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Deep survey of ape genetic diversity provides new insights into human-ape evolution millions of years ago

Deep survey of ape genetic diversity provides new insights into human-ape evolution millions of years ago

A new study by an international team of researchers has, for the first time, sequenced the genomes of a large number of Great apes from across Africa and South-East Asia. The work, lead by Dr. Tomas Marques Bonet of the Institut de Biologia Evolutiva (Universitat Pompeu Fabra and CSIC) in Spain and Dr Evan Eichler of the University of Washington, is focused on characterizing as much wild genetic diversity as possible from the worlds rapidly dwindling great ape populations. Javier Prado, predoctoral researcher at IBE, is the first author of the study today published in Nature.   
Reference article: Prado et al. 2013. 'Great ape genetic diversity and population history' Nature ahead of print. DOI 10.1038/nature12228.

04.07.2013

 

Deep survey of ape genetic diversity provides newinsights into human-ape evolution millions of years ago.

A new study by an international team of researchers has, for the first time, sequenced the genomes of a large number of Great apes from across Africa and South-East Asia. The work, lead by Dr. Tomas Marques Bonet of the Institut de Biologia Evolutiva (Universitat Pompeu Fabra and CSIC) in Spain and Dr Evan Eichler of the University of Washington focused on characterizing as much wild genetic diversity as possible from the worlds rapidly dwindling great ape populations. Great apes are a group of species made up of humans and our closest relatives, chimpanzees, gorillas and orangutans. These species all share a common ancestor about 14-16 million years ago, but chimpanzees, for example diverged from humans much more recently, ~6 million years ago.

"It's important to learn about the genetic diversity of great apes in order to put the history of our own genomes into context," says Peter Sudmant of the University of Washington, who cofirst authored the paper, which is published today in the journal Nature. The study provides one of the most detailed and comprehensive analyses of genetic diversity of wild-born great apes to date-pecies which are now all considered endangered.

Recent advances in genome sequencing technologies have allowed researchers to learn an enormous amount about human genomes and genetic diversity by sequencing individuals of our own species. In contrast however, far less attention has been focused on our great ape relatives.

This is largely due to the difficulty in obtaining DNA samples from these endangered species.

Though many apes exist in captivity, these individuals are a poor reflection of wild diversity. The

researchers instead tried to gather material from wild born individuals working internationally with conservation groups and researchers.

The researchers found that human genomes show relatively little variation between each other in comparison to most great apes. Few ape species are as shallow as human when it comes to genetic diversity. "This reduction in genetic diversity is commonly the result of an event called a population bottleneck." says Javier Prado-Martinez, a PhD student from Institut de Biologia Evolutiva who co-first authored the study. "What's striking is how severe this bottleneck must have been in ancestral humans in comparison to most great apes." The genomes of a pair of orangutans, for example differ at more than 2 out of every 1000 base-pairs, compared to 1 out of every 1000 base-pairs between any two humans. A few species of great apes, however, were more similar to humans in that they showed a dearth of genetic variation; namely Eastern lowland gorillas, Western chimpanzees and bonobos. All of these species showed evidence of severe bottlenecks in their ancient history possibly explaining the reduced genetic diversity.

The researchers focused particularly on the comparing the evolutionary history of our closest relatives, chimpanzees, who are dispersed across Africa and classified into four major groups, or, subspecies. An open question among evolutionary biologists has been how these four populations relate to one another. By sequencing multiple individuals from each group, the researchers were able to resolve the phylogenetic relationship among these subspecies distinguishing two genetically distinct groups of chimps. What also became apparent to the researchers was the complexity of the evolutionary history of chimps compared to humans. The patterns of genetic diversity were consistent with extensive gene flow or migration between ancestral populations with sudden expansions in population size followed by crashes. "Humans", in contrast "have a relatively simple evolutionary history," says Sudmant. "It's clear that over the last few million years chimpanzee populations fluctuated enormously in size and complexity." The basis for these population collapses is unclear but does coincide, in part, with a period of time when human populations began to thrive.

A companion paper published in the journal Genome Research today by Eichler and colleagues further explored how these fluctuations in the size and complexity of ape populations affected a larger form for genetic variation, known as copy number variation. They found in particular that chimpanzees harbored an excess number of gene deletion events more than 2 million years ago, coinciding with genetic bottlenecks in ancient chimpanzee populations. These findings suggest that the chimpanzee lineage actually lost more genes early in its history when compared to the human branch.

The work is underscored by sobering message however, "we need to do more to protect these species and preserve their natural environment," says Sudmant. "Some great ape populations are quite literally on the brink of extinction and they are, more so than ever, at the mercy of our species." Prado-Martinez expressed his hope that the resource would aid in conservation efforts, "knowing more about the genomes of these species will help to inform field biologists on the origin of poached great apes and the better management of captive breeding programs," he said.

Contacts:

University Pompeu Fabra-CSIC (Barcelona, Spain)
Tomàs Marquès Bonet (tomas.marques@upf.edu) and Javier Prado Martínez (javier.prado@upf.edu). Phone +34 93 316 08 87;

University of Washington (Seattle, USA)
Evan E. Eichler (eee@gs.washington.edu) and Peter Sudmant (psudmant@gmail.com). Phone +001

(206) 685-7336.

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