In the most comprehensive study of animal evolution ever attempted, an international consortium of scientists plans to assemble a genomic zoo--a collection of DNA sequences for 10,000 vertebrate species, approximately one for every vertebrate genus.
Known as the Genome 10K Project, it involves gathering specimens of thousands of animals from zoos, museums, and university collections throughout the world, and then sequencing the genome of each species to reveal its complete genetic heritage.
Launched in April 2009 at a three-day meeting at the University of California, Santa Cruz, the project now involves more than 68 scientists. Calling themselves the Genome 10K Community of Scientists, the group outlined its proposal to create a collection of tissue and DNA specimens for the project in a paper published online November 5 in the Journal of Heredity.
The project was conceived by the paper's three lead authors: David Haussler, professor of biomolecular engineering at UC Santa Cruz and a Howard Hughes Medical Institute investigator; Stephen J. O'Brien, chief of the Laboratory of Genomic Diversity at the National Cancer Institute; and Oliver A. Ryder, director of genetics at the San Diego Zoo's Institute for Conservation Research and adjunct professor of biology at UC San Diego.
"For the first time, we have a chance to really see evolution in action, caught in the act of changing whole genomes," Haussler said. "This is possible because the technology to sequence DNA is thousands of times more powerful now than it was just a decade ago, and is poised to get even more powerful very soon."
Among the authors is pioneering geneticist Sydney Brenner, a Nobel Laureate and senior distinguished fellow at the Salk Institute. "The most challenging intellectual problem in biology for this century will be the reconstruction of our biological past so we can understand how complex organisms such as ourselves evolved," Brenner said. "Genomes contain information from the past--they are molecular fossils--and having sequences from vertebrates will be an essential source of rich information."
At the UCSC meeting, 55 leading scientists representing major zoos, museums, research centers, and universities around the world hashed out the challenging logistics involved in carrying out this ambitious project. Participants included UCSC biologists Giacomo Bernardi, James Estes, Barry Sinervo, and Terrie Williams.
The scientists have identified specimens that span a broad range of evolutionary diversity. The species include living mammals, birds, reptiles, amphibians, and fishes, many of which are threatened or endangered, as well as some recently extinct species, O'Brien said.
"We are capturing what evolution left us with before the human population started impacting species--a set of genomes inclusive of the biota that a magnificent evolutionary process has produced," he said.
According to Ryder, genome sequences will be particularly valuable in efforts to assess genetic diversity in endangered populations. "Any tool used so far for evaluating genetic diversity and genetic variation is overshadowed by the resolving power of genomic information," he said.
The collection will include more than a thousand frozen samples of fibroblast cells derived from 602 different vertebrate species. These cell samples, maintained by the San Diego Zoo, the National Cancer Institute, and the world's cell repositories, are a valuable resource for genetic studies, Ryder said.
Because the evolution of species living today involved ancient genetic changes still preserved in their DNA, the Genome 10K project can help uncover answers to longstanding questions about the history of evolution. Having full genomes at hand will enable detailed studies of evolutionary changes throughout the genome.
"Differences in the DNA that makes up the genomes of the animals we find today hold the key to the great biological events of the past, such as the development of the four-chambered heart and the magnificent architecture of wings, fins, and arms, each adapted to its special purpose," Haussler said.
But now the most challenging parts of the project begin, O'Brien said. "The first challenge is to bring this whole promise into reality by actually getting samples, characterizing them, doing quality control on them, and delivering them to sequencing centers that can accomplish the goal," he said. "The second is to very quickly raise the money to pay for sequencing and analysis and annotation of the sequences."
