posted 16. May 2004 17:00                   

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ABSTRACT
The origin of organismal complexity is generally thought to be tightly coupled to the evolution of new gene functions arising subsequent to gene duplication. Under the classical model for the evolution of duplicate genes, one member of the duplicated pair usually degenerates within a few million years by accumulating deleterious mutations, while the other duplicate retains the original function. This model further predicts that on rare occasions, one duplicate may acquire a new adaptive function, resulting in the preservation of both members of the pair, one with the new function and the other retaining the old.
However, empirical data suggest that a much greater proportion of gene duplicates is preserved than predicted by the classical model. Here we present a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum. Focusing on the regulatory complexity of eukaryotic genes, we show how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions. The duplication-degeneration-complementation (DDC) model predicts that (1) degenerative mutations in regulatory elements can increase rather than reduce the probability of duplicate gene preservtion and (2) the usual mechanism of duplicate gene preservation is the partitioning of ancestral functions rather than the evolution of new functions. We present several examples (including analysis of a new engrailed gene in zebrafish) that appear to be consistent with the DDC model, and we suggest several analytical and experimental approaches for determining whether the complementary loss of gene subfunctions or the acquisition of novel functions are likely to be the primary mechanisms for the preservation of gene duplicates.

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My current work is an attempt to model the evolution of new protein functions through gene duplication. Gene duplication is purported to be a major pathway for the Darwinian evolution of biochemical novelty. However, as in other areas, Darwinists have not closely examined whether gene duplication can realistically do all that they ascribe to it. I hope to help them out in this area by asking those questions.

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The hitch, as always, is that Darwinists virtually never explain in any detail how natural selection would actually get from protein A to protein B after the gene for protein A duplicated. After all, gene duplication just leaves you with a second copy of the same gene --- nothing different. The problem is, as everyone agrees, that the duplicated gene is much more likely to suffer a deleterious mutation than a beneficial one. Nonetheless, Darwinists hope that the occasional beneficial mutation just might come along. However, they never look very deeply into the matter.
It turns out that to acquire some new functions, such as the capacity to bind a new molecule, multiple mutations would be expected to be needed, not just a single mutation. The requirement for multiple mutations would quickly render gene duplication an untenable explanation, since a duplicated gene would be riddled with deleterious mutations before acquiring several positive ones.

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Koszul, R., Caburet, S., Dujon, B., Fischer, G. (2004). Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J. 23: 234-243

Pielberg, G., Day, A. E., Plastow, G. S., Andersson, L. (2003). A Sensitive Method for Detecting Variation in Copy Numbers of Duplicated Genes. Genome Res. 13: 2171-2177

Panopoulou, G., Hennig, S., Groth, D., Krause, A., Poustka, A. J., Herwig, R., Vingron, M., Lehrach, H. (2003). New Evidence for Genome-Wide Duplications at the Origin of Vertebrates Using an Amphioxus Gene Set and Completed Animal Genomes. Genome Res. 13: 1056-1066

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Co-option occurs when natural selection finds new uses for existing traits, including genes, organs, and other body structures. Genes can be co-opted to generate developmental and physiological novelties by changing their patterns of regulation, by changing the functions of the proteins they encode, or both. This often involves gene duplication followed by specialization of the resulting paralogous genes into particular functions. A major role for gene co-option in the evolution of development has long been assumed, and many recent comparative developmental and genomic studies have lent support to this idea. Although there is relatively less known about the molecular basis of co-option events involving developmental pathways, much can be drawn from well-studied examples of the co-option of structural proteins. Here, we summarize several case studies of both structural gene and developmental genetic circuit co-option and discuss how co-option may underlie major episodes of adaptive change in multicellular organisms. We also examine the phenomenon of intraspecific variability in gene expression patterns, which we propose to be one form of material for the co-option process. We integrate this information with recent models of gene family evolution to provide a framework for understanding the origin of co-optive evolution and the mechanisms by which natural selection promotes evolutionary novelty by inventing new uses for the genetic toolkit

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For example, it is becoming clear that co-option has played a critical role in evolution and the homeotic genes are not exempt in this regard. To demonstrate this point we can point to the expression pattern of the homeotic gene Ubx in various arthropod groups and the most basic morphology of the segments within its expression domains.

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Like Dembski, Johnson is very fond of information theory. He is quite emphatic that natural selection acting on chance variations can not significantly increase the information content of the genome. Johnson offers a crude caricature of the arguments made in Dawkins’ article (41), but offers no explanation of why gene duplication with subsequent divergence can not account for the growth in genetic information. The closest he comes to addressing the subject is the following quote, in which he recounts a discussion with mathematical physicist Paul Davies:

“When I asked Davies about this, his reply gave me the impression that he thinks that natural selection increases genetic information by preserving copies that are made in the reproductive process. I am afraid this misses the point. When two rabbits reproduce there are more rabbits, but there is not any increase in information in the relevant sense. If you need to write out the full text of the encyclopedia and have only page one, you cannot make progress toward your goal by copying page one twenty times.” (59)



In reply I will simply quote John Maynard Smith and Eors Szathmary, from their book The Major Transitions in Evolution. The mere duplication of a gene adds no new information, but the divergence of the two copies does so.”

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