|
Author
|
Topic: Putting Limits on the Diversity of Life
|
Fernando Castro-Chavez
Member
Member # 1201
|
posted 24. March 2004 15:25
Putting Limits on the Diversity of Life
(Part One)
This outstanding study depicts the two explosions of life and the interval of destruction, with all the animal life on the ocean appearing at the same time in each explosion of life, without any "gradual appearing of new kinds of organisms". That's why Richard A. Kerr, in his review for 'Science' magazine entitled it:
"Putting Limits on the Diversity of Life":
Effects of sampling standardization on estimates of Phanerozoic marine diversification.
PNAS. May 22, 2001. Vol. 98, 11:6261-6266. Alroy et al.
Abstract
Global diversity curves reflect more than just the number of taxa that have existed through time: they also mirror variation in the nature of the fossil record and the way the record is reported. These sampling effects are best quantified by assembling and analyzing large numbers of locality-specific biotic inventories. Here, we introduce a new database of this kind for the Phanerozoic fossil record of marine invertebrates. We apply four substantially distinct analytical methods that estimate taxonomic diversity by quantifying and correcting for variation through time in the number and nature of inventories. Variation introduced by the use of two dramatically different counting protocols also is explored. We present sampling-standardized diversity estimates for two long intervals that sum to 300 Myr (Middle Ordovician-Carboniferous; Late Jurassic-Paleogene). Our new curves differ considerably from traditional, synoptic curves. For example, some of them imply unexpectedly low late Cretaceous and early Tertiary diversity levels. However, such factors as the current emphasis in the database on North America and Europe still obscure our view of the global history of marine biodiversity. These limitations will be addressed as the database and methods are refined.
Full text:
http://www.pnas.org/cgi/content/full/98/11/6261
Comment of that article in the same number by,
Mark Newman
From the Cover: A new picture of life's history on Earth
Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 11, 5955-5956, May 22, 2001
http://www.pnas.org/cgi/content/full/98/11/5955
(With a figure depicting the great contrast)
Comment of the article in the Journal "Science":
Putting Limits on the Diversity of Life
Richard A. Kerr
Science 2001 May 25; 292: 1481 (in News Focus)
A new way to analyze the fossil record is suggesting that life… long ago hit a limit to its diversity.
Abstract:
"In a paper published in The Proceedings of the National Academy of Sciences, 25 paleontologists demonstrate a fresh approach to extracting a history of life from an imperfect fossil record imperfectly sampled by paleontologists for 180 years. Preliminary results contradict previous studies that showed biodiversity increasing over time. Although far from the last word, the method marks a turning point in the study of paleontological databases, the researchers say".
From the figure:
Where Sepkowski's numbers told of steadily increasing marine diversity, a recount shows a plateau.
From the text:
"This paper represents a real step forward," says ecologist Michael Rosenzweig of the University of Arizona in Tucson. "For the first time, a large group of people is saying paleobiology has been making a mistake, that it's very important to deal with sampling issues. And when you try to get rid of the biases, the diversity curve looks a lot flatter."
Further quotations of the original PNAS article:
1-
PNAS | May 14, 2002 | vol. 99 | no. 10 | 6854-6859
Bambach, Knoll and Sepkoski Jr.
Anatomical and ecological constraints on Phanerozoic animal diversity in the marine realm
From the Abstract:
"The proportional representation of major functional groups was stably maintained ... Early Paleozoic radiations established stable ecosystem relationships, and thereafter only the great era-bounding mass extinctions were able to break patterns of incumbency..."
2-
PNAS | January 21, 2003 | vol. 100 | no. 2 | 599-604
Wilf et al.
Correlated terrestrial and marine evidence for global climate changes before mass extinction at the Cretaceous-Paleogene boundary
Conclusion:
"Our analysis of climate and facies considerations shows that the effects of bolide impact should be regarded as the most significant contributor to these plant extinctions."
3-
J. S. Crampton, A. G. Beu, R. A. Cooper, C. M. Jones, B. Marshall, and P. A. Maxwell
Estimating the Rock Volume Bias in Paleobiodiversity Studies
Science, July 18, 2003; 301(5631): 358 - 360.
From the Abstract:
"To interpret changes in biodiversity through geological time, it is necessary first to correct for biases in sampling effort related to variations in the exposure of rocks and recovery of fossils with age."
[ 07. April 2004, 17:10: Message edited by: Fernando Castro-Chavez ]
IP: Logged
|
|
Fernando Castro-Chavez
Member
Member # 1201
|
posted 26. March 2004 14:59
Putting Limits on the Diversity of Life
(Part Two):
Between the two abrupt and non gradual explosions of life, there was an interval of destruction: "the great impact", the great tsunamis, the "tohu-bohu", "the fall on earth of enormous ice-filled comets", leaving as an evidence the great craters, and is also called "the gap", see below:
PNAS Vol. 95, Issue 19, 11028-11029, September 15, 1998
This paper is a summary of a session presented at the Ninth Annual Frontiers of Science Symposium (Nov. 7-9, 1997):
Meteorite impact and the mass extinction of species at the Cretaceous/Tertiary boundary.
Pope et al.
"Confirmation that a large meteorite impact in Mexico correlates with a mass extinction… including the dinosaurs, is revolutionizing geology" "Georges Cuvier (1769-1832) first developed the concept of mass extinction based on the recognition of abrupt changes in the fossil record."
"Rejection of abrupt mass extinction [due to the blind belief in the writings of Darwin and of Charles Lyell, see original review, link below] prevailed until the late 1970s when a team of scientists lead by Luis and Walter Alvarez set out to measure the amount of cosmic dust in the K/T boundary. They hoped to use the dust influx rate to refine the duration of the inferred "gap" in the record." "On the basis of this finding, they hypothesized that the mass extinction at the K/T boundary was caused by the shutdown of photosynthesis by a global cloud of impact debris."
"Final confirmation of the impact came in the early 1990s with the discovery that the ~ 200 km in diameter Chicxulub crater in the Yucatan Peninsula of Mexico is the site of this catastrophic event."
"Confirmation of the impact portion of the Alvarez hypothesis marks a turning point in the study of the K/T mass extinction, away from speculations about possible causes, to linking the extinctions to a single catastrophic event. Here lies the frontier, which is in part ideological because many geologists still hold tight to the views of Lyell [and of Darwin, already mentioned]."
"Paleontologists have long known that a mass extinction of marine plankton occurred abruptly at the K/T boundary." "One of the first rigorous statistical tests of the abrupt extinction in larger animals is of ammonites (extinct relatives of the squid with coiled shells) from France and Spain." "This study provides good evidence for a link between the impact and an abrupt extinction of ammonites."
"There is much work ahead, but the course is clear"
To see this Summary and its References, with Full Access for an Article appeared in "Science":
http://www.pnas.org/cgi/content/full/95/19/11028
[To see from 'Science' a related search done in Mexico (in Spanish): http://www.geocities.com/fdocch/impact.htm]
[ 14. April 2004, 16:39: Message edited by: Fernando Castro-Chavez ]
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 26. March 2004 22:22
My I ask as to the nature of your argument? What specific limits on the diversity of life do you believe exist? Thanks for the links to some interesting papers but I would be interested in your personal interpretation of these papers and how they apply to ID.
IP: Logged
|
|
Fernando Castro-Chavez
Member
Member # 1201
|
posted 27. March 2004 12:55
Putting Limits on the Diversity of Life
(Part Three):
To approach an answer to Pim (thanks for your thought provoking post!), I must go back on time on my references and for now, just to quote them (some with Abstract excerpts).
I may welcome, if anybody have more references or reviews regarding this particular topic on "The Natural Limits to Biological Change", as it is also my desire to co-write some day an update on that, as I have stated elsewhere:
http://www.iscid.org/boards/ubb-get_topic-f-10-t-000077.html
So, in this part I want to link the past with the present to take back that good science that has been looking for order, laws and intelligent design (opposed to randomness, chaos and a lack of purpose for life).
Mendel's work and source of inspiration had a very clear and a very practical purpose, leading him to be considered "The Father of Genetics".
So, the first reference on the search for natural limits to biological change is the classic work of Mendel (Mendel, Gregor. 1865. Experiments in plant hybridization. Verhandlungen des naturforschenden Vereines in Brünn, Bd. IV für das Jahr 1865, Abhandlungen, 3-47), in which he writes:
“Species are fixed with limits beyond which they cannot change”
Definition of Fixed:
1. secured or made stable. 2. Constant, not subject to variation or alteration. 3. rigid or fastened. From the Latin fixus, which is the past participle of figere, meaning to fix or fasten.
The word "fixed" appears twice in the Bateson translation: first, in reference to the 2:1 ratio observed between the offspring of the F1 dominants that produced both dominant and recessive F2 characteristics and those that produced only dominant F2 characteristics; and second, in reference to the belief that there are definite limits to how species may be transformed through cross-breeding. An interesting analogy is thus drawn, in the English version, between the discovery of genetic ratios and the discovery of species boundaries. Mendel did not use the same word to describe the two situation in the original, however, using gesichert in the case of ratios, and fest in the case of species limits.
Reference: http://www.mendelweb.org/Mendel.html
As a logical "follow-up" of the work of Mendel being applied to populations, we can include here the important and brief (one page long) work of Hardy:
Hardy, G. H. 1908. Mendelian Proportions in a Mixed Population. Science, NS. XXVIII:49-50:
http://www.esp.org/foundations/genetics/classical/hardy.pdf
Most recently (06-24-2004), on reading one of the Classic Books on Genetics, I have found the next that I quote:
Statement by Thomas Hunt Morgan, A. H. Sturtevant, H. J. Muller, and C. B. Bridges (1915):
"The fact that more than one change may take place in the material at a given locus must not be taken to mean that the material is undergoing continuous fluctuating variability…" "…the change can not properly be said to be fluctuating, but is of a fixed nature." (pp. 170-171. The Mechanism of Mendelian Heredity. 1915. NY. Henry Holt and Co.)
http://www.esp.org/books/morgan/mechanism/facsimile
2- The next preliminary efforts that I have noticed (following after Mendel, Hardy, and Morgan et al) on the search for “The Natural Limits to Biological Change” are the works, first developed by the school of Alan Robertson (focused also on the mathematical aspect of the limits of biological change with a practical "breeding" purpose):
http://www.geocities.com/kubyimm3/alan_robertson.htm (a review)
Robertson, Alan. A Theory of Limits in Artificial Selection. Proceedings of the Royal Society of London. Series B, Biological Sciences 1960 Nov. 29; 153(951):234-249.
Hill WG, Robertson A. The effect of linkage on limits to artificial selection. Genet Res 1966 Dec;8(3):269-94 .
Robertson A, 1970, “A Theory of Limits in Artificial Selection With Many Linked Loci”. In: Mathematical Topics in Population Genetics. Ed. K. Kojima, Berlin. Sringer Verlag.
Robertson A, 1977, “Artificial Selection With a Large Number of Linked loci, pp. 307-22”. In: Proceedings of the International conference on Quantitative Genetics, edited by E. Pollak, O. Kempthorne & T. B. Baily. Iowa State University Press, Ames.
Nicholas, F. W. & A. Robertson, 1980, “The Conflict Between Natural and Artificial Selection in Finite Populations”. Theor. Appl. Genet. 56:57-64.
Gillian, L. Sharp, William G. Hill & Alan Robertson. "Effects of Selection on Growth, Body Composition and Food Intake in Mice" I. Responses in Selected Traits. 1984. Genet Res 43:75-95.
Forbes D. Brien, Gillian, L. Sharp, William G. Hill & Alan Robertson. "Effects of Selection on Growth, Body Composition and Food Intake in Mice" II. Correlated responses in Reproduction. 1984. Genet Res 44:73-85.
Shrimpton, A. E. & A. Robertson. "The Isolation of Polygenic Factors Controlling Bristle Score in Drosophila melanogaster." 1988a & 1988b, Genetics 118:437-43 & 445-9.
Roberts RC. The limits to artificial selection for body weight in the mouse. I. The limits attained in earlier experiments. Genet Res 1966 Dec;8(3):347-60.
Roberts RC. The limits to artificial selection for body weight in the mouse. II. The genetic nature of the limits. Genet Res 1966 Dec;8(3):361-75.
Cockerham, C.C.; Burrows, P.M. Selection limits and strategies. PNAS 1980 Jan;77(1):546-549.
Reeve JP. Predicting long-term response to selection. Genet Res 2000 Feb;75(1):83-94.
From the Abstract: "Models with biallelic loci have limits as to the amount of trait divergence possible".
Wang RL, Stec A, Hey J, Lukens L, Doebley J. The limits of selection during maize domestication. Nature 1999 Mar 18;398(6724):236-9.
From the Abstract: "Here we show that the effects of selection were limited to the gene's regulatory region."
Siegel PB, Dunnington EA. Genetic selection strategies--population genetics. Poult Sci 1997 Aug;76(8):1062-5.
From the Abstract: "Relationships between artificial and natural selection and among causes contributing to limits to artificial selection are discussed."
Barton NH. Linkage and the limits to natural selection. Genetics 1995 Jun;140(2):821-41.
From the Abstract: "The question is important both for understanding whether species approach this limit in nature".
Garte S. Locus-specific genetic diversity between human populations: an analysis of the literature. Am J Human Biol. 2003 Nov-Dec;15(6):814-23. From the Abstract: "These results do not support the idea that positive or diversifying natural selection plays an important role in increasing genetic diversity, even in genes that might be expected to be subject to selection pressure."
Betancourt AJ, Presgraves DC. Linkage limits the power of natural selection in Drosophila. Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13616-20.
From the Abstract: "Together these findings suggest that linkage limits the rate and degree of adaptation even in recombining genomes."
Barton N, Partridge L. Limits to natural selection. Bioessays. 2000 Dec;22(12):1075-84. Review.
From the Abstract: "We review the various factors that limit adaptation by natural selection. Recent discussion of constraints on selection and, conversely, of the factors that enhance "evolvability", have concentrated on the kinds of variation that can be produced."
Witting L. Interference competition set limits to the fundamental theorem of natural selection. Acta Biotheor. 2000 Jun;48(2):107-20.
From the Abstract: "The relationship between Fisher's fundamental theorem of natural selection and the ecological environment of density regulation is examined. Using a linear model, it is shown that the theorem holds when density regulation is caused by exploitative competition and that the theorem fails with interference competition."
Siegel PB, Dunnington EA. Genetic selection strategies--population genetics. Poult Sci. 1997 Aug;76(8):1062-5. Review.
From the Abstract: "This paper provides an overview of the association between population genetics and selection strategies in poultry. Relationships between artificial and natural selection and among causes contributing to limits to artificial selection are discussed. Homeostasis and resource allocations at the individual and at the population level are reviewed. Examples from poultry demonstrate where human intervention has circumvented biological limits. "
Polak M. Heritability of resistance against ectoparasitism in the Drosophila-Macrocheles system. J Evol Biol. 2003 Jan;16(1):74-82.
From the Abstract: "The present paper reports results of artificial selection for increased resistance in Drosophila nigrospiracula..." "This documented presence of additive genetic variation for resistance..."
Buckling A, Wills MA, Colegrave N. Adaptation limits diversification of experimental bacterial populations. Science. 2003 Dec 19;302(5653):2107-9.
From the Abstract: "Adaptation to a specific niche theoretically constrains a population's ability to subsequently diversify into other niches." "These results show that niche specialization may come with a cost of reduced potential to diversify."
3- The other that I also want to emphasize (as already has been done in ISCID) is the work on “Molecular Quality Control” inside the cell, which also contributes on "The Natural Limits to Biological Change”, with a practical purpose (like the Laws of Mendel were for the "breeders"):
Science (3 Dec. 1999, Vol 286:1881-1905).
http://www.geocities.com/fdocch/ctl.htm (Abstracts)
Welch WJ. Role of quality control pathways in human diseases involving protein misfolding. Semin Cell Dev Biol. 2004 Feb;15(1):31-8.
Abstract:
"Advances in connecting phenotype to genotype have led to new insights regarding the basis of human disease. Many inherited diseases are now known to arise due to specific mutations within a gene that then lead to a protein product unable to assume a stable conformation within the cell. Cellular machineries serving as "quality control monitors" recognize and target such abnormally folded proteins for rapid destruction. As a consequence, specific biochemical pathways requiring the protein of interest are adversely affected and lead to the disease phenotype. Yet in other cases, upon its misfolding the particular protein quickly aggregates, leading to the formation of inclusion bodies that eventually lead to cell demise. In what follows I discuss some classic examples of human diseases known to arise due to mutations that lead to altered protein folding, abnormal protein maturation and/or protein aggregation. In many cases simply altering the protein folding environment within the cell, via molecular or pharmacological approaches, can effectively rescue the maturation and stability of the mutant protein and thereby reduce the onset and/or progression of the disease phenotype. These new insights regarding the mechanisms underlying the disease phenotype, as well as new approaches to correct the protein folding defect, will undoubtedly prove to have a tremendous impact on clinical medicine."
Comment: I should include here also the background and the inspiration (those studies related with "real life being originated only from Life", the somehow passed-by "Law of Pasteur") behind the works of Pasteur against the "Spontaneous Generation" (which also had a very practical end, leading him to be considered "The Father of Microbiology").
If there is no "Spontaneous and Random Generation" today, there was none of that in any point in the past in any oceanic "soup". That was the first "Quality Control for Life"!
[ 01. July 2004, 12:35: Message edited by: Fernando Castro-Chavez ]
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 27. March 2004 20:34
I still fail to see the relevance of this literature bombing but there is one statement which needs some attention
Chavez quoting: “Species are fixed with limits beyond which they cannot change”
While this may be Mendel's thoughts on these matters, science has shown extensively that these ideas are contradicted by data.
Chavez, without much evidence, claims that "If there is no "Spontaneous and Random Generation" today, there was none of that in any point in the past in any oceanic "soup". "
But that of course is 'begging the question' since there may be and are some perfectly good reasons why one would not expect abiogenesis to be happening today.
So I still am not sure as to what Chavez is arguing here. That abiogenesis is not happening today. Fine, I could live with that conclusion. That thus abiogenesis could never have happened? Well that conclusion seems to be 'logical' and in fact given the data we do have available, perhaps a bit hasty.
I appreciate some of the old references and some may still have their relevance but science has reached many conclusions that reject the idea that species do not change. Evidence of speciation is plentiful.
Have you actually read all these papers or are you quoting mostly from their abstracts?
For a more relevant paper see
quote:
J Mol Evol. 2003;57 Suppl 1:S154-64.Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection by Sawyer SA, Kulathinal RJ, Bustamante CD, Hartl DL.
One of the principal goals of population genetics is to understand the processes by which genetic variation within species (polymorphism) becomes converted into genetic differences between species (divergence). In this transformation, selective neutrality, near neutrality, and positive selection may each play a role, differing from one gene to the next. Synonymous nucleotide sites are often used as a uniform standard of comparison across genes on the grounds that synonymous sites are subject to relatively weak selective constraints and so may, to a first approximation, be regarded as neutral. Synonymous sites are also interdigitated with nonsynonymous sites and so are affected equally by genomic context and demographic factors. Hence a comparison of levels of polymorphism and divergence between synonymous sites and amino acid replacement sites in a gene is potentially informative about the magnitude of selective forces associated with amino acid replacements. We have analyzed 56 genes in which polymorphism data from D. simulans are compared with divergence from a reference strain of D. melanogaster. The framework of the analysis is Bayesian and assumes that the distribution of selective effects (Malthusian fitnesses) is Gaussian with a mean that differs for each gene. In such a model, the average scaled selection intensity (gamma = N(e)s) of amino acid replacements eligible to become polymorphic or fixed is -7.31, and the standard deviation of selective effects within each locus is 6.79 (assuming homoscedasticity across loci). For newly arising mutations of this type that occur in autosomal or X-linked genes, the average proportion of beneficial mutations is 19.7%. Among the amino acid polymorphisms in the sample, the expected average proportion of beneficial mutations is 47.7%, and among amino acid replacements that become fixed the average proportion of beneficial mutations is 94.3%. The average scaled selection intensity of fixed mutations is +5.1. The presence of positive selection is pervasive with the single exception of kl-5, a Y-linked fertility gene. We find no evidence that a significant fraction of fixed amino acid replacements is neutral or nearly neutral or that positive selection drives amino acid replacements at only a subset of the loci. These results are model dependent and we discuss possible modifications of the model that might allow more neutral and nearly neutral amino acid replacements to be fixed.
Full article
[ 27. March 2004, 20:39: Message edited by: Pim van Meurs ]
IP: Logged
|
|
Fernando Castro-Chavez
Member
Member # 1201
|
posted 28. March 2004 22:57
Focusing on what Mendel said: “Species are fixed with limits beyond which they cannot change”.
The molecular basis to biological change clearly indicate that there is change within species but never one kind of organism is being transformed in another different kind of organism.
Somebody has said that there is “evolution” only within species. The variation that brings all the lines within species has a clear boundary, beyond which it cannot change.
It is as if putting in one graphic all the possible lines of Bos taurus, they never are going to become something else and different to Bos taurus. There is change and variation always within a boundary.
The trick of the evolutionary thinking is to unleash the imagination and to think that one kind of organism eventually, after millennia, was transformed into another totally different. Have you seen that absurd kind of programs that present a terrestrial mammal being gradually transformed into “a whale”, or the old fantasy of "the evolution of the horse" by taking species totally different and aligning them in a sequential form?
Life appeared suddenly, i.e., with all its possible kinds on the ocean, with no gradual improvement or transformism, allowing that same perfect design further variation in sizes and colors, and a plasticity to adaptation always with order, within a boundary.
So, the statement of Mendel stands as valid as when it was written. With the quality control mechanisms and other molecular discoveries, we are learning why it is not possible for a perfect kind of organism to be transformed into another, as the evolutionary thinking dreams.
IP: Logged
|
|
RBH
Member
Member # 380
|
posted 29. March 2004 00:18
Is that posting serious? I have to believe it's a parody, a caricature.
Castro-Chavez wrote quote:
The molecular basis to biological change clearly indicate that there is change within species but never one kind of organism is being transformed in another different kind of organism.
I just looove that seque from "species" to "kind." It almost (but not quite) makes one think that "kind" has some sort of biological meaning.
C-C further wrote quote:
Somebody has said that there is "evolution" only within species. The variation that brings all the lines within species has a clear boundary, beyond which it cannot change.
And somehody else said evolution can produce new species. And that somebody has actual data.
C-C further wrote quote:
It is as if putting in one graphic all the possible lines of Bos taurus, they never are going to become something else and different to Bos taurus. There is change and variation always within a boundary.
A boundary that's never been described or explained.
C-C went on quote:
Life appeared suddenly, i.e., with all its possible kinds on the ocean, with no gradual improvement or transformism, allowing that same perfect design further variation in sizes and colors, and a plasticity to adaptation always with order, within a boundary.
And those that couldn't swim promptly sank beneath the waves of that ocean (along with this thread).
Finally, C-C wrote quote:
So, the statement of Mendel stands as valid as when it was written.
Yup. It was invalid then and it's invalid now, hence it's precisely as valid now as it was when it was written.
RBH
IP: Logged
|
|
Fernando Castro-Chavez
Member
Member # 1201
|
posted 30. March 2004 23:27
To RBH:
1-) The concept of “Specie” is not absolute, it is rather imperfect and subject to change. The Word “Kind” stands out of that fallibility and goes beyond Linnaeus. If the Word “Kind” bothers some, don’t use it, but there is freedom if another individual wants to use it. The fallibility of the definition of “Specie” can be seen in the next point.
2-) Your ~ 41 data on “Speciation” shows that the same Kind of organisms are being compared in each of them. Where is the follow up of those old studies using today the same organisms described there?
3-) The search of a boundary led Mendel to become “the Father of Genetics”. The limits in artificial and natural selection have been described in phenotype and genotype and now those limits are starting to be described also at the molecular level, i.e. in the mechanisms of “quality control” (part three).
4-) This space is under Research Tools for Intelligent Design. “Part One” and “Part Two” are the main topic of this Review, as both describe the simultaneous and sudden appearance of life in the ocean, one of four different events of sudden appearance of life, non-linear, lacking gradual improvements or millions of years. Part three is an answer to Pim’s posting.
5-) Finally, your opinion contrasts the Conclusion of Mendel. His search for limits on variability took him to the discovery of the most common and important Laws of Heredity. Mendel’s Conclusions are dismissed and/or despised by “evolutionary thinking” (past and present), as your posting demonstrates.
Link to the grant of Bateson for his study on the Laws of Mendel applied to animals and plants, grant denied by the dominant evolutionism of his time, even when he attached his book defending the work of Mendel:
http://www.esp.org/foundations/genetics/classical/holdings/b/wb-02g.pdf
Book that Bateson Attached to his Grant Application:
http://www.esp.org/books/bateson/mendel/facsimile
Report that Bateson Attached to his Grant Application:
http://www.esp.org/foundations/genetics/classical/holdings/b/wb-02b.pdf
IP: Logged
|
|
Fernando Castro-Chavez
Member
Member # 1201
|
posted 01. April 2004 20:38
Putting Limits on the Diversity of Life
(Part 2)
Fragment of: "Chapter 1: "Darwinism in an Age of Molecular Revolution ("Evolution and the Molecular Revolution", Charles R. Marshall & J. William Schopf (eds.), 1996, Jones and Bartlett Publishers, Inc.)":
"A delightful example of the limits on variation is Wayne's (1986) study of variation in domestic animals. There are a great many types of domestic dogs, ranging from great danes to pugs, but there is much less diversity among domestic cats". "During its development, the relative proportions of a dog's skull change dramatically. Young dogs have broad and short skulls in comparison with those of adult dogs. In cats, however, the proportions of the face and head remain essentially constant during their growth to adulthood. This simple observation suggests that if there are large differences between the morphologies (the shape and form) of juveniles and adults in a species, a relatively greater range of varieties can be generated. This rule also holds for horses, the skulls of which show relatively little change of shape during growth and of which there are relatively few domestic varieties. On the other hand, pigs show dramatic face changes during their development and there are hundreds of different breeds. Wayne's analysis suggests that certain types of cat and horse skull morphologies are essentially impossible, not because they would be disadvantageous, but because the development of cats and horses proceeds in such a way that a whole suite of shapes simply cannot be readily generated. Clearly, the range of variation that can be produced by nature is not random with respect to the range of shapes and forms that can be imagined by humans!" [Quoted Article: Wayne, R.K. 1986. Cranial morphology of domestic and wild canids: The influence of development on morphological change. Evolution 40: 243-261]
[ 28. May 2004, 11:36: Message edited by: Fernando Castro-Chavez ]
IP: Logged
|
|
Fernando Castro-Chavez
Member
Member # 1201
|
posted 06. April 2004 01:22
For those with eyes to see a second and later instance of Cuvier's proposed research on Earth's Catastrophes (when compared with our References posted in Parts One and Two, presenting a first instance):
Geology: Vol. 32, No. 2, pp. 165–168.
Fossil whale preservation implies high diatom accumulation rate in the Miocene–Pliocene Pisco Formation of Peru.
Leonard R. Brand et al.
Abstract:
http://www.gsajournals.org/gsaonline/?request=get-abstract&doi=10.1130%2FG20079.1
"The well-preserved whales indicate rapid burial. The 346 whales within ~ 1.5 km^2 of surveyed surface... were distributed uninterrupted through an 80-m-thick sedimentary section..." "Current depositional models do not account for the volume of diatomaceous sediments or the taphonomic features of the whales...""...rapid burial due to high diatom accumulation...responsible for the superb preservation of these whales, leading to a higher upper limit on phytoplankton accumulation rates than previously documented."
Cover:
http://www.gsajournals.org/gsaonline/?request=get-static&name=0091-7613-32-2i
"...The unusual preservation of numerous whales in the Pisco Formation seems to require especially rapid burial from coalescence of several processes, including accumulation of current-transported diatom skeletons in shallow bays..."
----------------
The main author (Leonard R. Brand) answered two letters sent by Mike Brennan. The next are Brand's inspiring conclusions:
1-
"A more important conclusion to me is that when I take seriously a biblical concept of earth history, it opens my eyes to see things in nature that otherwise are likely to be overlooked, like the nature of these whales that imply rapid deposition of the sediments. Much more of that type of research will be good for science as well as for our faith."
2-
"I have not been limited in my research or publication opportunities because of my Christian beliefs."
[ 06. April 2004, 01:36: Message edited by: Fernando Castro-Chavez ]
IP: Logged
|
|
Fernando Castro-Chavez
Member
Member # 1201
|
posted 07. April 2004 17:21
Putting Limits on the Diversity of Life
(Part Four)
An extensive discussion with links can be found at:
http://www.iscid.org/ubbcgi/ultimatebb.cgi?ubb=get_topic&f=6&t=000488&p=3#000043
Taking one step further the study of “The Natural Limits to Biological Change” we can say that the concept of “Species” is fallible only because of the human ignorance. I.E., a simple and very old condition for the definition of living animals as ‘Kinds’ or ‘Species’ is:
" A fertile group of organisms capable to provide a fertile lineage."
More recent references on ‘Speciation’ can show the truth of ‘Speciation’ as being a complete Speculation, done under an ambiguous use of the word ‘Species’ and so, being deceptive:
If anybody wants to read these and more abstracts at will, these articles are available in:
http://www.ncbi.nlm.nih.gov/entrez
Evolution Int J Org Evolution. 2003 May;57(5):1049-60. Reproductive character displacement and the genetics of gamete recognition in tropical sea urchins. Geyer LB, Palumbi SR.
“Most documented cases of reproductive character displacement involve characters that are poorly understood at the genetic level, and rejecting alternative hypotheses for biogeographic shifts in reproductive traits is often very difficult.”
Evolution Int J Org Evolution. 2003 May;57(5):1031-48. Macroevolutionary consequences of developmental mode in temnopleurid echinoids from the Tertiary of southern Australia. Jeffery CH, Emlet RB.
“Analysis using phylogenetically independent contrasts is unable to confirm that the stratigraphic and geographic patterns are unbiased by the phylogenetic relationships of the included taxa.”
Nature. 2003 Jun 12;423(6941):715-9. Adaptive evolution drives divergence of a hybrid inviability gene between two species of Drosophila. Presgraves DC, Balagopalan L, Abmayr SM, Orr HA. [Comment in: Nature. 2003 Jun 12;423(6941):699-700.]
“Almost nothing is known about the genes involved in such hybrid incompatibilities or the evolutionary forces that drive their divergence.”
Nature. 2003 Jun 26;424(6943):979-82. The evolution of reproductive isolation through sexual conflict. Martin OY, Hosken DJ. [Comment in: Nature. 2003 Jun 26;424(6943):929-30.]
“Sexual conflict, potentially the strongest driver of speciation, is greater in larger, higher-density populations. This idea is highly controversial and has little experimental support.” “This result strongly suggests [it]…”
Heredity. 2003 Jul;91(1):28-35. Drosophila melanogaster and D. simulans rescue strains produce fit offspring, despite divergent centromere-specific histone alleles. Sainz A, Wilder JA, Wolf M, Hollocher H.
“A recent theory proposes that the independent evolution of centromere-binding proteins in isolated populations may be a universal cause of speciation among eukaryotes. In Drosophila the centromere-specific histone, Cid (centromere identifier), shows extensive sequence divergence between D. melanogaster and the D. simulans clade, indicating that centromere machinery incompatibilities may indeed be involved in reproductive isolation and speciation." "Through comparisons of cid sequence between nonrescue and rescue strains, we show that cid is not involved in restoring hybrid viability or female fertility. Further, we demonstrate that divergent cid alleles are not sufficient to cause inviability or female sterility in hybrid crosses." "cid... is not a speciation gene."”
Mol Ecol. 2003 Jul;12(7):1843-54. Wolbachia and genetic variability in the birdnest blowfly Protocalliphora sialia. Baudry E, Bartos J, Emerson K, Whitworth T, Werren JH.
“Current results… suggest that Wolbachia has not acted as a major barrier to gene flow between western and eastern-Midwestern populations”
Mol Phylogenet Evol. 2003 Jul;28(1):60-86. A molecular phylogeny of the Littorininae (Gastropoda: Littorinidae): unequal evolutionary rates, morphological parallelism, and biogeography of the Southern Ocean. Williams ST, Reid DG, Littlewood DT.
“The phylogeny shows considerable disagreement with earlier hypotheses derived from morphological data.” “The phylogenetic relationships of 'Littorina' striata have been controversial and it is here transferred to the genus Tectarius, a surprising relationship for which there is little morphological support. The relationships of the enigmatic Mainwaringia remain poorly resolved, but it is not a basal member of the subfamily.” “The fossil record of littorinids is poor…” “…there is no evidence for speciation events in the Plio-Pleistocene”
Infect Genet Evol. 2001 Dec;1(2):117-22. The population structure of Neisseria meningitidis serogroup A fits the predictions for clonality. Bart A, Barnabe C, Achtman M, Dankert J, van der Ende A, Tibayrenc M.
“The two interpretations are contradictory.” “This was not due to the overrepresentation of certain genotypes, in contrast to the expectations for an epidemic population.”
Plant Cell. 2003 Jun;15(6):1430-42. The basis of natural and artificial postzygotic hybridization barriers in Arabidopsis species. Bushell C, Spielman M, Scott RJ.
“…Much remains to be learned about the nature of hybridization barriers” “We conclude from these findings that the dominant cause of seed abortion in the diploid A. thaliana x tetraploid A. arenosa cross is parental genomic imbalance. Our results also demonstrate that manipulation of DNA methylation can be sufficient to erect hybridization barriers, offering a potential mechanism…”
Mol Biol Evol. 2003 Jul;20(7):1158-67. The major tick salivary gland proteins and toxins from the soft tick, Ornithodoros savignyi, are part of the tick Lipocalin family: implications for the origins of tick toxicoses. Mans BJ, Louw AI, Neitz AW.
“The origins of tick toxicoses remain a subject of controversy because no molecular data are yet available…” “The implications of this study are that the various forms of tick toxicoses do not have a common origin…”
Mol Ecol. 2003 Jun;12(6):1619-28. Evidence for interspecies transmission of viruses in natural populations of filamentous fungi in the genus Cryphonectria. Liu YC, Linder-Basso D, Hillman BI, Kaneko S, Milgroom MG.
“Based on these findings, we rule out the hypotheses that CHV-1 diverged from viruses in a common ancestor of the hosts…”
Evol Dev. 2003 May-Jun;5(3):269-80. Mimicry: developmental genes that contribute to speciation. Naisbit RE, Jiggins CD, Mallet J.
“Despite renewed interest in the role of natural selection as a catalyst for the origin of species, the developmental and genetic basis of speciation remains poorly understood.” “…is constrained by preexisting linked elements that may have arisen via tandem duplication rather than having been assembled by natural selection.” “…developmental and genomic …effects are probably not strong...”
Syst Biol. 2003 Apr;52(2):186-205. The geometry of the marmot (rodentia: sciuridae) mandible: phylogeny and patterns of morphological evolution. Cardini A.
“Marmots have a prominent role in the study of mammalian social evolution, but only recently has their systematics received the attention it deserves if sociobiological studies are to be placed in a phylogenetic context.” “…sciurid skeletal characters are considered to be inclined to convergence. However, no morphological study involving all marmot species has ever been undertaken.” “…the marmotine mandible may have evolved as a mosaic of characters and does not show convergence...” “…hypothesis… thought to have originated as isolated populations…”
Mol Phylogenet Evol. 2003 Jun;27(3):441-52. Molecular phylogeny of Crematogaster subgenus Decacrema ants (Hymenoptera: Formicidae) and the colonization of Macaranga (Euphorbiaceae) trees. Feldhaar H, Fiala B, Gadau J, Mohamed M, Maschwitz U.
“…On a wider geographic range (including North and North-East Borneo) some morphospecies turned out to be species complexes with genetically quite distinct taxa. Our phylogenetic analysis and host association studies do not indicate strict cocladogenesis…”
Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7169-74. Sympatric speciation through intraspecific social parasitism. Savolainen R, Vepsalainen K. [Comment in: Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6896-8.]
“We show that congeneric inquilines have originated independently several times. We also show that two of the inqulines are more closely related to their hosts than to any other species.”
Genetica. 2003 May;118(1):41-50. On the relative roles of faster-X evolution and dominance in the establishment of intrinsic postzygotic isolating barriers. Naveira HF.
“The modern theory of speciation assigns a prominent role to the recessivity of genetic incompatibilities in the two rules of speciation…” “…dominance considerations absolutely irrelevant” “…the relative roles currently assigned to faster-X evolution and dominance in the theory of speciation should be revised…”
Homo. 2003;53(3):201-24. Number of ancestral human species: a molecular perspective. Curnoe D, Thorne A.
“Despite the remarkable developments in molecular biology over the past three decades, anthropological genetics has had only limited impact…” “Published genetic distances between common chimpanzees and bonobos, along with evidence for interbreeding, suggest they should be assigned to a single species.”
[That author even suggests the aberration of putting chimpanzees in the ‘Homo’ category]
Genome Res. 2003 May;13(5):781-93. Complex evolution of 7E olfactory receptor genes in segmental duplications. Newman T, Trask BJ.
“The complex structure and history of the 7E SDs (Large Segmental Duplications) necessitates extension of the current model of large-scale DNA duplication. Despite their appearance as pseudogenes, some 7E genes exhibit a signature of purifying selection, and at least one 7E gene is expressed.”
Comp Biochem Physiol A Mol Integr Physiol. 2003 May;135(1):105-29. Thyroid rhythm phenotypes and hominid evolution: a new paradigm implicates pulsatile hormone secretion in speciation and adaptation changes. Crockford SJ.
“Recently I proposed a novel theory…” “THs (Thyroid Hormones) are produced in a distinctly pulsatile manner and appear to generate species-specific TH rhythms with distinct ontogenic shifts.” “The concept provides the first really plausible explanation…”
J Hum Evol. 2003 Apr;44(4):451-78. An integrated approach to taphonomy and faunal change in the Shungura formation (Ethiopia) and its implication for hominid evolution. Alemseged Z.
“…Discerning major biotic turnovers and linking them to global and regional climatic changes have been complicated by many factors, notably taphonomy and discontinuity of the fossil evidence, notwithstanding the considerable work of some researchers [mainly Vrba, E.S.]…”
Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5252-7. Directional selection has shaped the oral jaws of Lake Malawi cichlid fishes. Albertson RC, Streelman JT, Kocher TD.
“…Definitive evidence for the action of natural selection has been missing”
Am Nat. 2003 Mar;161(3):413-21. The evolution of body size in extant groups of North American freshwater fishes: speciation, size distributions, and Cope's rule. Knouft JH, Page LM.
“…Expectation that general trends exhibited in the fossil record will correspond to patterns in extant groups is not necessarily warranted.”
Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5302-7. A rapidly evolving MYB-related protein causes species isolation in Drosophila. Barbash DA, Siino DF, Tarone AM, Roote J.
“Matings among different species of animals or plants often result in sterile or lethal hybrids. Identifying the evolutionary forces that create hybrid incompatibility alleles is fundamental to understanding the process of speciation, but very few such alleles have been identified….” “We report here the cloning of the first, to our knowledge, Drosophila melanogaster gene involved in hybrid incompatibilities, Hybrid male rescue (Hmr). Hmr causes lethality and female sterility in hybrids among D. melanogaster and its sibling species …” “Our results suggest that hybrid lethality may result from disruptions in gene regulation…”
Oecologia. 2003 Jun;136(1):1-13. Toward an ecological synthesis: a case for habitat selection. Morris DW.
“…Future studies of habitat selection… will also continue to enrich the panoply of ideas that shape evolutionary ecology.”
Evolution Int J Org Evolution. 2003 Feb;57(2):205-15. Phylogeographic structure and cryptic speciation in the trans-Antarctic moss Pyrrhobryum mnioides. McDaniel SF, Shaw AJ.
“We find: (1) reciprocal monophyly of Australasian and South American populations, indicating a lack of intercontinental dispersal; (2) shared haplotypes between Australia and New Zealand, suggesting recent or ongoing migration across the Tasman Sea; and (3) reciprocal monophyly among Patagonian and neotropical populations, suggesting no recent migration along the Andes.” “These data are in accord with niche conservatism, but whether the morphological stasis is a product of stabilizing selection or phylogenetic constraint is unknown.”
Mol Biol Evol. 2003 May;20(5):831-41. Study on the evolution of the grande retrotransposon in the zea genus. Garcia-Martinez J, Martinez-Izquierdo JA.
“Phylogenetic analysis revealed a lack of concordance between the phylogenetic tree obtained from LTR (Long-Terminal Repeat, from the Retrotransposon, with around 5,700 copies per haploid genome) sequences and the conventional taxonomic tree”
Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4639-43. Positive selection in the egg receptor for abalone sperm lysin. Galindo BE, Vacquier VD, Swanson WJ.
“The mechanism of speciation is a central problem in evolutionary biology.” “Several mathematical simulations predict …” “…support for theoretical models…”
Mol Biol Evol. 2003 Mar;20(3):338-50. Multiple hybrid formation in natural populations: concerted evolution of the internal transcribed spacer of nuclear ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae). Koch MA, Dobes C, Mitchell-Olds T.
“Hybridization, reticulation, and apomixis are assumed to be the major forces driving speciation processes in this species complex. Analysis of conserved regions and secondary structures of the ITS region provided no evidence that, in this system, hybrid ITS evolution is predominantly driven in a particular direction.”
Mol Phylogenet Evol. 2003 Mar;26(3):369-88. Phylogeny of the eelpout genus Lycodes (Pisces, Zoarcidae) as inferred from mitochondrial cytochrome b and 12S rDNA. Moller PR, Gravlund P.
“Subdivision of the genus has been based on single or few morphological characters (e.g., lateral line configuration) with contradicting results and phylogenetic approaches have not been attended.” “This is not in accordance with earlier assumptions of the more elongate, deeper living species being the more derived…” “Small genetic differences between Arctic/Atlantic species indicate a rather recent radiation…”
Nature. 2003 Mar 6;422(6927):68-72. Engineering evolution to study speciation in yeasts. Delneri D, Colson I, Grammenoudi S, Roberts IN, Louis EJ, Oliver SG. [Comment in: Nature. 2003 Mar 6;422(6927):25-6.]
“The Saccharomyces 'sensu stricto' yeasts are a group of species that will mate with one another, but interspecific pairings produce sterile hybrids” “…translocations between the chromosomes of these species do not correlate with the group's sequence-based phylogeny (that is, translocations do not drive the process of speciation).” “Here, we report experiments that take an interventionist, rather than a retrospective approach…” “We demonstrate that this imposed genomic collinearity allows the generation of interspecific hybrids that produce a large proportion of spores that are viable, but extensively aneuploid.” “This controlled comparison of the effect of chromosomal translocation on species barriers suggests a mechanism…”
Mol Biol Evol. 2003 Feb;20(2):220-31. Evolution of bindin in the pantropical sea urchin Tripneustes: comparisons to bindin of other genera. Zigler KS, Lessios HA.
“…not correlated with phylogenetic affinities or molecular structure…”
Philos Trans R Soc Lond B Biol Sci. 2003 Jan 29;358(1429):87-97; discussion 97. Eukaryotic genome evolution: rearrangement and coevolution of compartmentalized genetic information. Herrmann RG, Maier RM, Schmitz-Linneweber C.
“Organelle exchanges, even between closely related species, can greatly disturb the intracellular genetic balance ("hybrid bleaching")” “We have studied the reciprocal Atropa belladonna-Nicotiana tabacum cybrids, which differ markedly in their phenotypes, and found that transcriptional and post-transcriptional processes can contribute to genome/plastome incompatibility. Allopolyploidy can influence this phenomenon by providing an increased, cryptic RNA editing potential and the capacity to maintain the integrity of organelles of different taxonomic origins.”
Proc R Soc Lond B Biol Sci. 2003 Jan 7;270(1510):53-9. Sex chromosome evolution and speciation in Ficedula flycatchers. Saetre GP, Borge T, Lindroos K, Haavie J, Sheldon BC, Primmer C, Syvanen AC.
“Speciation is the combination of evolutionary processes that leads to the reproductive isolation of different populations. We investigate the significance of sex-chromosome evolution on the development of post- and prezygotic isolation in two naturally hybridizing Ficedula flycatcher species [birds]. Applying a tag-array-based mini-sequencing assay to genotype single nucleotide polymorphisms (SNPs) and interspecific substitutions, we demonstrate rather extensive hybridization and backcrossing…” “However, gene flow across the partial postzygotic barrier (introgression) is almost exclusively restricted to autosomal loci…”
Evolution Int J Org Evolution. 2002 Dec;56(12):2445-58. Speciation by host switch and adaptive radiation in a fish parasite genus Gyrodactylus (Monogenea, Gyrodactylidae). Zietara MS, Lumme J.
“Four hundred Gyrodactylus species have been formally described, but the estimated number of species in this fish ectoparasite genus of Monogenean Platyhelminthes is more than 20,000. The unusually high species richness has lead to the hypotheses of speciation and adaptive radiation via host switching.” “In G. (Limnonephrotus), eight host switches crossing the host family barrier were observed…” “…the phylogenies are largely independent and disconnected.”
Nucleic Acids Res. 2003 Feb 15;31(4):1121-35. Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns. Bon et al.
“Taken together, our results indicate that the origin of spliceosomal introns is complex within a given genome…”
J Plant Res. 2002 Jun;115(3):225-35. Karyomorphology of Taiwanese Begonia (Begoniaceae): taxonomic implications. Oginuma K, Peng CI.
“The variation in chromosomal features is more complex than the variation in floral and fruit morphologies.”
Mol Phylogenet Evol. 2003 Feb;26(2):190-201. Rapid evolutionary divergences in reef fishes of the family Acanthuridae (Perciformes: Teleostei). Clements KD, Gray RD, Howard Choat J.
“Unweighted parsimony analysis produced two optimal trees. Both of these were highly incongruent with a previous morphological phylogeny…” “Split decomposition analysis identified conflict in the placement of long basal branches separated by short internodes, providing further evidence that long branch attraction is an important cause of disagreement between molecular and morphological trees. Parametric bootstrapping rejected hypotheses of monophyly…”
Genetica. 2002 Nov;116(2-3):359-70. Sexual isolation and speciation in bacteria. Cohan FM.
“[Bacterial] interspecies recombination is reduced by a variety of factors, including ecological isolation, behavioral isolation, obstacles to DNA entry, restriction endonuclease activity, resistance to integration of divergent DNA sequences, reversal of recombination by mismatch repair, and functional incompatibility of recombined segments.”
Genetica. 2002 Nov;116(2-3):291-300. Divergence and reproductive isolation in the early stages of speciation. Tregenza T.
“To understand speciation we need to identify the factors causing divergence between natural populations. The traditional approach to gaining such insights has been to focus on a particular theory and ask whether observed patterns of reproductive isolation between populations or species are consistent with the hypothesis in question. However, such studies are few and they do not allow us to compare between hypotheses, so often we cannot determine the relative contribution to divergence of different potential factors.” “There are only weak correlations between patterns of genetic divergence and phenotypic divergence and no correlation between premating and postmating isolation.” “I discuss the advantages and disadvantages of the general approach of simultaneously testing competing hypotheses…”
Genetica. 2002 Nov;116(2-3):205-14. Sexual signaling and speciation, a microevolutionary perspective. Boake CR.
“Despite the growing evidence that sexual selection can drive speciation, the evolution of sexual signals in natural populations is far from being well-understood.” “…it is less clear how multimodal signals evolve…” “”
Genetica. 2002 Nov;116(2-3):151-66. Divergence in mate choice systems: does evolution play by rules? Etges WJ.
[The author suggests the "genetic analysis of single phenotypes"]
Syst Biol. 2003 Feb;52(1):89-109. Molecular systematics and adaptive radiation of Hawaii's endemic Damselfly genus Megalagrion (Odonata: Coenagrionidae). Jordan S, Simon C, Polhemus D.
“Past phylogenetic analysis based on morphological characters has been problematic.” “Problems with distant outgroups were accommodated…” “Areas of disagreement are mainly confined to clades that are strongly supported by the mitochondrial DNA and weakly supported by the elongation factor 1alpha data because of lack of changes.” “Correlation between Bayesian posterior probabilities and bootstrap percentages decreased in concert with decreasing information in the data partitions.” “”
Mol Ecol. 2003 Feb;12(2):299-313. History and evolution of the arctic flora: in the footsteps of Eric Hulten. Abbott RJ, Brochmann C.
“Most molecular evidence fails to support his [Eric Hulten in his landmark book Outline of the History of Arctic and Boreal Biota during the Quarternary Period, published in 1937] proposal that contemporary east and west Atlantic populations of circumarctic and amphi-Atlantic species have been separated throughout the Quaternary. In fact, populations of these species from opposite sides of the Atlantic are normally genetically very similar, thus the North Atlantic does not appear to have been a strong barrier to their dispersal during the Quaternary…” “…for the intriguing taxonomic complexity of the arctic flora…” “Despite the progress made since Hulten wrote his book, there remain large gaps in our knowledge of the history of the arctic flora…” “Comprehensive analyses of the molecular phylogeography of arctic taxa and their relatives together with detailed fossil studies are required to fill these gaps.”
Genome Res. 2003 Jan;13(1):13-26. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Hardison et al.
“Regional variation in all processes is correlated with, but not completely accounted for, by GC content in human and the difference between GC content in human and mouse.”
Science. 2003 Jan 3;299(5603):107-9. Genetic evidence for local retention of pelagic larvae in a Caribbean reef fish. Taylor MS, Hellberg ME. [Erratum in: Science. 2003 Jun 27;300(5628):2033-4. Comment in: Science. 2003 Jan 3;299(5603):51-2. Science. 2003 Jun 13;300(5626):1657-9; author reply 1657-9.]
“The pelagic larvae of many marine organisms can potentially disperse across hundreds of kilometers, but whether oceanographic or behavioral mechanisms can constrain dispersal over periods sufficient for the evolution of genetic differentiation remains unclear.” “These results suggest that marine populations can remain demographically closed for thousands of generations despite extended larval duration…”
Evolution Int J Org Evolution. 2002 Nov;56(11):2103-11. Speciation despite gene flow when developmental pathways evolve. Porter AH, Johnson NA.
“Evolutionary biologists assume that species formation requires a drastic reduction in gene exchange between populations, but the rate sufficient to prevent speciation is unknown” “…in developmental pathway models with more than two loci, gene flow is more able to impede speciation.” “Development therefore… constrains the microevolutionary process…”
Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16835-40. Allopolyploidization and evolution of species with reduced floral structures in Lepidium L. (Brassicaceae). Lee JY, Mummenhoff K, Bowman JL.
“Previous phylogenetic studies using noncoding regions of chloroplast DNA and rDNA internal transcribed spacer were incongruent in most New World species relationships” “…did not provide enough information to infer the evolutionary pattern of flower structures.”
Mol Phylogenet Evol. 2003 Jan;26(1):46-55. A molecular phylogeny of the neotropical butterfly genus Anartia (Lepidoptera: Nymphalidae). Blum MJ, Bermingham E, Dasmahapatra K.
“Both the mitochondrial and nuclear gene phylogenies demonstrate that Anartia jatrophae is not sister to all other Anartia species” “Traditional biogeographic explanations for speciation across the genus relied on A. jatrophae being sister to its congeners” “…species range boundaries.”
J Theor Biol. 2003 Feb 7;220(3):323-43. Evolution was chemically constrained. Williams RJ, Frausto Da Silva JJ.
“The relationship to the manner in which particular species (gene sequences) were coincidentally changed, the molecular view of evolution, is left for additional examination.”
Curr Top Microbiol Immunol. 2002;270:1-21. Evolution of the TIR, tolls and TLRs: functional inferences from computational biology. Beutler B, Rehli M.
“The patterns of TLR expression are quite variable at the level of tissues, even among closely related species.” “In this review, we discuss the computational methods used to analyze divergence of the TIR…”
Evolution Int J Org Evolution. 2002 Oct;56(10):2083-9. The evolution of F1 postzygotic incompatibilities in birds. Price TD, Bouvier MM.
“Among our sample more than half the crosses between species in the same genus produce fertile hybrids” “…in contrast to Drosophila, fertility of the homogametic sex in the F1 appears to be lost before viability of the heterogametic sex in the F1.”
Cytogenet Genome Res. 2002;96(1-4):261-75. Patterns of karyotype evolution in complexes of sibling species within three genera of African murid rodents inferred from the comparison of cytogenetic and molecular data. Volobouev VT, Aniskin VM, Lecompte E, Ducroz JF.
“This observation suggests that karyotypic orthoselection documented in numerous groups is not so much a reflection of selection of a definite type of chromosomal mutation, as suggested by the classical concept, but is due to genome structure of a given species” “…the low sequence divergences distinguishing karyotypically distinct sibling species within Arvicanthis and Mastomys emphasizes the power of combining cytogenetic and molecular approaches for the characterization of unrecognized components of biodiversity.”
Cytogenet Genome Res. 2002;96(1-4):33-9. X-Autosome translocations, meiotic synapsis, chromosome evolution and speciation. Ashley T.
“Several theories have been proposed to explain the often-noted sterility of both reciprocal and Robertsonian X-autosome translocations in male mammals. However, there are a number of species in which all members of the species carry a Robertsonian X-autosome translocation.”
Parasitology. 2002;124 Suppl:S3-22. Revealing the faunal tapestry: co-evolution and historical biogeography of hosts and parasites in marine systems. Hoberg EP, Klassen GJ.
“Parasites… represent elegant tools to explore the origins, distribution and maintenance of biodiversity. Among these diverse assemblages, host and geographic ranges described by various helminths are structured and historically constrained by genealogical and ecological associations that can be revealed and evaluated using phylogenetic methodologies within the context of frameworks and hypotheses…” “Despite over 200 years of sporadic investigations of helminth systematics, knowledge of parasite faunal diversity in chondrichthyan and osteichthyan fishes, seabirds and marine mammals remains to be distilled into a coherent and comprehensive picture…”
Evolution Int J Org Evolution. 2002 Sep;56(9):1859-62. The evolution of reproductive isolation in spatially structured populations. Church SA, Taylor DR.
“These results counter the widespread notion that speciation is most likely to occur in allopatric populations and suggest that there are useful insights to be gained by incorporating increasingly realistic types of population structure into models of speciation.”
Mol Phylogenet Evol. 2002 Oct;25(1):125-137. Molecular phylogeny and historical biogeography of the Aphanius (Pisces, Cyprinodontiformes) species complex of central Anatolia, Turkey. Hrbek et al.
“Phylogenetic relationships among the six clades are only weakly supported, however, and differ among analytical methods. We therefore test and subsequently reject the hypothesis of simultaneous diversification among the six central Anatolian clades.” “Therefore, although bifurcating branching order is hypothesized to underlie this radiation, the exact branching order is difficult to estimate with confidence.”
Mol Phylogenet Evol. 2002 Oct;25(1):1-9. Evolution in Hawaiian cave-adapted isopods (Oniscidea: Philosciidae): vicariant speciation or adaptive shifts? Rivera MA, Howarth FG, Taiti S, Roderick GK.
“…The geographic and phylogenetic patterns are not sufficient to support a vicariant mode of speciation” “…it suggests that simple vicariance is insufficient to explain the evolution of troglobites in tropical zones.”
Genetika. 2002 Aug;38(8):1063-77. [Variation of the mitochondrial genome in the evolution of Drosophila] [Article in Russian] Mitrofanov VG, Sorokina SIu, Andrianov BV.
“In some species, mtDNA variation may serve as a reliable marker for population differentiation within a species, although evidence on the population dynamics of the mtDNA variation is very scarce.”
Trends Genet. 2004 Apr;20(4):182-7.
Zhaxybayeva O, Peter Gogarten J.
Cladogenesis, coalescence and the evolution of the three domains of life.
"Simulations of genes and organismal lineages suggest that there was no single common ancestor that contained all the genes ancestral to those shared among the three domains of life." "Each contemporary molecule has its own history... likely to be present in different organisms and at different times."
J Exp Zoolog Part B Mol Dev Evol. 2004 Jan 15;302(1):69-91.
Evo-devo aspects of classical and molecular data in a historical perspective.
Sander K, Schmidt-Ott U.
"Darwin and his "continental apostle" Haeckel put the striking similarity between early vertebrate embryos in an evolutionary context. Haeckel's partly illicit generalizations discredited evolutionary thinking among early experimental embryologists who moreover noted riddles incompatible..."
Evolution Int J Org Evolution. 2003 Nov;57(11):2557-65.
Divergent environments and population bottlenecks fail to generate premating isolation in Drosophila pseudoobscura.
Rundle HD.
"I conducted a laboratory speciation experiment using Drosophila pseudoobscura involving 78 replicate populations assigned in a two-way factorial design to both bottleneck (present vs. absent) and environment (ancestral vs. novel) treatments... . Bottlenecks alone did not generate any premating isolation, despite an experimental design that was conducive to bottleneck-induced speciation...
Reduced mating success of derived males will hamper speciation by enhancing the mating success of immigrant, ancestral males. Novel environments are generally thought to promote ecological speciation by generating divergent natural selection. In the current experiment, however, the novel environment did not cause the evolution of any premating isolation and it reduced the likelihood of speciation through its effects on male mating success."
Curr Opin Genet Dev. 2003 Dec;13(6):588-92.
Evolution and diversity of fish genomes.
Venkatesh B.
"Fish genomes seem to be 'plastic' in comparison with other vertebrate genomes..."
J Evol Biol. 2003 Mar;16(2):200-7.
Testing the link between the latitudinal gradient in species richness and rates of molecular evolution.
Bromham L, Cardillo M.
"We find no support for an effect of latitude on rate of molecular evolution. This result casts doubt on the generality of a key component of Rohde's hypothesis linking climate and speciation."
Mol Phylogenet Evol. 2003 Dec;29(3):507-18.
Genes that determine flower color: the role of regulatory changes in the evolution of phenotypic adaptations.
Durbin ML, Lundy KE, Morrell PL, Torres-Martinez CL, Clegg MT.
"The molecular bases for these adaptive shifts can be dissected because the biosynthetic pathways that determine floral pigmentation are well understood and many of the genes of flavonoid biosynthesis have been isolated and extensively studied. We present a comparative analysis of the level of gene expression in Ipomoea for several key genes in flavonoid biosynthesis. Specifically we ask: how frequently are adaptive shifts in flower color phenotypes associated with changes in regulation of gene expression versus mutations in structural genes? The results of this study show that most species differences in this crucial phenotype are associated with changes in the regulation of gene expression."
Syst Biol. 2003 Oct;52(5):618-40.
Phylogenetic relationships among calyptraeid gastropods and their implications for the biogeography of marine speciation.
Collin R.
"Closely related species can, however, occur in such divergent regions as Southern California and South Africa."
Parasitol Res. 2003 Nov;91(5):398-406. Epub 2003 Sep 18.
Phylogeny of sheep and goat Theileria and Babesia parasites.
Schnittger L, Yin H, Gubbels MJ, Beyer D, Niemann S, Jongejan F, Ahmed JS.
"The recently reported pathogenic sheep/goat Theileria sp. 1 (China) seems to be identical with a Theileria sp. isolated from Japanese serow. Furthermore, our results suggest that T. ovis represents a single species."
Genetics. 2003 Aug;164(4):1645-56.
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.
Rannala B, Yang Z.
"Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models."
J Mol Evol. 2003;57 Suppl 1:S277-85.
Molecular clock and gene function.
Saccone C, Caggese C, D'Erchia AM, Lanave C, Oliva M, Pesole G.
"The porin gene redundancy found in invertebrates and possibly in some fishes may indicate a tendency to duplicate the genetic material, rather than a real need for function innovation."
Trends Genet. 2004 Feb;20(2):80-6.
Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision.
Graur D, Martin W.
"Because the appearance of accuracy has an irresistible allure, non-specialists frequently treat these estimates as factual. In this article, we show that all of these divergence-time estimates were generated through improper methodology on the basis of a single calibration point that has been unjustly denuded of error. The illusion of precision was achieved mainly through the conversion of statistical estimates (which by definition possess standard errors, ranges and confidence intervals) into errorless numbers. By employing such techniques successively, the time estimates of even the most ancient divergence events were made to look deceptively precise."
Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2507-11. The Tre2 (USP6) oncogene is a hominoid-specific gene. Paulding CA, Ruvolo M, Haber DA.
“TBC1D3 is derived from a recent segmental duplication, which is absent in most other mammals… [but present] through the primate lineage” “Remarkably, the chimeric gene Tre2 exists only in the hominoid lineage of primates. This hominoid-specific oncogene…” “In contrast to the broad expression pattern of USP32 and TBC1D3, expression of Tre2 is testis-specific, a pattern proposed for novel genes implicated in the emergence of reproductive barriers...” “Sudden emergence of chimeric proteins, such as that encoded by Tre2”
Genetica. 2003 Jul;118(2-3):193-208.
Nahon JL.
"The heretical concept of 'human-specific' genes has recently received some supporting data."
More references to come...
IP: Logged
|
|
gordon
Member
Member # 781
|
posted 08. April 2004 11:32
Is there a point in posting these carefully selected quotes?
IP: Logged
|
|
Fernando Castro-Chavez
Member
Member # 1201
|
posted 09. April 2004 01:10
Putting Limits on the Diversity of Life. Part Four. Continued...
We need to remember that this is a Reference source for ID Researchers. There are other sites that explore evolution assuming that evolution is a reality, those sites are best suited for anyone offended by the References presented here.
The search strategy used to post these references is that I went to Pubmed and I searched only for two words: 'speciation' and 'evolution', putting limits in Title and Abstract. More than 700 references appeared. If we search in Full Text, as the last contributed reference demonstrates, much more references will appear.
As I can not read all of them at once; I am reading and then posting them, quoting significant aspects of their Abstracts that impacted me, aspects being in a need, either to be corrected, or discarded, or analyzed more carefully. Isn't that one preliminary way to integrate Reference Records for our research papers? At least I was told in class to do so. Who quotes a full abstract in his own articles? The full References are there for anyone wanting to see the full abstract or article:
Am J Hum Genet. 2002 Oct;71(4):695-714. Neocentromeres: role in human disease, evolution, and centromere study. Amor DJ, Choo KH.
"Current evidence from human and fly studies indicates that neocentromere activity is acquired epigenetically rather than by any alteration to the DNA sequence."
Genetics. 2002 Aug;161(4):1517-26. Hybrid sterility, Haldane's rule and speciation in Heliconius cydno and H. melpomene. Naisbit RE, Jiggins CD, Linares M, Salazar C, Mallet J.
"Most genetic studies of Haldane's rule, in which hybrid sterility or inviability affects the heterogametic sex preferentially, have focused on Drosophila. It therefore remains unclear to what extent the conclusions of that work apply more generally, particularly in female-heterogametic taxa such as birds and Lepidoptera." "Sterility may result from the production of normal but infertile eggs, production of small infertile eggs, or from a complete failure to develop ovarioles…" "The two species are broadly sympatric and hybridize in the wild, so that female hybrid sterility forms one of several strong but incomplete barriers to gene flow in nature. The effect of female sterility is comparable to that of selection against non-mimetic hybrids, while mate choice forms a much stronger barrier to gene transfer."
Dev Genes Evol. 2002 Aug;212(7):307-18. The evolution of engrailed genes after duplication and speciation events. Gibert JM.
"Members of the engrailed class encode transcription factors involved in major steps of metazoan development. Few developmental regulatory genes have been studied in such a wide range of animals. Furthermore duplications of an ancestral engrailed gene independently generated multiple engrailed paralogues in several organisms." "However, in all engrailed duplications studied, even in ancient chromosomal duplications, the paralogues have kept redundant functions. In fact, selection seems to maintain a certain redundancy between engrailed paralogues."
Toxicon. 2002 Jun;40(6):803-13. Characterization, primary structure and molecular evolution of anticoagulant protein from Agkistrodon actus venom. Tani et al.
"The ratios of the numbers of nucleotide substitutions per nonsynonymous site (K(A)) and per synonymous site (K(S)) in the mature protein-coding region in the cDNA pairs were about three times greater than those for the ordinary isoprotein genes…"
J Mol Evol. 2002 Jul;55(1):92-103. SRY evolution in Cebidae (Platyrrhini: Primates). Moreira MA.
"Estimates of the number of synonymous and nonsynonymous substitutions indicated the absence of positive selection acting on SRY…" "Available data on the fertility of natural and captive interspecific hybrids failed to show any relationship between SRY evolution and speciation for the genera herein studied."
Contributed Reference:
PNAS, Vol. 96, Issue 19, 10752-10757, September 14, 1999. The molecular clock of HIV-1 unveiled through analysis of a known transmission history, Thomas Leitner and Jan Albert.
From the Full Text:
"...in the original molecular clock hypothesis, proposed by Zuckerkandl and Pauling, the observed rates of evolution were suggested to be approximately described by a simple Poisson process." "Thus, this model predicts that the variance in the number of substitutions should be equal to the mean. However, many authors have reported the evolutionary rates of other organisms than HIV to be more dispersed than predicted by a Poisson process (overdispersion) (30-32), i.e., there is more variation in branch lengths in a tree than expected from a Poisson process. Several potential explanations for overdispersion have been proposed. It has been suggested that overdispersion may exist because mutant sites do not evolve independently (32). Another hypothesis invokes a generation-time effect, i.e., that the number of mutational errors will increase with increasing number of replication cycles." "However... must be investigated further."
More to come, depending on time...
IP: Logged
|
|
gordon
Member
Member # 781
|
posted 09. April 2004 09:04
"We need to remember that this is a Reference source for ID Researchers."
To what end? What do these citations hold for the ID researchers out there?
If I may say so, it looks more and more like the beginnings of an addendum to the 'creationist quote book'.
You seem to be focusing on titles that deal with the concept of the molecular clock - is there a reason fro that?
I am especially interested in the quote you used from the Graur and Martin paper - why not this one:
"For almost a decade now, a team of molecular evolutionists has produced a plethora of seemingly precise molecular clock estimates for divergence events ranging from the speciation of cats and dogs to lineage separations that might have occurred approximately 4 billion years ago."
Have you read that paper?
If you have, you should know that it is a condemnation of a particular group of researchers, not the concept and methodology as a whole.
I suggest you cut down on quantity and focus more on quality.
Keyowrd searches are typically not the best way to amass relevant material.
IP: Logged
|
|
Fernando Castro-Chavez
Member
Member # 1201
|
posted 10. April 2004 18:25
Putting Limits on the Diversity of Life.
(Part Four. Continued... 2)
As ID researchers, we need to make evident, using the published material, the weakness behind the concept of 'speciation', used over and over as the strongest evidence for 'evolution'.
Molecular clock was not my search strategy used this time. Articles dealing with that topic appear as a side product of the words 'speciation-evolution' or as contributed articles. The reason of why I don't use full quotations here is because the source is given for everybody to see the originals if desired. PubMed: http://www.ncbi.nlm.nih.gov/entrez
Adv Mar Biol. 2002;43:1-86. Ecology and biogeography of marine parasites. Rohde K.
"Even rough estimates of the richness of most parasite groups in the oceans are premature for the following reasons: species numbers of host groups, in particular in the deep sea and the meiofauna, are not known; most host groups have been examined only insufficiently for parasites or not at all; even in some of the best known groups, latitudinal, longitudinal and depth
gradients in species richness are only poorly understood or not known at all; effects of hosts on parasite morphology and geographical variation have been studied only in a few cases; there are few studies using techniques of molecular biology to distinguish sibling species" "…most parasitic species are concentrated in a few taxa." "Few studies on metapopulations of marine parasites have been made. A new approach, that of fuzzy chaos modelling, is discussed." "The practical importance of marine parasites in mariculture, as monitors of pollution… are also discussed."
Mol Ecol. 2002 Aug;11(8):1377-92. Historical biogeography and molecular systematics of the
Indo-Pacific genus Dascyllus (Teleostei: Pomacentridae). McCafferty et al.
"Our data rejected a model based on body size but not one based on phylogenetic inertia." "…this study highlights the importance of adequate geographical sampling…"
Syst Biol. 2000 Mar;49(1):65-86. The quality of the fossil record and the accuracy of phylogenetic
inferences about sampling and diversity. Wagner PJ.
"Because phylogenies can be estimated without stratigraphic data and because estimated phylogenies also infer gaps in sampling, some workers have used phylogeny estimates as templates for evaluating sampling from the fossil record and for "correcting" historical diversity patterns. However, it is not known how sampling intensity (the probability of sampling taxa per unit time) and completeness (the proportion of taxa sampled) affect the accuracy of phylogenetic inferences, nor how phylogenetically inferred estimates of sampling and diversity respond to inaccurate estimates of phylogeny." "Parsimony estimates of simulated phylogenies become less accurate as sampling decreases, and inaccurate trees chronically underestimate sampling. Biotic factors such as rates of morphologic change and extinction both affect the accuracy of phylogenetic estimates and thus affect estimated gaps in sampling, indicating that differences in implied sampling need not reflect actual differences in sampling. Errors in inferred diversity are concentrated early in the history of a clade. This, coupled with failure to account for true extinction times (i.e., the Signor-Lipps effect), inflates relative diversity levels early in clade histories. Because factors other than differences in sampling predict differences in the numbers of gaps implied by phylogeny estimates, inferred phylogenies can be misleading templates for evaluating sampling or historical diversity patterns."
Genetics. 2002 Jul;161(3):1187-96. Codon bias differentiates between the duplicated amylase loci following gene duplication in Drosophila. Zhang et al.
"…the difference in the GC content at third synonymous sites between the duplicated genes is not due to the temporal or regional changes in mutation bias."
Syst Biol. 2000 Mar;49(1):114-29. Mitochondrial phylogeny of notothenioids: a molecular approach to Antarctic fish evolution and biogeography. Bargelloni et al.
"Phylogenetic trees, reconstructed on the basis of sequence data by different methods, indicate that traditional hypotheses on notothenioid systematics and biogeography might be in need of reexamination." "Likewise, multiple, independent transitions from benthic to pelagic habit are inferred from molecular data, at variance with the more conservative hypothesis based on cladograms reconstructed from morphological data."
Syst Biol. 2000 Sep;49(3):463-79. Age rank/clade rank metrics--sampling, taxonomy, and the meaning of "stratigraphic consistency". Wagner PJ, Sidor CA.
"Paleontologists frequently contrast clade rank (i.e., nodal or patristic distance from the base of a
cladogram) with age rank (i.e., relative first known appearances of the analyzed taxa) to measure the degree of congruence between the estimated phylogeny and the fossil record. Although some potential biases of these methods have been examined (e.g., the effect of tree imbalance), other properties of age rank/clade rank (ARCR) comparisons have not been studied in detail." "These results suggest several plausible explanations for patterned differences in ARCR metrics among clades, thereby compromising their validity as measures of the quality of the fossil record."
Syst Biol. 2000 Sep;49(3):422-34. Testing hybridization hypotheses based on incongruent gene
trees. Sang T, Zhong Y.
"Hybridization is an important evolutionary mechanism in plants and has been increasingly documented in animals. Difficulty in reconstruction of reticulate evolution, however, has been a long-standing problem in phylogenetics. Consequently, hybrid speciation may play a major role in causing topological incongruence between gene trees." "Here we characterized certain distinctions between hybridization and other biological processes, including lineage sorting,
paralogy, and lateral gene transfer, that are responsible for topological incongruence between gene trees." "…the model could not test hypotheses of hybridization versus lateral gene transfer as the cause of incongruence..."
---------------
If we only use the word 'speciation', we find many articles dealing with radioactive elements and other metals (by the way, further evidence that also every non-molecular 'dating' system (concept and methodology) is only based in 'fortunate guesses'):
J Environ Radioact. 2002;62(3):263-76. Modelling the physico-chemical speciation of plutonium in the eastern Irish Sea: a further development. Perianez R.
"In the earlier version of the model, a one-step kinetic model was used to describe the transfers of radionuclides between the dissolved and solid phases. Although with this kind of model the contamination of the sediments can be properly simulated, it is clearly not able to describe the re-dissolution of radionuclides from a contaminated sediment once the external source to the sea is reduced. Thus, the model has been improved by substituting the one-step model with a two-step kinetic model consisting of two consecutive reversible reactions."
To be continued…
IP: Logged
|
|
|
Printer-friendly view of this topic