Posted by: Dan | November 11, 2009

10,000 Genomes

This is an example of big science which could drive discoveries regarding evolution and more for years to come. A consortium of researchers are proposing in the Journal of Heredity to sequence the genomes of 10,000 vertebrate species! This would of course be a huge expansion from the already-sequenced 32 mammals and 24 nonmammalian vertebrate genomes.

While the Introduction and the Proposal itself are quite interesting, I thought that the Discussion really bears sharing and discussion with a wider audience. So I hope that no one objects to me re-printing it here where interested parties can comment on it…


DISCUSSION

Careful observations of the morphological and functional adaptations in vertebrates have formed the basis of biological studies for a millennium, but it is only recently that we have been able to observe the action of evolution directly at the genetic level. It is not known whether convergent adaptations in independent lineages are often governed by analogous changes in a small number of orthologous genome loci or if macroevolutionary events in separate lineages usually result from entirely idiosyncratic combinations of mutations. The evidence from several recent studies points toward the former hypothesis (Eizirik et al. 2003; Nachman et al. 2003). For example, adaptive hind-limb reduction occurred independently many times in different lineages and even within the same species, just as sticklebacks in different lakes adapted from an oceanic to a freshwater environment (Shapiro et al. 2006). These stickleback adaptations are all traced to independent deletions of the same distal enhancer of the PITX2 development gene, demonstrating remarkable convergent evolution at the genomic level (Kingsley D, HHMI, personal communication). By cataloging the footprints of adaptive evolution in every genomic locus on every vertebrate lineage, the G10K project will provide the power to thoroughly test the “same adaptation, same loci” hypothesis, along with other fundamental questions about molecular adaptive mechanisms.

In the course of this investigation, we will discover the genetic loci governing fundamental vertebrate processes. The study of the evolution of viviparity is an outstanding example. Birds, crocodiles, and turtles all lay eggs, whereas apart from monotremes, mammals are all live bearers. Thus, there was one fundamental transition from oviparity to viviparity in these amniotes, which caused a fundamental reorganization in the developmental program and large-scale change in gene interactions that we are only just beginning to understand. Remarkably, however, nonavian reptiles have over 100 independent evolutionary origins of viviparity (Blackburn 2000). Fish have an equally spectacular variety of such transitions, along with some amphibians, such as the frog genus Gastrotheca, which includes species with placental-like structures (Duellman and Trueb 1986). These many independent instances of the evolution of viviparity afford an extraordinary opportunity to explore the genomics behind this reproductive strategy.

The architecture of sex determination in vertebrates is similarly diverse, with examples of XY, ZW, and temperature-dependent mechanisms. The G10K project thus provides an equally exciting opportunity for dissection of this diversity. In fact, a few vertebrate species have abandoned sex altogether. What happens when an asexual genome descends from an ancestral sexual genome, as has occurred repeatedly in Aspidoscelis lizard lineages? Are the independent parthenogenetic genomes parallel in any way? In one group of lizards, genus Darevskia, the formation of unisexual species is phylogenetically constrained (Murphy et al. 2000), yet in others, for example, Aspidoscelis, it is not. Many species of lizards and snakes are also known to have facultative parthenogenesis: Unmated females produce viable eggs and offspring. Unisexuality also occurs in amphibians and fishes by gynogenesis, hybridogenesis, and in amphibians by kleptogenesis (Bogart et al. 2007). Sequential hermaphrodite fishes can change their sex. Do these parallel convergent changes involve the same genes? The evolution of longevity remains another question of great interest. What mechanisms are responsible for the 2 orders of magnitude differences among vertebrates and what sets the limits for long-lived species found in each of the vertebrate clades? By identifying genomic loci that support different evolutionary innovations such as these, the data from the G10K project will drive fundamental progress in molecular and developmental biology.

The symphony of vertebrate species that cohabit on our planet attests to underlying life processes with remarkable potential. Genomics reveals a unity behind these life processes that is unrivaled by any other avenue of investigation, exposing the undeniable relatedness and common origin of all species. By revealing genetic vulnerabilities in endangered species and tracking host–pathogen coevolution, genomics also plays an increasing role in sustaining biodiversity and combating emerging infectious diseases. Thus, the information in the genomes of threatened and endangered species revealed by the G10K project will be crucial to conservation efforts (Ryder et al. 2000; O’Brien 2003; Ryder 2005; Kohn et al. 2006; Schwartz et al. 2009). In studying the genomes of recently extinct species as well, molecular aspects of species’ vulnerability can be revealed and vital gaps in the vertebrate record restored. In all these ways, the G10K project will engage the public in the quest for the scientific basis of animal diversity and in the application of the knowledge we gain to halt extinctions and improve animal health.

As the printing of the first book by Johannes Gutenberg altered the course of human history, so did the human genome project forever change the course of the life sciences with the publication of the first full vertebrate genome sequence. When Gutenberg’s success was followed by the publication of other books, libraries naturally emerged to hold the fruits of this new technology for the benefit of all who sought to imbibe the vast knowledge made available by the new print medium. We must now follow the human genome project with a library of vertebrate genome sequences, a genomic ark for thriving and threatened species alike, and a permanent digital record of countless molecular triumphs and stumbles across some 600 million years of evolutionary episodes that forged the “endless forms most beautiful” that make up our living world.


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