In the forests of Borneo and Sumatra, orangutans -- the "men of the forest" in the language of Malaysia-swing among the trees, an endangered primate population so similar and yet different from man -- and from each other, according to a recently published genome analysis of the two populations of orangutans still existing in the world.
The multi-national study led by scientists from Baylor College of Medicine and Washington University in St. Louis, Mo., define many of the similarities between the two populations -- one in Sumatra and one in Borneo -- and the differences between these members of the Great Ape family and their human cousins.
"As more information about primates becomes known, we find additional genes for which there is positive selection," said Dr. Kim Worley, associate professor in the Baylor College of Medicine Human Genome Sequencing Center and an author of the report that appears in the recent issue of the journal Nature. The study includes a "deep" or intricately defined genome sequence of a Sumatran orangutan and less detailed genomic studies of five Sumatran and five Bornean orangutan genomes.
One unique feature they have identified is a neocentromere, a centromere that appears in a novel location on a chromosome. (Normal centromeres are the center of the "X" form of the chromosomes that appears during mitosis or cell division.)
"This variant in the chromosome 12 centromere position appears in both populations of orangutan," said Worley. "It attracts the centromeric protein sequences in the same way that a normal centromere does." Discovery of this neocentromere will help researchers understand how centromeres, and therefore chromosomes, change and evolve.
Dr. Jeffrey Rogers, associate professor in the BCM sequencing center and a primatologist, said that while orangutans were once thought to be a single species, geneticists find that the two populations are quite different, leading to their identification as two different species.
Variation within group
While behavioral and physical studies have identified differences between the two groups, Rogers said, "What the genome sequence found is that there is a large amount of genetic variation within the Sumatran and Bornean orangutans. Each population separately has more genetic variation than is found in humans. Add in the variation between the two populations and there is twice as much variation among orangutans as is found in humans."
What came as a surprise is that in some ways the orangutan genome has evolved more slowly than that of humans, chimps or gorillas, said Rogers. What that means is that the genome has not been structurally rearranged to the same degree as other primates. These structural rearrangements are often considered one important way in which evolution occurs.
There are fewer duplications and deletions or rearrangements of genetic material in orangutans. There are also many fewer Alu elements -- short stretches of DNA that insert themselves into the genome and make up roughly 10 percent of the total genome itself. Alu elements are associated with new mutations and gene recombinations within the genome. The lack of newer Alu elements could be one of the reasons that the orangutan genome does not have the structural variation found in other great apes, said Worley.
"This was a surprise," said Rogers. "From this perspective, the genome as a whole has evolved more slowly than those for humans, chimps and gorillas. We don't know what is driving that."
The orangutan genome will be important in "trying to reconstruct evolutionary history," said Rogers. As more primate genomes are sequenced, the information will help scientists understand better how genomes evolve and how the human species and its genome evolved. "It will help us understand what is unique about the process that produced humans."
Orangutan studies are particularly important because these primates are under tremendous ecological pressure. Their numbers have dwindled as man has encroached on their habitat. In 2004, experts estimated that 7,000-7,500 Sumatran and 40,000 to 50,000 Bornean orangutans remained in the wild.
"Their genetic variation is good news because, in the long run, it enables them to maintain a healthy population," said Rogers. Future efforts to conserve orangutans will only be bolstered by the information in the genome sequencing project, said Rogers.
"But, if the forest disappears, then the genetic variation won't matter. Habitat is of course absolutely essential," said Rogers. "If things continue as they have for the next 30 years, we won't have orangutans in the wild."
Others who took part in the sequencing efforts come from 34 institutions in several different countries.
Many other BCM researchers took part in this work including the Baylor Human Genome Sequencing Center's director, Dr. Richard Gibbs.
Funding for the study came from the National Human Genome Research Institute, National Science Foundation, David and Lucile Packard Foundation, Cornell University Provost's Fellowship, United Kingdom Medical Research Council, Marie Curie Fellowship, Ministerio de Ciencia e Innovación-Spain (MCI-Spain) and Fundación M. Botín, MCI-Spain, Spanish National Institute for Bioinformatics (INAB) and the Fundação para a Ciência e a Tecnologia, PRIN and CEGBA, and the Commission of the European Communities.
- 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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