mole rats in Asia Minor correlated with increased ecological stress. Nevo et al.
"The evolutionary forces causing chromosomal speciation and adaptation are still enigmatic" "...subterranean mole rats... supporting... the biological species status of most tested populations." "This haplotype diversity may contribute to population adaptation to climatic stress and ecological unpredictability in space and time."
Microbiol Rev. 1994 Sep;58(3):563-602. Bacterial gene transfer by natural genetic transformation in the environment. Lorenz MG, Wackernagel W.
"Natural genetic transformation is the active uptake of free DNA by bacterial cells and the heritable incorporation of its genetic information. Since the famous discovery of transformation in Streptococcus pneumoniae by Griffith in 1928 and the demonstration of DNA as the transforming principle by Avery and coworkers in 1944, cellular processes involved in transformation have been studied extensively by in vitro experimentation with a few transformable species. Only more recently has it been considered that transformation may be a powerful mechanism of horizontal gene transfer in natural bacterial populations. In this review the current understanding of the biology of transformation is summarized to provide the platform on which aspects of bacterial transformation in water, soil, and sediments and the habitat of pathogens are discussed. Direct and indirect evidence for gene transfer routes by transformation within species and between different species will be presented, along with data suggesting that plasmids as well as chromosomal DNA are subject to genetic exchange via transformation. Experiments exploring the prerequisites for transformation in the environment, including the production and persistence of free DNA and factors important for the uptake of DNA by cells, will be compiled, as well as possible natural barriers to transformation. The efficiency of gene transfer by transformation in bacterial habitats is possibly genetically adjusted to submaximal levels." "...natural transformation has been detected among bacteria from all trophic and taxonomic groups including archaebacteria..."
Genetics. 1994 Aug;137(4):903-17. Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli. Rosenzweig RF, Sharp RR, Treves DS, Adams J.
"Populations of Escherichia coli initiated with a single clone and maintained for long periods in glucose-limited continuous culture, become polymorphic. In one population, three clones were isolated and by means of reconstruction experiments were shown to be maintained in stable polymorphism, although they exhibited substantial differences in maximum specific growth rates and in glucose uptake kinetics. Analysis of these three clones revealed that their stable coexistence could be explained by differential patterns of the secretion and uptake of two alternative metabolites acetate and glycerol."
Curr Opin Genet Dev. 1992 Dec;2(6):844-9. Population cytogenetics. Hewitt GM.
"The current explosion of molecular techniques is facilitating the localization of many DNA sequences, while a reassessment of the fitness of chromosome mutants challenges some classical views on polymorphism and polytypy."
Mol Phylogenet Evol. 1995 Dec;4(4):408-19. Mhc-DRB genes and the origin of New World monkeys. Trtkova K, Mayer WE, O'Huigin C, Klein J.
“…bootstrap values fail to provide statistically significant support for the separation of these two clades” “…and thus contradicts the results of an earlier study in which some exon 2 DRB sequences appeared to…” “The inconsistency in the DRB gene phylogeny can be explained by…”
Curr Biol. 1995 Oct 1;5(10):1129-39. Pattern of ecological shifts in the diversification of Hawaiian Drosophila inferred from a molecular phylogeny. Kambysellis et al.
“Founder events and accompanying random drift, together with shifts in sexual selection… do not account for their spectacular ecological diversification into a wide array of breeding niches. Although recognized as contributing to the success of this group, the precise role of adaptive shifts has not been well defined” “…we conclude that this ecological divergence and the correlated changes in ovarian patterns that adapt species to their ecological habitats were contributing factors in the major phyletic branching…”
Genetics. 1995 Sep;141(1):223-36. Molecular evolution of the duplicated Amy locus in the Drosophila melanogaster species subgroup: concerted evolution only in the coding region and an excess of nonsynonymous substitutions in speciation. Shibata H, Yamazaki T.
“From the nucleotide sequence data, we show a strong within-species similarity between the duplicated loci in the Amy coding region. This is in contrast to a strong similarity in the 5' and 3' flanking regions within each locus (proximal or distal) throughout the species subgroup” “…D. erecta… is a "specialist" species for host plants…”
J Mol Evol. 1995 Aug;41(2):250-2. The genomic sequence for Prader-Willi/Angelman syndromes' loci of human is apparently conserved in the great apes. Luke S, Verma RS.
“Certain pericentric inversions are too minute to be detected cytogenetically, thus hindering the complete reconstruction of hominoid phylogeny” “…the nature of these pericentric inversions remains relatively unknown.” “"Genetic" divergence in the speciation process which occurs through "chromosomal" rearrangement needs to be reevaluated and further explored using newer techniques.”
J Theor Biol. 1995 Jul 12;175(2):197-202. Entropy, irreversibility and evolution. Berry S.
“There is no direct connection between evolutionary events such as speciation and thermodynamic entropy changes…”
Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6389-93. Evolution of single and double Wolbachia symbioses during speciation in the Drosophila simulans complex. Rousset F, Solignac M.
“Maternally inherited bacteria of the genus Wolbachia are responsible for the early death of embryos in crosses between uninfected females and infected males in several insect species. This phenomenon, known as cytoplasmic incompatibility, also occurs between strains infected by different symbionts in some species, including Drosophila simulans.” “Wolbachia was found… to cause [not] incompatibility in… D. mauritiana.” “Some D. simulans and D. sechellia cytoplasmic lineages harbor two bacteria as a consequence of a double infection…” “…little variation of incompatibility types has occurred within maternal lineages beyond that related to the density of symbionts in their hosts.”
Chromosome Res. 1995 May;3(3):143-50. Karyotype evolution in holocentric chromosomes of three related species of triatomines (Hemiptera-Reduviidae). Panzera et al.
“…cytogenetic traits that differ from all other triatomines: large autosomes, C-heterochromatic blocks and meiotic heteropycnotic chromocenters formed by autosomes and sex chromosomes. In spite of these similarities, each species presents different chromosomal behavior during male meiosis, distinct DNA content and a specific amount and localization of the C-heterochromatin” “…the differences in distribution and amount of heterochromatin do not play a direct role in speciation in this group.”
J Hered. 1995 May-Jun;86(3):216-27. Chromosomal evolution in gazelles. Vassart M, Seguela A, Hayes H.
“The main novelties [of this phylogenetic reconstruction] are the proximity of G. rufifrons and G. thomsoni and the inclusion of Antilope cervicapra in the gazelle group.”
Genetics. 1995 Apr;139(4):1805-13. The population genetics of speciation: the evolution of hybrid incompatibilities. Orr HA.
“Speciation often results from the accumulation of "complementary genes," i.e., from genes that, while having no deleterious effect within species, cause inviability or sterility when brought together with genes from another species. Here I model speciation…”
Mol Biol Evol. 1995 Mar;12(2):219-30. Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer. Springer MS, Tusneem NA, Davidson EH, Britten RJ.
“Rates of synonymous substitution for reverse transcriptase are similar to rates of single-copy DNA evolution and to rates of synonymous substitution for the H3 and H4 histone genes, contradicting the assumption that rates of evolution are accelerated in retrotransposons.”
Virology. 1995 Feb 20;207(1):334-7. Interspecific reassortment of genomic segments in the evolution of cucumoviruses. White PS, Morales F, Roossinck MJ.
“…we describe a cucumovirus isolate that is composed of genomic segments from two distinct viral species [which also are cucumovirus].”
Cell. 1995 Feb 10;80(3):507-15. Interspecies gene exchange in bacteria: the role of SOS and mismatch repair systems in evolution of species. Matic I, Rayssiguier C, Radman M.
“Analysis of interspecies matings between S. typhimurium and E. coli indicates that the genetic barrier that separates these (and perhaps many other) related species is primarily recombinational. The structural component of this barrier is genomic sequence divergence. The mismatch repair enzymes act as potent inhibitors of interspecies recombination, whereas the SOS system acts as an inducible positive regulator. Interspecies mating triggers a RecBC-dependent SOS response in female bacteria that increases recombination mainly through overproduction of the RecA protein. Mismatch repair acts to reduce the mutation rate and recombination between similar sequences, whereas SOS acts to increase both. These opposing activities allow mismatch repair and SOS systems to determine both the rate of accumulation of sequence divergence…”
Proc Natl Acad Sci U S A. 1995 Jan 3;92(1):280-4. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Wendel JF, Schnabel A, Seelanan T.
“Polyploidy is a prominent process in plant evolution; yet few data address the question of whether homeologous sequences evolve independently subsequent to polyploidization.”
Virus Genes. 1995;11(2-3):163-79. Reverse transcriptase: mediator of genomic plasticity. Brosius J, Tiedge H.
“Reverse transcription has been an important mediator of genomic change” “…the current cellular role(s) of reverse transcriptase are not yet completely understood.” “Reverse transcriptase generates, for example, extra gene copies (retrogenes), using as a template mature messenger RNAs. Such retrogenes do not always end up as nonfunctional pseudogenes but form, after reinsertion into the genome, new unions with resident promoter elements that may alter the gene's temporal and/or spatial expression levels. More frequently, reverse transcriptase produces copies of nonmessenger RNAs, such as small nuclear or cytoplasmic RNAs. Extremely high copy numbers can be generated by this process. The resulting reinserted DNA copies are therefore referred to as short interspersed repetitive elements (SINEs).” “SINEs… can give rise to novel genes encoding small RNAs, and are the migrant carriers of numerous control elements and sequence motifs that can equip resident genes with novel regulatory elements [Brosius J. and Gould S.J., Proc Natl Acad Sci USA 89, 10706-10710, 1992]. Retrosequences, such as SINEs and portions of retroelements (e.g., long terminal repeats, LTRs), are capable of donating sequence motifs for nucleosome positioning, DNA methylation, transcriptional enhancers and silencers, poly(A) addition sequences, determinants of RNA stability or transport, splice sites, and even amino acid codons for incorporation into open reading frames as novel protein domains.”
Annu Rev Microbiol. 1995;49:55-94. Genetics, physiology, and evolutionary relationships of the genus Buchnera: intracellular symbionts of aphids. Baumann et al.
“Buchnera can synthesize methionine, cysteine, and tryptophan and supply these amino acids to the aphid host. In the case of some fast-growing species of aphids, the overproduction of tryptophan by Buchnera involves plasmid-amplification of the gene coding for anthranilate synthase, the first enzyme of the tryptophan biosynthetic pathway.”
Int J Parasitol. 1994 Dec;24(8):1213-26. The evolutionary expansion and host-parasite relationships of the Digenea. Gibson DI, Bray RA.
“In a detailed examination of three zoogonid genera, few indications of co-evolution with their vertebrate hosts were detected, and geographical information from the data-base appeared to shed no light upon the geographical origins of the Digenea.”
Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):6787-94. Molecular genetics of speciation and human origins. Ayala FJ, Escalante A, O'Huigin C, Klein J.
"In some genes there are extensive and ancient polymorphisms that have passed from ancestral to descendant species and are shared among contemporary species." "The data are consistent with, but do not provide specific support for, the claim that human populations throughout the World were at that time replaced by populations migrating from Africa."
Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):6758-63. The role of extinction in evolution. Raup DM.
"The extinction of species is not normally considered an important element of neodarwinian theory, in contrast to the opposite phenomenon, speciation. This is surprising in view of the special importance Darwin attached to extinction, and because the number of species extinctions in the history of life is almost the same as the number of originations..." "For an evolutionary biologist to ignore extinction is probably as foolhardy as for a demographer to ignore mortality. The past decade has seen a resurgence of interest in extinction, yet research on the topic is still at a reconnaissance level, and our present understanding of its role in evolution is weak" "...there is little evidence that extinction is selective in the positive sense argued by Darwin."
Proc Natl Acad Sci U S A. 1994 May 24;91(11):5129-32. Columbines: a geographically widespread species flock. Hodges SA, Arnold ML.
"Species in the columbine genus, Aquilegia, are known for their broad variation in ecology and floral morphology. Aquilegia is also known for the large degree of intercompatibility among its species, which has led to the suggestion that the genus has arisen recently" "...the columbines are the result of a recent, rapid radiation."
Am J Phys Anthropol. 1994 May;94(1):89-113. Molecular evolutionary processes and conflicting gene trees: the hominoid case. Ruvolo M.
"...involucrin repeats are difficult to align, and published alignments are contradictory..." "...gorillas are polymorphic in that some do not have repeats reported to be synapomorphies linking chimpanzees and gorillas."
J Mol Evol. 1994 May;38(5):506-32. Nucleotide composition as a driving force in the evolution of retroviruses. Bronson EC, Anderson JN.
"All complete retrovirus sequences in the GenEMBL database were examined with the goal of assessing possible relationships between the nucleotide composition of retroviral genomes..." "By analogy to microbial species, we suggest that the variations arise from group-specific patterns of directional mutations..." "It is most likely that the mutational patterns are introduced during reverse transcription, and a direct participation of reverse transcriptase in the process is suspected." "...viruses with radically different base frequencies most often inhabit the same cell type..." "The variants with the most extreme compositional differences would have a selective advantage because their different precursor requirements would enable them to occupy different ecological niches within a single cell."
Virology. 1994 Feb 15;199(1):56-66. Genetic analysis and molecular phylogeny of simian T-cell lymphotropic virus type I: evidence for independent virus evolution in Asia and Africa. Song et al.
"...our data are consistent with an archaic presence of STLV-I in Asia..."
Genet Res. 1994 Feb;63(1):11-7. Genetic basis and evolution of species-specific courtship song in the Drosophila auraria complex. Tomaru M, Oguma Y.
"The interpulse interval (IPI) of courtship song in the Drosophila auraria complex is the only parameter that is consistently species-specific among the several courtship elements examined within the complex. The genetic basis of the species-specific courtship song was examined by analysing the song of interspecific hybrids and of backcross progeny. IPI of all interspecific hybrids except two showed intermediate values, suggesting autosomal control of species-specific IPI. However, significant deviation for shorter IPI from midparent was found in thirteen out of 20 crosses" "…it is concluded that each autosome acts additively in the determination of species-specific IPI."
J Med Vet Mycol. 1994;32(5):331-41. Phylogeny of dermatophytes and dimorphic fungi based on large subunit ribosomal RNA sequence comparisons. Leclerc MC, Philippe H, Gueho E.
"From our data, teleomorphs of E. parva, Paracoccidioides brasiliensis and H. farciminosum, three dimorphic fungi known only under their anamorphic states, should belong to the family of Onygenaceae and the genus Ajellomyces. Among Arthrodermataceae, a family containing the most keratinophilic species, it was not possible to establish a clear hierarchy of species. Only Ctenomyces serratus, the species adapted to degrade keratin of feathers, Trichophyton ajelloi and Trichophyton terrestre were significantly separated."
J Mol Evol. 1993 Dec;37(6):590-9. Evolution of regulatory genes and patterns: relationships to evolutionary rates and to metabolic functions. Thorpe PA, Loye J, Rote CA, Dickinson WJ.
"...cause and effect are difficult to discern." "There are highly significant differences between individual enzymes, but no obvious correlations to functional categories."
Mol Biol Evol. 1993 Nov;10(6):1303-16. Molecular phylogeny of the symbiotic actinomycetes of the genus Frankia matches host-plant infection processes. Cournoyer B, Gouy M, Normand P.
"This region of the nif operon is variable enough to classify most infective Frankia strains at the species level."
Mol Biol Evol. 1993 Nov;10(6):1259-72. The lepidopteran mitochondrial control region: structure and evolution. Taylor MF, McKechnie SW, Pierce N, Kreitman M.
"Recent speciation was supported by the observation of low interspecific sequence divergence. Thus, no useful phylogeny could be constructed for the genus." "Analysis of secondary structure indicated only one possible feature in common--inferred stem loops with higher-than-random folding energies--although the positions of the structures in different species were unrelated to regions of primary sequence similarity" "...determination of flanking sequences for one Jalmenus species indicated... only weak support for the available model of insect 12S rRNA structure..."
Proc R Soc Lond B Biol Sci. 1993 Jul 22;253(1336):117-22. Honesty, perception and population divergence in sexually selected traits. Schluter D, Price T.
"...populations may drift apart in arbitrary directions if choice of different male traits yields equivalent benefits to females."
Am J Phys Anthropol. 1993 Jun;91(2):161-71. Human taxonomic diversity in the pleistocene: does Homo erectus represent multiple hominid species? Kramer A.
"Recently, nomina such as "Homo heidelbergensis" and "H. ergaster" have been resurrected to refer to fossil hominids that are perceived to be specifically distinct from Homo sapiens and Homo erectus. This results in a later human fossil record that is nearly as speciose as that documenting the earlier history of the family Hominidae. However, it is agreed that there remains only one extant hominid species: H. sapiens." "Cranial variation in a taxonomically mixed sample of fossil hominids, and in a modern human sample, is analyzed with regard to the variation present in the fossils attributed to H. erectus. The data are examined using both univariate (coefficient of variation) and multivariate (determinant) analyses. Employing randomization methodology to offset the small size and non-normal distribution of the fossil samples, the CV and determinant results reveal a pattern and degree of variation in H. erectus that most closely approximates that of the single species H. sapiens. It is therefore concluded that the null hypothesis cannot be rejected."
Genetics. 1993 May;134(1):251-60. The genetic basis of Haldane's rule and the nature of asymmetric hybrid male sterility among Drosophila simulans, Drosophila mauritiana and Drosophila sechellia. Zeng LW, Singh RS.
"Haldane's rule (i.e., the preferential hybrid sterility and inviability of heterogametic sex) has been known for 70 years, but its genetic basis, which is crucial to the understanding of the process of species formation, remains unclear." "An introgression of D. sechellia Y chromosome into a fairly homogenous background of D. simulans did not show any effect of the introgressed Y on male sterility. The substitution of D. simulans Y chromosome into D. sechellia, and both reciprocal Y chromosome substitutions between D. simulans and D. mauritiana were unsuccessful. Introgressions of cytoplasm between D. simulans and D. mauritiana (or D. sechellia) also did not have any effect on hybrid male sterility. These results rule out the X-Y interaction hypothesis as a general explanation of Haldane's rule in this species group and indicate an involvement of an X-autosome interaction."
Proc Natl Acad Sci U S A. 1993 May 1;90(9):4117-21. Coevolution of persistently infecting small DNA viruses and their hosts linked to host-interactive regulatory domains. Shadan FF, Villarreal LP.
"...virus-host "co-speciation" appears incongruent with some prevailing views of viral evolution..." "…the conserved retinoblastoma binding domain is characteristic and inclusive of the entire polyomavirus family, but the conserved p53-like binding domain is characteristic and inclusive of three entire families of small DNA viruses: polyomaviruses, papillomaviruses, and parvoviruses."
Proc Natl Acad Sci U S A. 1993 Apr 1;90(7):2734-8. Rate variation of protein and mitochondrial DNA evolution as revealed by sea urchins separated by the isthmus of Panama. Bermingham E, Lessios HA.
"Acceptance of the rough constancy of rates of molecular evolution, averaged over tens of millions of years, is widely used to date the splitting between taxa. However, for the study of speciation a hypothesis of rough constancy over tens of millions of years is of little use."
Proc R Soc Lond B Biol Sci. 1993 Feb 22;251(1331):119-25. Bimodal echolocation in pipistrelle bats: are cryptic species present? Jones G, van Parijs SM.
"The pipistrelle bat Pipistrellus pipistrellus is the most widespread in Europe, and is often the most abundant bat species in northern and central Europe. P. pipistrellus has traditionally been considered as one species throughout Europe." "The sympatric occurrence of two phonic types, the lack of mixing of types between colonies, and the morphological divergence between phonic types suggests that P. pipistrellus may actually consist of at least two cryptic sibling species."
Riv Biol. 1993;86(1):101-11. The "blind alley". Its significance for evolutionary theory. Davison JA.
"Several scientists have apparently independently used the term "Blind Alley" to indicate that major evolutionary change has ceased. The failure to observe speciation through selection would indicate that obligatory sexual reproduction is incapable of producing progressive evolution."
Acta Trop. 1992 Dec;52(2-3):175-87. Evolution of the retrotransposons TRS/ingi and of the tubulin genes in trypanosomes. Braun R, Behrens K, Glauser A, Brun R.
"The African trypanosomes have genomes of high plasticity, as demonstrated for instance by their ability to shuffle their genes around, coding for variant-specific surface glycoproteins (VSGs). Another indication of their genome plasticity is the presence of multiple retro-elements. The retrotransposon-like element TRS/ingi is present in many copies in the genome of trypanosomes" "...TRS/ingi is unlikely to be involved directly in VSG switching, it may have contributed to the genome plasticity of trypanosomes."
Genetika. 1992 Dec;28(12):5-17. [The role of mobile genetic elements (MGE) in microevolution] [Article in Russian] Ratner VA, Vasil'eva LA.
"The MGEs of Drosophila and other objects contain open reading frames (ORFs) encoding transposition enzymes, and "motifs" similar to functional sites: promoters, enhancers, heat shock regulatory sites, those of reception of different stress external signals and hormones, recombination sites, etc. In other words, MGE play a role of "movable cassettes of regulatory elements" in the genomes. The patterns of genome MGE localization are the important components of polygenic systems of character expression..." "...stress induction (temperature, treatment, dysgenic cross, etc.) stimulated the MGE transpositions and excisions, mass in population and multiple in individuals. The temperature induction acts probably through the system of response to heat shock treatment. The totality of MGE patterns make up the genomic system capable of quick reorganizations after stress external and genomic influences. The stress external influences are often correlated with passing of the population through the "bottle-neck" stage. The rate of transpositions has an upper limiting border, so named "boundary of regulation error catastrophe", that corresponds to approx. 1 transposition per genome, per generation. After the stress induction of transpositions this boundary could be exceeded, the state of the population norm becoming disrupted."
Hum Immunol. 1992 Sep;35(1):29-39. Evolutionary stability of transspecies major histocompatibility complex class II DRB lineages in humans and rhesus monkeys. Slierendregt et al.
“…the data indicate that distinct species may not have inherited or lost transspecies Mhc-DRB lineages in evolution, because several allele lineages in rhesus monkeys appear to be absent in humans and vice versa.”
Nature. 1992 Aug 13;358(6387):578-81. Genetic divergence, speciation and morphological stasis in a lineage of African cichlid fishes. Sturmbauer C, Meyer A.
“…we report a case of surprisingly large genetic divergence among populations of the endemic Tropheus lineage of Lake Tanganyika. This lineage of six species contains twice as much genetic variation as the entire morphologically highly diverse cichlid assemblage of Lake Malawi and six times more variation than the Lake Victoria species flock. Although it is highly variable in coloration, this group of species and its closest relatives have not undergone appreciable morphological change.”
Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3310-4. Evolutionarily different alphoid repeat DNA on homologous chromosomes in human and chimpanzee. Jorgensen AL, Laursen HB, Jones C, Bak AL.
“…the alphoid DNA on these human and chimpanzee chromosomes is not orthologous but originates from two evolutionarily different repeat families.”
Mol Gen Genet. 1992 Apr;232(3):479-88. Evolution of the alcohol dehydrogenase (ADH) genes in yeast: characterization of a fourth ADH in Kluyveromyces lactis. Shain DH, Salvadore C, Denis CL.
“…K. lactis and S. cerevisiae use different compartments for their metabolism of ethanol. Our results also indicate that the complex regulatory circuits controlling the glucose-repressible SADH2 in S. cerevisiae are a recent acquisition from regulatory networks used for the control of genes other than SADH2.”
J Theor Biol. 1992 Feb 7;154(3):391-8. A two-locus model of speciation. Gregorius HR.
“In the presence of recombination between the object and mating modifier locus speciation may be prevented by forces maintaining gametic phase imbalance between these loci such as can result from unidirectional gene flow between parapatric populations.”
Nature. 1992 Feb 6;355(6360):511-5. Genetics and speciation. Coyne JA [Comment in: Nature. 1992 Oct 29;359(6398):781]
“Called the "mystery of mysteries" by Darwin, speciation is still a little-understood area of evolution. Genetic analysis, however, has yielded new generalizations about speciation...”
Biosystems. 1992;27(3):125-8. M.V. Volkenstein, evolutionary thinking and the structure of fitness landscapes. Conrad M, Ebeling W.
“…connection between the neutral and punctuated aspects of evolution and evolution on moving landscapes. The paper is written in honor of M.V. Volkenstein (October 23rd, 1912-February 18th, 1992), who devoted his last papers to uniting dynamics with evolutionary thinking.”
Immunol Today. 1991 Nov;12(11):411-4. Shared epitopes among HLA class II alleles: gene conversion, common ancestry and balancing selection. Erlich HA, Gyllensten UB.
"The extent and pattern of HLA class II sequence polymorphism raise a variety of evolutionary questions..." "The striking patchwork pattern of polymorphism with different alleles containing common sequence motifs can be accounted for by... depending on the location of the shared epitope."
Neuron. 1991 May;6(5):845-58. Evolutionary studies of the nerve growth factor family reveal a novel member abundantly expressed in Xenopus ovary. Hallbook F, Ibanez CF, Persson H.
“Northern blot analysis of different tissues from Xenopus showed NT-4 mRNA only in ovary, where it was present at levels over 100-fold higher than those of NGF mRNA in heart.”
Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2326-30. Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution. Kido et al.
"The salmon Sma I family is present in the genomes of two species of the genus Oncorhynchus but not in other species, including five other species of the same genus. The charr Fok I family is present only in four species and subspecies of the genus Salvelinus. The third family, the salmonid Hpa I family, appears to be present in all salmonid species but is not present in species that are not members of the Salmonidae." "We speculate that amplification and dispersion of retroposons may have played a role in salmonid speciation."
Proc Natl Acad Sci U S A. 1991 Feb 15;88(4):1256-60. Seismic communication in a blind subterranean mammal: a major somatosensory mechanism in adaptive evolution underground. Nevo E, Heth G, Pratt H.
“Seismic communication, through low-frequency and patterned substrate-borne vibrations that are generated by head thumping, and which travel long distances underground, is important in the nonvisual communication of subterranean mole rats of the Spalax ehrenbergi superspecies (2n = 52, 54, 58, and 60) in Israel.” “Neurophysiologic, behavioral, and anatomic findings in this study suggest that the mechanism of long-distance seismic communication is basically somatosensory and is independent of the auditory mechanism… that display major adaptation to life underground.”
Ann Genet. 1991;34(3-4):137-42. The malignant primate? de Grouchy J.
"Speciation and carcinogenesis result from genomic instability at the gametic or at the somatic levels." "Evolution and malignancy are interweaved by viruses and oncogenes..." "Cancer uses its intelligence to expand and to destroy the other tissues, using subtle metabolic pathways and a variety of tricks to metastasize other cells. It always wins but saws the branch on which it sits. Mankind also... modifies his genome or that of other species, and develops new technologies for his reproduction." "To be or not to be the malignant primate..."
Brain Behav Evol. 1991;38(4-5):226-39. Pedigrees of neurobehavioral circuits: tracing the evolution of novel behaviors by comparing motor patterns, muscles, and neurons in members of related taxa. Paul DH.
“When the pedigree of a particular behavior can be traced-by comparing motor patterns and their neural substrates in related taxa whose phylogeny is known from other (non-neurobehavioral) criteria-divergent and convergent evolutionary changes can be distinguished and the order of their occurrence reconstructed. An example of reconstructing a behavioral pedigree (for the novel mode of swimming in the crab Emerita [Hippidae]) is presented...”
Proc Natl Acad Sci U S A. 1990 Dec;87(24):9732-5. Polymorphism at the self-incompatibility locus in Solanaceae predates speciation. Ioerger TR, Clark AG, Kao TH.
“Sequences of 11 alleles of the gametophytic self-incompatibility locus (S locus) from three species of the Solanaceae family have recently been determined. Pairwise comparisons of these alleles reveal two unexpected observations: (i) amino acid sequence similarity can be as low as 40% within species and (ii) some interspecific similarities are higher than intraspecific similarities. The gene genealogy clearly illustrates this unusual pattern of relationships.”
Proc Natl Acad Sci U S A. 1990 Dec;87(24):9558-62. Evolution of Drosophila mitochondrial DNA and the history of the melanogaster subgroup. Satta Y, Takahata N.
“The nucleotide sequences of a common region of 15 mitochondrial DNAs (mtDNAs) sampled from the Drosophila melanogaster subgroup were determined. The region is 2527 base pairs long, including most of the NADH dehydrogenase subunit 2 and cytochrome oxidase subunit 1 genes punctuated by three tRNA genes. The comparative study revealed (i) the extremely low saturation level of transitional differences, (ii) recombination or variable substitution rates even within species, (iii) long persistence times of distinct types of mtDNA in Drosophila simulans and Drosophila mauritiana, and (iv) an apparent lack of within-type variations in island species” “…geographic isolation is so weak as to show no evidence for further speciation. Moreover, one type of mtDNA shared by D. simulans and D. mauritiana suggests either recent divergence or ongoing introgression.”
J Am Mosq Control Assoc. 1990 Dec;6(4):593-9. Classical taxonomy of mosquitoes--a memorial to John N. Belkin. Zavortink TJ.
"The major contributions of John N. Belkin to the field of mosquito systematics are noted." "It is argued that mosquito systematics is still largely at the alpha taxonomy level, that at best only 25-50% of mosquito species are known, and that we have not even begun to develop a natural classification for the Culicidae. It is concluded that there will be little improvement in the status of mosquito taxonomy unless there is increased support for systematics."
Genomics. 1990 Nov;8(3):536-40. The dystrophin gene is autosomally located on a microchromosome in chicken. Dominguez-Steglich M, Meng G, Bettecken T, Muller CR, Schmid M.
“The dystrophin gene has been mapped to a pair of microchromosomes in Gallus domesticus. In situ hybridization using a pool of biotinylated human cDNA probes allowed detection of this huge single-copy sequence without having to employ isotopic labeling. The autosomal nature of the DMD gene in chicken is supported by molecular data from quantitative Southern blot analysis and is in sharp contrast to that in all eutherian mammals studied, where it is a characteristically X-linked locus.”
Mol Biol (Mosk). 1990 Sep-Oct;24(5):1181-99. [Molecular drive] [Article in Russian] Vol'kenshtein MV (Volkenstein MV).
“The review of the concept of molecular drive developed by Dover is presented” ...the non-equal crossing-over and the conversion of genes are considered... and the transposition of genes... non-Mendelian and non-Darwinian.
J Exp Med. 1990 Jul 1;172(1):53-9. Major histocompatibility complex class II-restricted antigen presentation across a species barrier: conservation of restriction determinants in evolution. Bontrop RE, Elferink DG, Otting N, Jonker M, de Vries RR.
“The existence of at least three alleles of the HLA-DRB3 gene within the human population is evident. These alleles express DRw52 determinants and react with monoclonal antibody (mAb) 22.214.171.124... also expressed on chimpanzee (Pan troglodytes) class II-positive cells” “…"biomutants" may thus be more useful to study the biological significance of MHC molecules than MHC variants that have been generated by in vitro mutagenesis experiments.”
Prog Clin Biol Res. 1990;335:49-69. Geomyid evolution: the historical, selective, and random basis for divergence patterns within and among species. Patton JL.
“The focus of this paper is on those factors contributing to differentiation among geographic segments of species, or among different species...”
J Hered. 1990 Jan-Feb;81(1):30-42. Evolution of the mojavensis cluster of cactophilic Drosophila with descriptions of two new species. Ruiz A, Heed WB, Wasserman M.
“The mojavensis cluster of the repleta species group of Drosophila (Drosophilidae: Diptera) consists of three species. One is newly described as D. navojoa. A second species, described here as D. arizonae, replaces D. arizonensis, which has become a junior subjective synonym for D. mojavensis, the third species in the cluster. A phylogeny of the three species is presented, based on chromosomal inversions, morphology, and the ability to produce hybrids” “...show a sequential northwest movement (D. navojoa----D. arizonae----D. mojavensis) from southern Mexico to southern California and northern Arizona” “...D. navojoa breeds in Opuntia cactus, an ancestral behavior, whereas the other two species breed chiefly in Stenocereus cacti, a derived behavior.”
Immunogenetics. 1990;31(4):229-32. A SINE insertion provides information on the divergence of the HLA-DQA1 and HLA-DQA2 genes. Del Pozzo G, Guardiola J.
“…DQ subregion contains a pair of closely related A genes, HLA-DQA1 and HLA-DQA2, whose phylogenetic relationship is uncertain…”
Am J Med Genet Suppl. 1990;7:38-51. Reflections on the pathogenesis of Down syndrome. Opitz JM, Gilbert-Barness EF.
“…a reductionist approach to explain the Down syndrome phenotype in a "linear" manner from the DNA sequence of the segment will be doomed to failure from the outset because of the open, complex, nonlinear, hierarchical nature of morphogenetic systems. Neo-Darwinism is under strong attack; most genetic changes accumulated over time may very well be of neutral effect... independent of one another” ...biology lacks a theory of ontogenetic and phylogenetic development, and that a purely "genocentric" view of biology at the expense of the complexly hierarchical intrinsic epigenetic attributes of developmental systems is "out of focus with respect to ... biological organization and morphogenesis," and may be "a residue of nineteenth century..." “…the pathogenesis of Down syndrome is best viewed in terms of the mechanisms of speciation.”
Immunogenetics. 1990;32(3):157-74. Immunoglobulin lambda light chain evolution: Igl and Igl-like sequences form three major groups. Hayzer DJ.
“...all mammalian species contain Igl-V genes of each group. A similar comparison between the protein sequences encoded by the known Igl-C genes indicates that the duplication of the Igl-J-C gene pairs occurred independently in each species... the Igl-V-(J-C)(J-C) gene clusters of the mouse may not have their homologues in other species.”
Genetica. 1990;83(1):67-72. Chromosomal and molecular evolution in Asiatic wild asses. Ryder OA, Chemnick LG.
"Chromosomal studies of Tibetan wild ass, Equus kiang holdereri are reported for the first time. A Robertsonian polymorphism resulting in diploid numbers of 2n = 51 and 2n = 52 was identified. This polymorphism involves the same elements that participate in the polymorphic Robertsonian rearrangement producing diploid numbers of 54-56 in E. hemionus kulan and E. hemionus onager."
Prog Clin Biol Res. 1990;344:701-42. Molecular evolutionary genetics of isozymes: pattern, theory, and application. Nevo E.
"The human genetics laboratory compared isozyme structure of Jewish and non-Jewish populations." "Jews from diverse countries, and in spite of 2,000 years of Diaspora, retain in the frequencies of some isozymes their Near Eastern origins."
Prog Clin Biol Res. 1990;335:129-53. The Spalacidae: evolutionary history, speciation and population biology. Savic IR, Nevo E.
“We concluded that the taxonomy of Spalacidae needs a modern revision based on chromosome and molecular-genetic data, beside that of morphology, physiology and behavior." "More than 30 karyotypes (2n = 38-62; NF = 72-124) earlier represented by 8 classical species." "Most karyotypes represent biospecies adapted at multiple organizational levels to their different ecologies. A short overview is presented on population biology and life history parameters of the Spalacidae which result in K-selected, "equilibrium species".”
Proc Natl Acad Sci U S A. 1989 Dec;86(24):9961-5. Evolution of immunoglobulin light chains: cDNA clones specifying sandbar shark constant regions. Schluter SF, Hohman VS, Edmundson AB, Marchalonis JJ.
"Sharks are living fossils that are indistinguishable morphologically from their Devonian ancestors..." "Shark immunoglobulins are polydisperse like those of mammals, but these species lack homogeneous myeloma proteins." "The sandbar shark (Carcharhinus plumbeus) has at least four distinct light-chain constant regions, and these can be considered homologs of mammalian lambda chains. Approximately 40% identity was found in comparison from sharks to mammals." "One hexapeptide (Ala-Thr-Leu-Val-Cys-Leu) occurred in lambda constant regions of all vertebrate species. There was a universal conservation of certain cysteines, phenylalanines, tryptophans, and glycines and strong identities in the block of residues from Ser-176 to Trp-186. Comparison of the shark sequence with that of the characterized human lambda myeloma protein Mcg indicates a strong conservation of three-dimensional structure in this light-chain domain..." "The shark light-chain sequence contains primordial features shared by mammalian kappa and lambda chains and by T-cell receptor beta chains."
Nature. 1989 Nov 30;342(6249):542-3. Genetic correlations between morphology and antipredator behaviour in natural populations of the garter snake Thamnophis ordinoides. Brodie ED 3rd.
"...changes in behaviour will result in changes in morphology and vice versa. This might explain nonadaptive differences in morphology through indirect selection on correlated characters of other categories." "Morphology and behaviour are often correlated in nature and a genetic basis for such couplings has been demonstrated. I present here evidence that colour pattern and antipredator behaviour are genetically coupled in natural populations of the garter snake Thamnophis ordinoides. Similar phenotypic correlations between pattern and behaviour exist among species of North American snakes, indicating that selection for particular combinations of traits may help to maintain genetic covariances and colour polymorphism in Thamnophis ordinoides."
Biochemistry. 1989 Sep 19;28(19):7953-61. Isolation and complete structure of the lymphocyte serine protease granzyme G, a novel member of the granzyme multigene family in murine cytolytic T lymphocytes. Evolutionary origin of lymphocyte proteases. Jenne DE, Masson D, Zimmer M, Haefliger JA, Li WH, Tschopp J.
"...no experimental evidence for the existence of a [murine] granzyme C-D-E-F-G equivalent was found in humans... [or]... in the primate lineage."
Genome. 1989 Aug;32(4):538-42. The role of sex chromosomes in black fly evolution. Feraday RM, Leonhardt KG, Brockhouse CL.
"Arguments are presented here against the case that frequent differences between species in their sex chromosomes are based on (i) different average rates of differentiation of sex-linked and autosomal loci or (ii) the fact that the X and Y chromosomes are less numerous than autosomal chromosomes and so are more subject to the effects of drift and the random fixation of chromosome rearrangements."
J Theor Biol. 1989 Jul 10;139(1):69-83. The inheritance of acquired epigenetic variations. Jablonka E, Lamb MJ.
"There is evidence that the functional history of a gene in one generation can influence its expression in the next. In somatic cells, changes in gene activity are frequently associated with changes in the pattern of methylation of the cytosines in DNA; these methylation patterns are stably inherited. Recent work suggests that information about patterns of methylation and other epigenetic states can also be transmitted from parents to offspring. This evidence is the basis of a model for the inheritance of acquired epigenetic variations. According to the model, an environmental stimulus can induce heritable chromatin modifications which are very specific and predictable, and might result in an adaptive response to the stimulus" "...fungi and plants... lack distinct segregation of the soma and germ line" "...inherited epigenetic changes in the structure of chromatin can influence neo-Darwinian evolution as well as cause a type of "Lamarckian" inheritance."
Proc Natl Acad Sci U S A. 1989 Jul;86(14):5483-6. The homeotic gene spalt (sal) evolved during Drosophila speciation. Reuter D, Schuh R, Jackle H.
"To our surprise, sal sequences appear to be conserved in the Sophophora subgenus of the Drosophila genus but not in the Drosophila subgenus. On the other hand, the segmentation and other homeotic genes are conserved in the Drosophila subgroup as well. Our data suggest that sal encodes an accessory function that evolved relatively late during Drosophila speciation rather than playing a fundamental evolutionary role similar to that of other homeotic genes."
Mol Biol Evol. 1989 Jan;6(1):80-102. Rapid evolution of variants in a rodent multigene family encoding salivary proteins. Dickinson DP, Mirels L, Tabak LA, Gross KW.
"A survey of polypeptides encoded by RNA isolated from the submandibular glands of members of the Muridae (species of Mus and Rattus), in conjunction with cDNA cloning, has identified a class of salivary proteins that we term "spot proteins." Although clearly homologous, these proteins show dramatic differences between species in their polypeptide length." "There is extensive divergence in sequence between the mouse and rat mRNAs and their encoded proteins. The pattern of amino acid replacements and nucleotide substitutions is consistent with little, if any, selection constraint on the precise sequence of the spot proteins, suggesting that it is the overall architecture of the molecule, rather than the precise structure, that is important for function."
Biosystems. 1989;23(1):1-5. Speciation and bifurcations. Volkenstein MV, Livshits MA.
"The interrelations of physics and biology are discussed. It is shown that Darwin can be considered as one of the founders of the important field of contemporary physics called physics of dissipative structures or synergetics. The theories of gradual and punctual evolution are presented. The contradiction between these theories can be solved on the basis of molecular theory of evolution and on the basis of the phenomenological physical treatment. The general physical properties of living systems, considered as open systems being far from equilibrium, are listed and simple non-linear mathematical models describing gradual and punctual speciation are suggested. The usual pictures which present these two kinds of speciation can possess physico-mathematical sense. Punctuated speciation means bifurcation, a kind of non-equilibrium phase transition."
Genome. 1989;31(1):361-7. Aging, evolution and individual health span: introduction. Cinader B.
"… identification of the particular system that is responsible for the limit of health span in subpopulations… depends on a subset of allelic products of many genes and their relative functional capacity....reverse genetics..." "…should be possible to identify appropriate probes for degenerative diseases of old age that can be used for detection of corresponding human genes" "...we should learn how to identify individuals at risk from degenerative diseases of old age and how to treat them preventively."
Biol Cybern. 1989;62(2):167-75. Saltatory transitions are a naturally occurring property of evolving systems. Zimmerman ID, Rapp PE.
"On the basis of paleological evidence, it has been suggested that biological evolution need not necessarily be characterized by gradual change. Rather, evolutionary history may display saltatory periods of rapid speciation alternating with periods of relative quiescence, the whole dynamic being called punctuated equilibria. The empirical evidence that has been presented in support of this hypothesis has been the object of a vigorous dispute" "...these networks do not constitute a model of biological evolution."
Immunogenetics. 1989;30(6):432-9. RFLP analysis of the HLA-, ChLA-, and RhLA-DQ alpha chain gene regions: conservation of restriction sites during evolution. Bontrop RE, Otting N, Broos LA, Noort MC, Kenter M, Jonker M.
"The ChLA-DQA1 and -DQA2 gene-associated RFLP patterns are identical in man and chimpanzee, whereas such restriction site conservation is not seen in the rhesus monkey."
Comp Biochem Physiol A. 1989;93(2):309-12. Comparative physiology and biochemistry: challenges for the future. Prosser CL.
"Comparative physiology is distinguished from other types of physiology by treating the diversity of solutions of functional problems and by using kind of animal as a functional variable." "The strength of comparative physiology is its capacity to give some solutions to problems in basic biology."
Med Hypotheses. 1988 Oct;27(2):115-26. RISH. VI: General evolutionary aspects of the immune system. Daunter B.
"...sexual reproduction... only like-cells could associate to exchange genetic information" "...in the protozoa cell-surface, antigens are demonstrable in mating, whereas alloincompatability is intracellular" "...lectins could be expressed intracellularly as well as on the plasma membrane" "...cell-surface components for the identification of like-cells. This represents, in part, the histocompatability antigens of the organisms... the regulation of differentiation, and... as immunological reactions."
Mol Gen Genet. 1988 Aug;213(2-3):297-309. Divergence of the mitochondrial leucyl tRNA synthetase genes in two closely related yeasts Saccharomyces cerevisiae and Saccharomyces douglasii: a paradigm of incipient evolution. Herbert CJ, Dujardin G, Labouesse M, Slonimski PP.
"We studied the NAM2 genes of Saccharomyces douglasii and Saccharomyces cerevisiae, and showed that they are interchangeable for all the known functions of these genes, both mitochondrial protein synthesis and mitochondrial mRNA splicing. This confirms the prediction that the S. douglasii NAM2D gene encodes the mitochondrial leucyl tRNA synthetase (EC 126.96.36.199.). The observation that these enzymes are interchangeable for their mRNA splicing functions, even though there are significant differences in the intron/exon structure of their mitochondrial genome, suggests that they may have a general role in yeast mitochondrial RNA splicing. A short open reading frame (ORF) precedes the synthetase-encoding ORF, and we showed that at least in S. cerevisiae this is not essential for the expression of the gene; however, it may be involved in a more subtle type of regulation" "...S. douglasii and S. cerevisiae provide an ideal system for the study of molecular evolution, being two yeasts "caught in the act" of speciation."
Mol Biol Evol. 1988 Jul;5(4):442-54. Evolution of androgen-regulated mRNA expression in mouse kidney. Tseng-Crank J, Schonfeld C, Berger FG.
"...RP2, ornithine decarboxylase, and beta-glucuronidase mRNAs have each evolved independently... the pattern of variation among species is unique for each. This suggests a role for gene-specific, cis-acting genetic elements." "Alternatively, the variations may have preexisted within the progenitor population as polymorphisms that were fixed during establishment of individual lineages."
Nature. 1988 Apr 14;332(6165):651-4. The origin of MHC class II gene polymorphism within the genus Mus. McConnell TJ, Talbot WS, McIndoe RA, Wakeland EK.
"Speculation on the origin of this polymorphism, which is believed to be essential for the function of the class II proteins in immune responses to disease, has given rise to two hypotheses."
Immunogenetics. 1988;28(1):22-9. Class II genes of miniature swine. I. Class II gene characterization by RFLP and by isolation from a genomic library. Sachs DH, Germana S, el-Gamil M, Gustafsson K, Hirsch F, Pratt K.
"...unique alpha genes were obtained which showed no evidence of cross-hybridization, while beta genes showed extensive cross-hybridization and were frequently detected in the library by more than one human beta gene probe."
Heredity. 1987 Oct;59 ( Pt 2):253-8. Inter and intraspecific variation in nuclear DNA content in Aedes mosquitoes. Rao PN, Rai K.
"Haploid nuclear DNA of 23 species of Aedes, as determined by Feulgen cytophotometry, was found to vary 3-fold. This was accompanied by a 2-fold variation in total chromosomal length. There was a significant correlation (r = 0.765, P less than 0.001) between these two parameters. Genome size varied from 0.87 pg to 1.3 pg among 10 strains of Aedes albopictus, from wide geographic regions."
Genetica. 1987 Aug 15;72(3):193-8. Pleiotropic effects of environment-sensitive genes affecting fitness in relation to postmating reproductive isolation. Hutter P.
"With regard to speciation in sexually reproducing organisms, some population geneticists continue to argue about the relative merits of sympatry versus allopatry. However, all workers seem quite comfortable with the conventional scenario depicting how reproductive isolation arises between subpopulations in the state of incipient speciation. This view according to which the evolution of reproductive isolation mainly results from some genetic divergence consecutive to a substantial restriction in gene flow is questioned here... it places two important constraints on the properties of the genetic elements involved in it. One of them is concerned with the environment-sensitivity of the mutations implicated in the process, and the other with their presumed pleiotropic action on a behavioural trait."
Mol Biol (Mosk). 1987 May-Jun;21(3):630-9. [Molecular biology, darwinism and nomogenesis] [Article in Russian] Vol'kenshtein MV (Volkenstein MV).
“The theory of nomogenesis put forward by L. S. Berg in 1922 is discussed. It is shown that side by side with some erroneous anti-darwinian ideas the theory contains a series of important suggestions which anticipate the further development of the synthetic theory of evolution. Berg has foreseen the development of molecular biology. Thus he was the fore-teller of our branch of science. The theory of nomogenesis emphasized the limitations of natural selection which determine the directionality of evolution. Berg treated the speciation as a kind of phase transition. Even the most conscientious critics of Berg have misrepresented the real sense of his works. It is totally groundless to treat nomogenesis as an idealistic of Lamarkian theory. Berg was superior to his critics. However the enthusiasm about nomogenesis in our time shows the inability to separate "the grains from weeds".”
Ann Parasitol Hum Comp. 1987;62(6):542-76. [Original adaptive characters of intestinal Digenea of Sarpa salpa (Teleostei, Sparidae) and their interpretation in terms of evolution] [Article in French] Bartoli P.
"...original and yet unknown features are pointed out. Among these unusual structures, several correspond to adaptive characteristics favouring the settlement of the Digenean on the peculiar digestive gut wall of this herbivorous fish. Indeed, the intestinal mucous membrane of Sarpa salpa exhibits very few villi giving it an unusual smooth aspect. Therefore, the Mesometridae which always have just a single sucker (monostomatous) have selected a new kind of compensatory adhesive structure. Sometimes, the anterior end of the body becomes a sucker due to the particular distribution of the muscle strings; in other examples, the whole body becomes a sucker and its edges become considerably thinner to improve the tightness of the adhesive system. Other original anatomical features have been selected to allow survival in a medium rich in plant detritus." "The Digenea of Sarpa salpa are not interpreted by the author as true parasites but as endocommensal symbionts. These inquiline species are not immunogenic, or at least only slightly so, since they do not feed upon the host itself but upon its intestinal chyme. In most cases this results in a high parasite density (post larvae and adults) together with a cohabitation of the various species along the various intestinal segments. Coexistence of several species, systematically very close, evidently raises the question of their reproductive isolation."
Immunogenetics. 1987;25(5):290-8. DNA polymorphism of MHC III genes in inbred and wild mouse strains. Falus A, Wakeland EK, McConnell TJ, Gitlin J, Whitehead AS, Colten HR.
"The C4-Slp gene duplex, on the other hand, showed extensive polymorphism by DNA blot analysis. This polymorphism correlated poorly with the C2/factor B restriction fragment length polymorphism, suggesting independent evolution of these two segments of the S region."
Proc Natl Acad Sci U S A. 1986 Apr;83(7):2157-61. Overreplication and recombination of DNA in higher eukaryotes: potential consequences and biological implications. Schimke RT, Sherwood SW, Hill AB, Johnston RN.
“We propose that a fundamental problem in the faithful replication of complex chromosomes of higher eukaryotes is the proper control of both the number and timing of the multiple initiations of replication on single chromosomes. When replication patterns are disrupted by any of a variety of agents, overreplication of DNA can occur. We propose a model that accounts for the generation of a wide variety of chromosomal aberrations-rearrangements, resulting from the various ways in which the overreplicated strands can undergo recombination. We also discuss certain implications of the generation of chromosomal alterations in higher eukaryotes as they may relate to cancer chemotherapy, cancer progression, aging...”
Arkh Anat Gistol Embriol. 1986 Feb;90(2):12-8. [Evolutionary histology and the theory of evolution (on the 100th anniversary of the birth of Academician A. A. Zavarzin] [Article in Russian] Mirzoian EN.
“Darwin's theory did not touch upon the problem of evolution of tissues. An attempt made by Heckel to explain phylogeny of tissues, basing on principles of selection and divergence, failed.” “A. A. Zavarzin demonstrated that darwinism developed predominantly at the theory of speciation.” “The synthetic theory of evolution does not take into consideration evolution of tissues. A. A. Zavarzin's theory [the parallelism theory, a certain principle on specific regularities for each level of organization in the alive, i.e., tissues] contributed to reorganization of methodology of the evolutional biology.”
Ann Genet. 1986;29(2):69-75. [Role of chromosomes in evolution: a new interpretation] [Article in French] Dutrillaux B.
“The number of possible meiotic segregations of paternal and maternal chromosomes is 2N (N = haploid chromosome number). In eutherian Mammals, where large variations of N exist, 2N may be very different in related species, genes, or families. For instance, in Cercopithecidae, species with the highest value (N = 36) make 2(15) = 32,768 more gametic chromosome combinations than those with the lowest value (N = 21). It is also shown that the number of chiasmata varies from species to species and is proportional to the haploid number of arms NF/2 of the karyotype. Thus, increase or decrease of both N and NF/2, often concomitant, both increase or decrease genetic mixing.” “It is concluded that dichotomic evolution, which should be favoured by the transmission of groups of linked mutant alleles, is prevented, in most instances, by the high recombination rate in karyotypes with high values of N and NF/2.”
J Theor Biol. 1985 Dec 7;117(3):363-83. Thermodynamics and the conceptual structure of evolutionary theory. Wicken JS.
“Thermodynamics and evolutionary theory have spent most of their shared history in adversarial relationship to one another” “…with the general obstruction of constructive dialogue between evolution and the physical sciences it fosters, come the perennial accusations that Darwinism deals in adaptational teleology but not mechanisms.”
Chromosoma. 1985;92(2):156-63. Oncogenes and linkage groups: conservation during mammalian chromosome evolution. Stallings RL, Munk AC, Longmire JL, Jett JH, Wilder ME, Siciliano MJ, Adair GM, Crawford BD.
“Proto-oncogenes, which represent the cellular progenitors of the transforming genes harbored by acute transforming oncogenic retroviruses, have been highly conserved…”
Ann Parasitol Hum Comp. 1985;60(5):613-30. [Morphology of adult and sub-adult Wuchereria bancrofti. Differential characteristics among the strains] [Article in French] Bain O, Dissanaike AS, Cross JH, Harinasuta C, Sucharit S.
“No morphological character of adult W. bancrofti distinguishes the geographic origin of the different collections studied. By contrast, the morphological characters of the microfilariae and their biological features are significantly different, but are not inter-correlated.”
Genetics. 1984 Jun;107(2):331-41. On the theory of speciation induced by transposable elements. Ginzburg LR, Bingham PM, Yoo S.
“…several speculations concerning the role of transposons in evolution.”
C R Acad Sci III. 1984;299(7):195-8. [Isoenzymatic strains of Trypanosoma cruzi: recent or ancient, homogeneous or heterogeneous origin?] [Article in French] Tibayrenc M, Solignac M, Cariou ML, Le Ray D, Desjeux P.
“The possibility of a heterogeneous origin of the strains is discussed.”
Cytogenet Cell Genet. 1984;38(1):39-44. Unusual C-band patterns in three karyotypically rearranged forms of Scapteromys (Rodentia, Cricetidae) from Brazil. Freitas TR, Mattevi MS, Oliveira LF.
“Chromosome studies of 30 specimens of the rodent Scapteromys collected at nine localities in southern Brazil revealed the occurrence of three karyotypic taxa with 2n = 36 (one locality), 34 (two localities), and 24 (six localities), although all three had 40 autosomal arms (AN).” “The broad genomic reorganization which has occurred in this genus, in which the chromosomes do not have large amounts of constitutive heterochromatin, argues against the idea that a large amount of constitutive heterochromatin favors chromosome evolution and speciation.”
Cytogenet Cell Genet. 1977;19(5):241-9. Chromosomes of Peromyscus (rodentia, cricetidae). VI. The genomic size. Deaven LL, Vidal-Rioja L, Jett JH, Hsu TC.
"In the genus Peromyscus cells of all species contain 48 chromosomes; however, the fundamental number varies from 56 (P. Crinitus, P. boylei) to 96 (P. eremicus)."
Biosystems. 1983;16(1):57-63. A test of the karyotypic fissioning theory of primate evolution. Stanyon R.
“Karyotypic fissioning theory has been put forward by a number of researchers... Most recently, Giusto and Margulis (BioSystems, 13 (1981) 267-302) hypothesized that karyotypic fissioning best explains the evolution...” “That hypothesis is tested here by comparing the G-banded chromosomes of humans and great apes with eight species of Old World monkeys” “...extensive karyological similarities are not in accordance with, or predicted by karyotypic fissioning. Apparently, karyotypic fissioning is an extremely uneconomical model of chromosomal evolution.”
Acta Biotheor. 1983;32(1):29-41. On a functional-morphological approach to phylogenetic reconstruction: a critique. Sluys R.
“…direction of the adaptation process cannot be determined because of lack of knowledge about particular selective forces…” “…theories of model reconstruction are not open… in the sense of Popperian falsification” "...remains unclear how to proceed when morphoclines show contradictory polarities. Moreover, it is doubtful whether polarities of morphoclines can be determined independently of phylogenetic hypotheses, and also whether the use of multistate morphoclines is methodologically valid. By relying on a particular evolutionary theory, i.e. the neo-Darwinian theory, and consequently assigning natural selection as the major agent of directional progress, the Senckenburg method of phylogenetic reconstruction [proposed by a number of scientists of the Senckenberg Research Institute, based on functional-morphological studies, the evolutionary adaptation principle of Bock and Von Wahlert (1965) and so-called model reconstruction] restricts itself to microevolutionary change and, therefore, cannot be used when other hypotheses on the evolutionary process appear to explain the speciation process more plausibly, i.e. hypotheses on macroevolution. Furthermore, it is an unproved statement that evolution always proceeds according to the principle of economy."
Proc Natl Acad Sci U S A. 1982 Aug;79(15):4681-5. Evolution of mouse immunoglobulin lambda genes. Selsing E, Miller J, Wilson R, Storb U.
"Other than the region between the genes, very little homology exists in the C lambda flanking regions. In contrast, V lambda 1 and V lambda 2 genes show considerable homology extending into the 5' flanking regions." "there are fewer silent changes than amino acid replacement changes between the V lambda 1/V lambda 2 genes, suggesting either that a selective pressure acted on the silent sites or that V lambda genes have only recently been duplicated."
Cytogenet Cell Genet. 1982;34(1-2):35-42. The chromosomes of the Hadada ibis and comments on the karyotype evolution in Threskiornithidae (Aves, Ciconiiformes). Capanna E, Civitelli MV, Geralico C.
"The karyotype of Hagedashia hagedash differs from that of the other ibises karyotyped and introduces further karyotypic variability within the family Threskiornithidae. This variability is in contrast with the generalized karyotypic uniformity of birds and the karyotypic identity displayed by the family Ciconidae, which is closely related to the ibises."
Chromosoma. 1982;85(2):149-62. Genome evolution in pocket gophers (genus Thomomys). I. Heterochromatin variation and speciation potential. Patton JL, Sherwood SW.
“Populations with extensive heterochromatin variation and those with similar amounts meet and hybridize freely in nature.”
Acta Biotheor. 1981;30(3):171-6. Tumourigenesis: the subterfuge of selection. Pearson RD.
"Variation of rearrangement of regulatory genes is responsible for cellular malignant change" "...neoplasia represents a cellular 'macroevolutionary' event, and a tumour can be said to be an evolved population of cells. To understand this cellular evolution to malignancy, it may be necessary to go beyond a 'clonal selection' (adaptationist) explanation of neoplastic alteration" “…success for the neoplasm depends not upon 'clonal selection', but solely upon a genetic methodology-the function of which is to elude selection [the organizational restraints of surrounding cells as well as the host's immunological surveillance and non-specific monocyte-macrophage systems, 'natural selection' in the pericellular environment].” “By reverting to juvenile (embryonic) repertoire of cellular behaviour a tumour secures its own tenure or niche by usurping the host's armamentarium of selection forces, employing many of the same or similar methods by which implanting and invading tissues of the mammalian embryo forestall maternal detection and rejection. A number of ways by which the tumour blocks, subverts or evades selection are discussed.”
Chromosoma. 1981;82(3):409-27. The DNA sequences of cloned complex satellite DNAs from Hawaiian Drosophila and their bearing on satellite DNA sequence conservation. Miklos GL, Gill AC.
“Direct sequencing methods thus reveal a widespread sequence heterogeneity in both invertebrate and mammalian satellite systems of long or short repeat length. This heterogeneity does not support the strict sequence conservation implied by the "library" hypothesis, which claims a functional role in speciation for the rigid conservation of satellite DNA sequences (Fry and Salser, 1977)” "...Drosophila and primate data reveal that satellite DNAs can change rapidly, though nonrandomly, at the nucleotide sequence level..."
Chromosoma. 1978 Mar 31;66(2):141-59. Conservation and chromosomal localization of DNA satellites in balenopterid whales. Arnason U, Purdom IF, Jones KW.
"DNA satellites were isolated from three balenopterid species, viz. the minke, sei, and fine whales." "The function of satellite DNA is considered to imply the introduction of both chromosomal and genic polymorphisms and thus being of great importance in speciation, Based upon these concepts a model is postulated for the function of satellite DNA. According to this model at meiotic pairing euchromatin-heterochromatin overlapping between homologous chromosomes is considered to be of a general occurrence."
Chromosoma. 1980;76(3):339-63. Restriction endonuclease and molecular analyses of three rat genomes with special reference to chromosome rearrangement and speciation problems. Miklos GL, Willcocks DA, Baverstock PR.
"When differences are found between related species of organisms, it is often assumed that the differences themselves are causal factors either in speciation itself or in processes related to speciation. Two recent proposals..." "We have chosen two very closely related species of rat which are phenotypically almost indistinguishable and which have undergone massive genome reorganization. They differ by 11 major centric rearrangements (2n = 32, 2n = 50)" "...and have found that they have virtually no highly repeated DNA. Thus the 11 major chromosomal rearrangements have been fixed in present day genomes with hardly any highly repeated DNA, centric or otherwise" "...a large amount of highly repeated DNA is not obligatory for the formation and fixation of chromosome rearrangements. In addition, the existing literature reveals that one can find almost any situation at all, from species groups with high amounts of satellite DNA and no gross chromosomal rearrangements, to ones such as those described here, with tiny amounts of highly repeated DNA and massive chromosomal reorganisation. Since direct experimental data indicates that satellite DNA differences per se between homologous chromosomes do not cause infertility, speculations concerning modes of speciation based on satellite DNA differences between otherwise homologous chromosomes [Hatch et al., 1976 and Fry and Salser 1977] would appear to be ill founded."
Genetics. 1980 Apr;94(4):1011-38. The theory of speciation via the founder principle. Templeton AR.
"The founder principle has been used to explain many instances of rapid speciation. Advances from theoretical population genetics are incorporated into Mayr's original founder-effect genetic-revolution model to yield a newer model called the genetic transilience [a rapid shift to a new adaptive peak, most likely to occur when the founder event causes a rapid accumulation of inbreeding without a severe reduction in genetic variability]" "...tested in the laboratory, using systems and techniques that already exist--a rare attribute of most models of speciation."
Chromosoma. 1979 Aug 10;73(2):207-26. Expermental hybridization within the genus Triturus (Urodela: Salamandridae). III. Evidence for crossing-over, true chiasmata and chomosomal homologies in the spermatogenesis of F1 species hybrids, T. cristatus carnifex female X T. marmoratus male. Mancino G, Ragghianti M, Bucci-Innocenti S.
"Spermatogenesis in the F1 hybrid (2n=24=12 female + 12 male) between the closely related newt species T. cristatus carnifex and T. marmoratus was apparently normal up to pachytene." "Chiasmata between corresponding heterospecific chromosomes can be reported as true: real crossing over has taken place, proving the presence of primary chromosomal homologies between the 2 sets of the parental species."
Cytogenet Cell Genet. 1977;18(4):197-211. Chromosomal evolution in Malagasy lemurs. II. Meiosis in intra- and interspecific hybrids in the genus Lemur. Dutrillaux B, Rumpler Y.
"The chromosome analysis of meiosis in four lemurs, Lemur fulvus fulvus, L. f. collaris, L. f. albocollaris, and L. macaco, and particular hybrid crosses is reported." "The absence of chain multivalents elements in the pachytene stages of hybrid meiosis, where a chain is detected later in diakinesis, may offer evidence on the possible existence of a two-step pairing mechanism in meiotic homolog pairing."
Cell. 1979 Jul;17(3):623-34. The distribution of endogenous chicken retrovirus sequences in the DNA of galliform birds does not coincide with avian phylogenetic relationships. Frisby DP, Weiss RA, Roussel M, Stehelin D.
"Domestic chickens carry the genome of the endogenous retrovirus RAV-O as DNA sequences integrated into host chromosomes transmitted through the germ line." "The presence of RAV-O-related sequences in avian DNA does not correlate with phylogenetic relationships." "No fragments with sequences related to chicken retroviruses were found, however, in digests of DNA prepared from Sonnerat's, Ceylonese and Green Junglefowl, from two other Pheasant genera (Chrysolophus and Lophura), or from one Quail genus (Coturnix). Thus the DNA of three Junglefowl species closely related to Gallus gallus lacked RAV-O sequences while the DNA of more distantly related Phasianus species showed significant homology."
Proc R Soc Lond B Biol Sci. 1979 Apr 11;204(1155):267-86. Symbionticism revisited: a discussion of the evolutionary impact of intracellular symbioses. Taylor FJ.
"Wallin (1927) first published the notion that the fusion of bacteria with host cells was the principal source of genetic novelty for speciation. He suggested that mitochondria are transitional elements in this process... the significance that he attributed to symbiosis now seem excessive..." "The current status of the 'serial endosymbiosis hypothesis' is briefly reviewed." "Mitochondrial origins are more obscure..." "Together with the potential effects of viral vectors, symbiosis serves as a supplementary speciation mechanism..." "It is likely that these processes will explain some of the apparent anomalies in evolutionary rates and direction which are not readily explicable by the conventional synthetic theory of evolution."
Sem Hop. 1979 Feb 8-15;55(5-6):286-91. [Populational speciation or chromosomal speciation? About the book of Jean de Grouchy "From the birth of species to the aberrations of life" (author's transl)] [Article in French] Ruffie J.
"According to Jean de Grouchy, the emergence of a new species is dependent on an "acceptable" chromosomic rearrangement..." "He is thus using the idea of karyotype to develop the typological theory put forward at the beginning of the century which postulates that a single mutant is at the origin of a new species." "J. Ruffie demonstrates by arguments taken from population genetics and from the immunological polymorphism of wild populations that speciation is almost always the result of the evolution of an entire group..."
J Biol Chem. 1978 Sep 10;253(17):6068-75. Evolution of immunoglobulin subclasses. Primary structure of a murine myeloma gamma1 chain. Adetugbo K.
"An expansion-contraction mechanism is proposed for the evolution of gamma genes."
J Hered. 1978 Sep-Oct;69(5):316-30. G-band patterns, hemoglobin, and transferrin types of the bharal: chromosomal evolutionary relationships with sheep and goats. Bunch TD, Nadler CF, Simmons L.
"G-band patterns of the bharal (Pseudois nayaur), 2n = 54, were compared with those of wild sheep (Ovis dalli stonei), 2n = 54, and the Persian wild goat (Capra hircus), 2n = 60."
Proc Natl Acad Sci U S A. 1977 Nov;74(11):5083-7. Is evolution gradual or rectangular? Evidence from living fishes. Avise JC.
"The traditional view that most evolutionary change is gradual and cumulative within lineages (phyletic gradualism) has recently been challenged by the proposition that the majority of evolutionary change is concentrated within speciation events (rectangular evolution). The logical implications of these competing hypotheses for the means and variances of genetic distance among living members of rapidly and slowly speciating phylads are examined." "Results are inconsistent with predictions of rectangular evolution, but are not demonstrably incongruent with predictions of phyletic gradualism."
Chromosoma. 1976 Nov 29;58(4):341-53. Robertsonian metacentrics in the mouse. Capanna E, Gropp A, Winking H, Noack G, Civitelli MV.
"...sex chromosomes are never included in a metacentric" "...karyotype rearrangements of Robertsonian type may initiate reproductive isolation, which prepares the ground for further genetic diversification and, as in the case of the mouse, of incipient speciation."
Am J Clin Pathol. 1978 Jan;69(1):41-7. Evaluation of a multitest system for identification of saccharolytic pseudomonads. Morris MJ, Young VM, Moody MR.
"...further modifications are needed to eliminate identification problems..."
Proc Natl Acad Sci U S A. 1975 Feb;72(2):646-50. A theory of evolution above the species level. Stanley SM.
"Gradual evolutionary change by natural selection operates so slowly within established species that it cannot account for the major features of evolution."
Science. 1975 Oct 24;190(4212):382-3. Clades versus clones in evolution: why we have sex. Stanley SM.
"...asexual species cannot speciate in the normal sense. Asexual clones seldom diversify rapidly enough to overcome normal rates of extinction. In contrast, phylogenetic groups of sexual species (clades) commonly develop broad, heterogeneous adaptive zones rapidly enough to ensure survival."
Surv Biol Prog. 1957;3:109-47. Some general problems of chromosomal evolution and speciation in animals. White MJ.
As bacteria are naturally able to mutually exchange genetic material (i.e., unilaterally: plasmids), do you think impossible to classify all of them as one 'species' ('kind') with an extensive amount of possible combinations, with 'millions' of sub-species? Always being nothing else but a prokaryotic 'bacteria', never evolving to become even the smallest unicellular eukaryote? That is nearer to the facts than to say that one bacteria has 'evolved' into another bacteria, ‘winding-up’ the illusion of ‘evolution’ and its ‘speciation’. Those still bacteria and what happened is that humans just discovered that inside the full pool of bacteria there were also genes for processing, i.e., 'cooper' or 'oil', etc., such bacteria under a specific environment became dominant. Do you know if “archaeabacterias” also freely exchange genetic material with “bacterias”? If that’s the case, they also need to be included in the “bacteria” species, each of them as “sub-species” of bacteria.
The same can be said regarding yeast, “yeast still yeast” even if some claim to have "caught [them] in the act" of speciation: "…enzymes… interchangeable for their mRNA splicing functions..." "...S. douglasii and S. cerevisiae provide an ideal system for the study of molecular evolution, being two yeasts "caught in the act" of speciation" [Mol Gen Genet. 1988 Aug;213(2-3):297-309]
Member # 276
posted 21. April 2004 00:26
"As bacteria are naturally able to mutually exchange genetic material (i.e., unilaterally: plasmids), do you think impossible to classify all of them as one 'species' ('kind') with an extensive amount of possible combinations, with 'millions' of sub-species?"
I think it is no less impossible to group all the eubacteria as one species than it is to group all the vertebrates as a single species. Which is to say, no, I do not think it is reasonable to classify them all as one species. The genetic and biochemical diversity found within the bacteria easily exceed that of mammals and even eukaroytes. But the interesting thing is that much of the diversity within bacteria still tends to track within hierarchies, suggesting that despite horizontal transfer, there is still a strong linear component within bacterial evolution.
On a related note, it appears that we have indulged in horizontal transfer with eubacteria some time in the distant past during the endosymbiotic acquisition of mitochondria. Would that make us part of one bacterial species too?
"The same can be said regarding yeast, “yeast still yeast” even if some claim to have "caught [them] in the act" of speciation:...
If you look at the yeasts, you again see a great amount of diversity. For example, the basic biochemical differences between S. pombe and S. cerevisiae easy exceed that of all mammals and reptiles. They also make very different beers. I think it is a mistake to consider evolution from the viewpoint of gross external morphologies (skin-deep differences, really) and miss the underlying biochemistry. If one is willing to grant that the bacteria represent an 'acceptable' amount of natural variation within a single 'kind', then that is conceeding a huge amount to organic evolution -- Something that makes vertebrate evolution appear simple in comparison.
Seriously, if you ignore bacteria from any serious analysis, you are ignoring most of the biosphere.
[ 21. April 2004, 00:27: Message edited by: Argon ]
Member # 1201
posted 23. April 2004 09:11
If any organism is naturally able to multiply itself, at least for two generations after an exchange of nucleic acids, it must be of the same species.
>all the vertebrates as a single species
No, because the hybrid product of two different true species is sterile.
>The genetic and biochemical diversity found within the bacteria easily exceed that of mammals and even eukaroytes.
Yes, that is the natural variability within species, but that is secondary to the first rule of fertility in the second generation. That's an amazing trait of the natural variability within bacteria.
>it appears that we have indulged in horizontal transfer with eubacteria some time in the distant past during the endosymbiotic acquisition of mitochondria. Would that make us part of one bacterial species too?
No, because that is only a speculation without any foundation. My own findings disprove that imaginary view, as when we switched down one storage gene, the intricate and precise energetic mechanism directed by the nuclei of the cell increased the production of the mRNAs for the proteins needed inside the mitochondria, i.e.: SdhB, Cox7a1, Cox8b, Sco2, etc. So, in order to properly function, they needed to be designed "irreducibly complex" from their very beginning.
>They also make very different beers.
Also the dogs bark very different but still are of the same true species because of the rule of fertility in the second generation.
>gross external morphologies
That has been the blunt mistake on the definitions of species by T.D., E.M., K.L. and C.D. That's why the fertility rule in the second generation also is vital.
>miss the underlying biochemistry
Even that is only a secondary trait after the fertility rule in the second generation.
To move on from only the philosophical and theoretical realm, I am proposing today on these posting boards to ISCID members, an organized and exhaustive project based also on ID Research. I propose them to request a government grant to start a research on "second generation fertility" of the American fauna, flora and micro-organisms, to set also a higher standard in our understanding of which of them are true species and which of them are just sub-species.
This statement complements my posting of today in my 'Brainstorms'.
Member # 179
posted 23. April 2004 12:20
It occurs to me that your criteria re: species make plants "off-limits" or otherwise not subject to your speculations or models. Some might question the usefulness of ideas that claim to apply to life in general, when virtually all living things in fact are not "covered" by these same ideas.
Also, FWIW, it's pretty well-known that the "limits on the diversity of life" are pretty broad, based on observations made in plants (at least - I'm not dissing entomologists or microbiologists here ).
Member # 276
posted 23. April 2004 19:39
"If any organism is naturally able to multiply itself, at least for two generations after an exchange of nucleic acids, it must be of the same species."
So any horizontal transfer of DNA is sufficient to classify two organisms as a single species? I do not think so. After all, we have seen horizontal transfer from humans into mice, yeasts, and bacteria. Viral transduction of DNA between organisms is also not an unheard of mechanism.
I agree with Art on this subject. There is rather a lot of literature in taxonomy which deals with the shortcomings of the biological species concept ('mating criterion') for many biological groups. I will add that bacterial conjugation tends to be limited to similar species with specialized mechanisms, in contrast to other modes of transduction where only fragments may be transferred. This, and clonal reproduction is what makes possible the ability to place bacteria like E. coli and S. typhimurium into coherent species and divide the various species further into higher groups (like the purple bacteria and gram positives). Further, if all of bacterial diversity is considered simply 'natural diversity' or 'secondary traits' then that concedes a huge degree of capability to evolution that makes most of vertebrate evolution (and certainly human/ape evolution) simple in comparison.
Commenting on the endosymbiotic origins of mitochondria:
"...that is only a speculation without any foundation."
There is rather extensive genetic evidence for the endosymbiotic origins of the mitochrondria. Additionally, and as might be expected from the model, we find there are related groups of organisms whose mitochondrial genes can be found in different states of transfer to the nuclear genome (i.e. in some species the active gene is located in the mitochondrion while others have an inactive gene in the mitochondrion but an active gene in the cell nucleus). One might want to check out work and reviews by Michael W. Gray of Dalhousie University for more details. The 'without foundation' comment just is not so (& this applies doubly for the chloroplasts).
Member # 1201
posted 03. May 2004 16:39
Putting Limits on the Diversity of Life
After reviewing every abstract available on speciation, I can see no evidence of any kind of speciation today or in the past.
The central issue is that organisms can multiply by natural cloning (bacteria, yeast, plants, mammal twins, etc.) and organisms also can multiply by cross-breeding (again bacteria, yeast, plants, and animals, etc.) always reproducing the designed pattern "after their kind". That applies even in the recent case of the artificial cloning of mules.
A working definition of 'Species' as synonymous of 'True Species' or 'Kind' (Heb. Miyn):
"A group of organisms that actually or potentially can experience natural cloning and/or interbreeding to produce a fertile offspring resembling its progenitors."
This definition relies in the fertility of at least the first two generations of organisms (P, F1) experiencing recombination of their genetic material, and goes beyond phenotype (morphology, anatomy, proteins, regulatory mechanisms, etc.), genotype (disposition of nucleic acids, DNA, RNA, etc.), karyotype (disposition of chromosomes and its banding, etc.), embryology, behavior, reproductive patterns, etc. All of these secondary considerations can be useful for the definition of 'Sub-species' within 'True Species', but not as the primary source to differentiate them. The primary source is always the fertility of the first two generations. Research can be extended to the evaluation of fertility on the third generation to make the conclusion more stringent. Similarities between organisms can be studied as 'Comparative Biology' to understand functional relatedness without making any subjective 'evolutionary' inference.
It will require long-term experimentation, i.e. cross-breeding two different viruses, yeast, bacteria or animal 'species' (according to the old definitions), then following their genetic cross-flow; also in animals, artificial insemination may be needed, and then the verifying of the offspring fertility, i.e., parental fertility (P), then fertility of the F1 (immediate offspring) by producing an F2 (a new offspring from the F1), then the corroboration of
the F2 fertility by producing an F3, etc.
Quality control molecules are important in these natural limits to biological change, together with other characteristics, such as the chromosomal and genomic global size, etc.
Members of the same 'True Species' in bacteria, yeast and plants can interbreed, but also can reproduce themselves "vegetatively" (cloning). Artificially, this also can be done now in animals (see below).
Members of the same 'True Species' in yeast and plants, etc. can exhibit polyploidy, in which its full genome duplicates or triplicates, some of them being able to reproduce "vegetatively" or sexually within themselves, given that most of the plants have both sexes in the same individual plant. Polyploid animals are sterile and only can be multiplied through cloning. Partial polyploidy in bacteria (amplicons, plasmid-like structures) includes the intense amplification of particular genes or segments of the genome that are urgently needed for their survival-adaptation. In plants and animals, a similar phenomenon may occur inside a specific organelle.
Sterile hybrids (i.e., mule, tiglon, etc.), commonly a product of two different species with high similarities, can only be multiplied by artificial cloning. These sterile clones are not members of new 'species', but a dead end.
Viruses also can experience recombination among themselves or to be incompatible. We are just starting to understand such processes.
We use the words 'True Species' to differentiate them from the conventional and fallible classification of 'species' based only on morphology, on physical incompatibility, and/or reproductive isolation.
Sub-speciation is the proven variability and change within 'True Species' (Kinds). "Species are fixed with limits beyond which they cannot change" [Gregor Mendel (Experiments in plant hybridization. Verhandlungen des naturforschenden Vereines in Brünn, Bd. IV für das Jahr 1865, Abhandlungen, 3-47)]. However, some creatures will be harder to handle experimentally and hence, to classify than others. Those 'though' creatures will be subject to further review.
The fossil record can be approached mainly indirectly, exploring alternative views to the hypotheses on 'evolution', and always subject to further review, as no direct evidence can be obtained from them as from living organisms. Fossils of sterile hybrids, or of same 'species' with high variability escape precise classifications. "Dating" will be, either unnecessary for 'real-time' experiments and/or in a need of calibration to include in their equation the evidence of waters covering the full earth; always subject to further review also, for their intrinsic highly speculative nature.
FORMER DEFINITIONS OF 'SPECIES' PROVEN TO BE WRONG:
'Species' are organisms "physiologically incapable of interbreeding" (proposed by the geneticist Theodosius Dobzhansky and called the 'strong evolutionary' definition).
A female Chihuahua and a male Great Dane are physiologically incapable to mate but are members of the same 'True Species', as their artificial interbreeding produces fertile offspring.
'Species' are "groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups" " (proposed by the zoologist Ernst Mayr and called the 'weak evolutionary' definition).
The fifteen isolated subspecies of the Galapagos tortoises certainly correspond to the same 'Species', living today near extinction in at least ten separate islands, reproductively isolated one from the others; however, when put together are able to interbreed and to produces fertile offspring. The same can be said of the other fauna found in the Galapagos Islands [iguanas, finches, etc. (see below)]
The "morphological concept"" of Karl Linnaeus.
Again, dogs or finches have a very different morphology (phenotype) but are able to provide a fertile offspring. This system is internationally used and can still be used, 'fine-tuning' it after verifying the offspring's fertility, then performing the proper corrections [the finches are in need to be re-classified under one 'True Species' with many 'Sub-species' (see a previous posting)]
'Species' are "a set of individuals closely resembling each other…it does not essentially differ from the term variety which is given to less distinct and more fluctuating forms", statement by Charles Darwin.
By confusing 'True Species' with 'Sub-species' (varieties, lines, races, strains, etc., which exist within the 'True Species'), Darwin paved the way for the confusing of 'Speciation' with 'Sub-speciation', making that confusion a highly convenient 'trademark' in the promotion of 'evolution' (in Darwin's own words, that term was "arbitrarily given for the sake of convenience").
DARWIN'S WEAKNESS HAS BEEN PRESENTED IN THE NEXT TERMS:
"Regrettably, 140 years after the publication of Darwin's Origin of Species, we face the grotesque situation that we still do not know what is a species whose origin Darwin wanted to explain"
(Trends Parasitol. 2002 Mar;18(3):121-4. When is a parasite species a species? Kunz W. [Comment in: Trends Parasitol. 2002 Oct;18(10):439-40; author reply 440.])
"Despite the title, Darwin's Origin of Species doesn't really explain how new species are born. Scientists have been struggling with that thorny problem ever since its publication"
(Sudden Origins: Fossils, Genes, and the Emergence of Species, by Jeffrey H. Schwartz, Wiley, 2000, preface, 432 pp.)
"It is an irony of evolutionary genetics that, although it is a fusion of Mendelism and Darwinism, it has made no direct contribution to what Darwin obviously saw as the fundamental problem: the origin of species"
(Richard Lewontin, The Genetic Basis of Evolutionary Change, Columbia University Press, 1974, p. 159; 346pp.)
HOWEVER, AND BASED ON THE PREVIOUSLY PROVEN WRONG DEFINITIONS OF 'SPECIES' EVOLUTION HAS COINED THE TERM:
Speciation: The unproven assumption that one organism can be transformed into another different.
Thanks for your postings,
>make plants "off-limits"
Only if they were totally unable to crossbreed. Plants can multiply by natural cloning and by crossbreeding.
>we have seen horizontal transfer from humans into mice, yeasts, and bacteria
Natural exchange of nucleic acids between similar organisms.
>Viral transduction of DNA between organisms
Natural interchange, not a pathology.
>bacterial conjugation... transduction...
In my personal works every Rhizobium, and Agrobacterium and E. coli were able to interchange nucleic acids between themselves.
>this applies doubly for the chloroplasts
Without mitochondria (or chloroplasts) since the very beginning, how could those cells have been able to work in any way? I.E., has somebody done experiments excluding every mitochondria of a cell to see how, if... can the cell survive?
>Michael W. Gray of Dalhousie University
Do you have the title?
[ 14. May 2004, 08:24: Message edited by: Fernando Castro-Chavez ]
Member # 380
posted 03. May 2004 22:09
quote:That's a pretty amazing project to have completed. Just for the heck of it I did a couple of searches on "speciation." These are the results:
After reviewing every abstract available on speciation I can see no evidence of any kind of speciation today or in the past.
PubMed: 3,919 hits
PNAS: 2,818 hits
JBC Online: 12,980 hits
JCB Online: 2,971 hits
That's a whole lot of abstracts, even allowing for overlap.
Member # 276
posted 04. May 2004 23:49
"In my personal works every Rhizobium, and Agrobacterium and E. coli were able to interchange nucleic acids between themselves."
Agrobacterium transfers DNA to plants all the time. It's "natural".
See also: http://www.nature.com/nsu/011122/011122-4.html
"Without mitochondria (or chloroplasts) since the very beginning, how could those cells have been able to work in any way? I.E., has somebody done experiments excluding every mitochondria of a cell to see how, if... can the cell survive?
Look up the term "petite" in the yeast literature. Note: There are species of eukaryotes without mitochondria and plants without chloroplasts. Many seem to have lost them over time and so apparently, these organelles are not universally necessary within eukaryotes.
Regarding Michael W. Gray of Dalhousie University...
"Do you have the title?"
Titles. Try Medline. He has written a bunch of reviews and book chapters too.
[ 04. May 2004, 23:50: Message edited by: Argon ]
Member # 1201
posted 07. May 2004 15:24
Putting Limits on the Diversity of Life
(Expanding Part 3.3)
Quality Control Molecules:
Molecules needed in the quality control mechanisms to identify, correct, and prevent mistakes in the ongoing processes inside the cell (DNA replication, translation, transcription, protein folding, regulation of expression, etc.) in order to maintain an effective internal regime and to prevent an attack by external factors.
"The consequences of faulty quality control range from the cell death of neurodegeneration to the uncontrolled cell growth that is cancer"
[Stella M. Hurtley, Science 1999 December 3; 286: 1881]
"Faithful maintenance of the genome is crucial to the individual and to species. DNA damage arises from both endogenous sources such as water and oxygen and exogenous sources such as sunlight and tobacco smoke. In human cells, base alterations are generally removed by excision repair pathways that counteract the mutagenic effects of DNA lesions"
"...these restricted procedures require special strategies to function at high accuracy, such as protection of reactive DNA intermediates by protein-DNA interactions, and access to a high-fidelity DNA-copying machine with editing capacity"
"The well-characterized DNA mismatch correction system (J. Jiricny, Replication errors: cha(lle)nging the genome, EMBO J. 17, 6427, 1998) further minimizes replication errors by a systematic survey of newly synthesized strands. In addition, accessory factors such as the DNA helicases encoded by the genes defective in Werner syndrome and Bloom syndrome apparently serve to improve accuracy during DNA elongation, possibly due to resolution of stalled replication forks"
"A comprehensive overview of quality control in DNA would include a discussion of DNA polymerase fidelity and postreplicative mismatch correction and would also consider the damage-responsive cell-cycle checkpoints and the signal transduction systems that lead to cellular effects"
"...correction of uracil in DNA is a major biological problem that demands substantial and partly overlapping activities to retain a high extent of DNA quality control. Even in nongrowing cells, expedient removal of uracil from DNA appears necessary to avoid transcriptional base substitution that would generate mutant proteins and phenotypic changes (A. Viswanathan, H. J. You, P. W. Doetsch, Phenotypic Change Caused by Transcriptional Bypass of Uracil in Nondividing Cells, Science 284, 159, 1999). Additional distinct uracil- or thymine-DNA glycosylases, not clearly related to mammalian enzymes, have been described in thermophilic Archaea; such organisms also have DNA polymerases with read-ahead functions that stall incorporation when a uracil residue is detected in the template strand (M. A. Greagg, et al., A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil, Proc. Natl. Acad. Sci. U.S.A. 96, 9045, 1999)"
"A surprisingly large number of nuclear proteins bind specifically to double-strand breaks. Besides protecting the lesion, they apparently serve to signal the presence of such damage and to instruct cell-cycle control proteins about the imminent hazard"
"Repair of double-strand breaks by homologous recombination with another allele can be achieved with high fidelity"
"...nondistorting adducts such as seemingly harmless modifications of sugar residues are readily removed, if the altered nucleoside is placed within a mismatch (M. T. Hess, H. Naegeli, M. Capobianco, J. Biol. Chem. 273, 27867, 1998)"
"UV-DDB is specialized for detecting damage within chromatin (V. Otrin, M. McLenigan, M. Takao, A. Levine, M. Proti , J. Cell Sci. 110, 1159, 1997)"
"One fascinating feature of mammalian NER (Nucleotide Excision Repair) proteins is that most of them have dual functions, participating in other aspects of DNA metabolism. For example, RPA is the major single-strand DNA binding protein in cells, necessary for semiconservative replication and recombination"
"DNA replication and transcription take place in localized factories within cell nuclei (P. R. Cook, The Organization of Replication and Transcription, Science 284, 1790, 1999), which seems reasonable for processes that require a systematic progression along DNA"
"… During NER, gaps of ~30 nucleotides are filled in by one of these enzymes [DNA polymerases, POL] (R. Wood and M. Shivji, Carcinogenesis 18, 605 (1997); M. E. Budd and J. L. Campbell, Mutat. Res. 384, 157, 1997), so the reaction should proceed at a level of faithfulness similar to that seen in replication"
"Following the same strategy as used by the E. coli Pol III holoenzyme where the dnaE and dnaQ genes encode separate subunits for polymerization and editing (R. H. Scheuermann and H. Echols, Proc. Natl. Acad. Sci. U.S.A. 81, 7747, 1984), a distinct mammalian 3' exonuclease can remove the mismatched residue, creating a second opportunity for correct gap-filling"
"A human homolog of the DnaQ 3' exonuclease was identified recently that allows error-free processing of mistakes during DNA short-patch gap filling by POL in vitro, making the new enzyme the main candidate for an editing role during BER (M. Höss, et al., EMBO J. 18, 3868 (1999); D. J. Mazur and F. W. Perrino, J. Biol. Chem. 274, 19655, 1999)"
"The existence of human diseases associated with defects in DNA repair graphically illustrates the importance of this process of quality control"
[Quality Control by DNA Repair. Tomas Lindahl and Richard D. Wood. Science 1999 December 3; 286: 1897-1905]
More to come, given the time, etc.
I refer here to the exchange of nucleic acids amongst bacteria only.
A. tumefaciens produces tumors in plants.
Also I refer here to cells that naturally have mitochondria and that in some way may be artificially eliminated.
It is not granted any speculative linear descent.
Smith et al:
As it was stated before, the search strategy selected was to use two words in Pubmed: speciation and evolution. Why? Because if you only use the word 'speciation' alone you carry over all the 'noise' of mineralogical speciation, maybe somebody can define that for us.
Even 'charlie d' has argued elsewhere that it is not sufficient to guideline the search strategies, and I agree, it is necessary to provide details, not only of the reference but also of some of the internal information; by other side gordon don't even likes to see any reference or quotations. Anybody is welcomed to post articles that he thinks are lacking to the representative ones that I have already posted here. We know that no matter how we present the evidences, some are just never going to accept them.
Thanks, have a good weekend, today is Friday.
[ 07. May 2004, 15:33: Message edited by: Fernando Castro-Chavez ]