Title

Comparative and demographic analysis of orang-utan genomes

Authors

Devin P. Locke, Washington University School of Medicine in St. Louis
Ladeana W. Hillier, Washington University School of Medicine in St. Louis
Wesley C. Warren, Washington University School of Medicine in St. Louis
Kim C. Worley, Baylor College of Medicine
Lynne V. Nazareth, Baylor College of Medicine
Donna M. Muzny, Baylor College of Medicine
Shiaw Pyng Yang, Washington University School of Medicine in St. Louis
Zhengyuan Wang, Washington University School of Medicine in St. Louis
Asif T. Chinwalla, Washington University School of Medicine in St. Louis
Pat Minx, Washington University School of Medicine in St. Louis
Makedonka Mitreva, Washington University School of Medicine in St. Louis
Lisa Cook, Washington University School of Medicine in St. Louis
Kim D. Delehaunty, Washington University School of Medicine in St. Louis
Catrina Fronick, Washington University School of Medicine in St. Louis
Heather Schmidt, Washington University School of Medicine in St. Louis
Lucinda A. Fulton, Washington University School of Medicine in St. Louis
Robert S. Fulton, Washington University School of Medicine in St. Louis
Joanne O. Nelson, Washington University School of Medicine in St. Louis
Vincent Magrini, Washington University School of Medicine in St. Louis
Craig Pohl, Washington University School of Medicine in St. Louis
Tina A. Graves, Washington University School of Medicine in St. Louis
Chris Markovic, Washington University School of Medicine in St. Louis
Andy Cree, Baylor College of Medicine
Huyen H. Dinh, Baylor College of Medicine
Jennifer Hume, Baylor College of Medicine
Christie L. Kovar, Baylor College of Medicine
Gerald R. Fowler, Baylor College of Medicine
Gerton Lunter, University of Oxford
Stephen Meader, University of Oxford
Andreas Heger, University of Oxford
Chris P. Ponting, University of Oxford
Tomas Marques-Bonet, University of Washington School of Medicine
Can Alkan, University of Washington School of Medicine
Lin Chen, University of Washington School of Medicine

Document Type

Article

Publication Date

1-27-2011

Abstract

Orang-utan- is derived from a Malay term meaning man of the forest- and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N e) expanded exponentially relative to the ancestral N e after the split, while Bornean N e declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts. © 2011 Macmillan Publishers Limited. All rights reserved.

Publication Source (Journal or Book title)

Nature

First Page

529

Last Page

533

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