A large international consortium -- involving more than 30 laboratories from eight different countries -- has published the full sequence of the orangutan genome. The work is featured on the title page of the journal Nature and Carolin Kosiol from the Institute of Population Genetics at the University of Veterinary Medicine, Vienna, is among the authors.
The direct ancestors of orangutans were once widely distributed in south-east Asia but the two modern orangutan species are confined to the islands of Sumatra and Borneo. Both species are endangered, largely as a consequence of destruction of their rainforest habitat. The orangutans are the only great apes that spend most of their time in trees. Nevertheless, the species share a number of features with other apes: they are adept in their use of tools and live in complex social groups that show evidence of cultural learning.
A wide-ranging international consortium has now presented the full genomic sequence of a female Sumatran orangutan named Susie. An analysis of the sequence reveals the orangutan genome to be remarkably stable: it has suffered far fewer duplication events than the human or chimpanzee genome. As a result of the slow rate of genomic evolution, the orangutan is genetically closest to a putative ancestral great ape. Comparing the new sequence with that of the human genome and other mammalian genomes thus provides unique insights into the evolution of man. Kosiol has examined a total of nearly 14,000 human genes that are also found in the orangutan, chimpanzee, macaque and dog genomes. She was able to show that genes involved in two processes have been particularly subject to natural selection in primate evolution: visual perception and the metabolism of glycolipids. Intriguingly, defects in glycolipid metabolism are known to be associated with a number of neurodegenerative diseases in humans.
"Changes in lipid metabolism may have played a big part in neurological evolution in primates, as well as being involved in the diversity of diets and life history strategies," Kosiol believes. "Apes, especially orangutans, have slower rates of reproduction and much lower energy usage than other mammals. It would be very valuable to sequence more primate genomes to enable more comparative analysis of this kind and thus help us understand the evolution of primates and our own species."
In fact, the scientists have accomplished far more than merely sequencing a single genome. Taking advantage of the new next generation sequencing technologies, they also sequenced the genomes of ten additional orangutans, five from Sumatra and five from Borneo. Examining all the sequences together permits an estimate of when the two species separated from one another -- about 400,000 years ago, which is considerably more recent than previously believed -- and enables an assessment of the diversity among them. The surprising finding is that the Sumatran orangutan is genetically much more variable than its close cousin on Borneo despite now having a much smaller population. There are thought to be about 40,000-50,000 Bornean orangutans left in the wild but the Sumatran orangutan is believed to number only 7,000-7,500 individuals and the International Union for Conservation of Nature lists the species as critically endangered.
As Kosiol says, "the greater diversity of Sumatran orangutans compared with Bornean orangutans could be very important for conservation efforts. We need to do all we can to maintain the diversity of both species."
- Devin P. Locke, LaDeana W. Hillier, Wesley C. Warren, Kim C. Worley, Lynne V. Nazareth, Donna M. Muzny, Shiaw-Pyng Yang, Zhengyuan Wang, Asif T. Chinwalla, Pat Minx, Makedonka Mitreva, Lisa Cook, Kim D. Delehaunty, Catrina Fronick, Heather Schmidt, Lucinda A. Fulton, Robert S. Fulton, Joanne O. Nelson, Vincent Magrini, Craig Pohl, Tina A. Graves, Chris Markovic, Andy Cree, Huyen H. Dinh, Jennifer Hume, Christie L. Kovar, Gerald R. Fowler, Gerton Lunter, Stephen Meader, Andreas Heger, Chris P. Ponting, Tomas Marques-Bonet, Can Alkan, Lin Chen, Ze Cheng, Jeffrey M. Kidd, Evan E. Eichler, Simon White, Stephen Searle, Albert J. Vilella, Yuan Chen, Paul Flicek, Jian Ma, Brian Raney, Bernard Suh, Richard Burhans, Javier Herrero, David Haussler, Rui Faria, Olga Fernando, Fleur Darré, Domènec Farré, Elodie Gazave, Meritxell Oliva, Arcadi Navarro, Roberta Roberto, Oronzo Capozzi, Nicoletta Archidiacono, Giuliano Della Valle, Stefania Purgato, Mariano Rocchi, Miriam K. Konkel, Jerilyn A. Walker, Brygg Ullmer, Mark A. Batzer, Arian F. A. Smit, Robert Hubley, Claudio Casola, Daniel R. Schrider, Matthew W. Hahn, Victor Quesada, Xose S. Puente, Gonzalo R. Ordoñez, Carlos López-Otín, Tomas Vinar, Brona Brejova, Aakrosh Ratan, Robert S. Harris, Webb Miller, Carolin Kosiol, Heather A. Lawson, Vikas Taliwal, André L. Martins, Adam Siepel, Arindam RoyChoudhury, Xin Ma, Jeremiah Degenhardt, Carlos D. Bustamante, Ryan N. Gutenkunst, Thomas Mailund, Julien Y. Dutheil, Asger Hobolth, Mikkel H. Schierup, Oliver A. Ryder, Yuko Yoshinaga, Pieter J. de Jong, George M. Weinstock, Jeffrey Rogers, Elaine R. Mardis, Richard A. Gibbs, Richard K. Wilson. Comparative and demographic analysis of orang-utan genomes. Nature, 2011; 469 (7331): 529 DOI: 10.1038/nature09687
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