Comparative and demographic analysis of orang-utan genomes
Devin P. Locke,LaDeana W. Hillier,Wesley C. Warren,Kim C. Worley,Lynne V. Nazareth,Donn20KN万能材料实验机a 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,Step沙浆拉伸粘结强度实验机hen 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,Dom&eg电线电缆燃烧实验机rave;nec Farré,Elodie Gazave,Meritxell Oliva,Arcadi Navarro,Roberta Roberto,Oronzo Capozzi,Nicoletta Archidiacono,Giuliano Della Valle,Stefania Purgato,Mariano Rocchi,Miriam K. Konkel,Jeril触摸屏划线实验机yn 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. Ordo?ez,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岩石剪切实验机. Gutenkunst,T阀门耐用性实验机homas 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
‘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 pygma缠绕膜拉力实验机eus (Bornean), are the most phylogenetically distant great apes from humans, there拉力实验机by providing an informative perspective on hominid evolution. Here we present a Sumatran o胶带剥离力实验机rang-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中底纤维板曲折实验机 gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, 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, 400,000?years 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 (Ne) expanded exponentially防水实验机 relative to the ancestral Ne after the split, while Bornean Ne decline铝合金抗拉压强度实验机d 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.
Genome Res. doi: 10.1101/gr.114751.110
Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan spe纯弯疲劳实验机ciation and widespread selection
Asger Hobolth1, Julien Y. Dutheil1, John Hawks2, Mikkel H. Schierup1,3 and Thomas Mailund1水平冲击实验机
We search the complete orangutan genome for regions where humans are more closely related to orangutans than to chimpanzees due to incomplete lineage sorting (ILS) in the ancestor of human and chimpanzees. The search uses our recently developed coalescent HMM framework. We find ILS present in ~1% of the genome, and that the ancestral species of human and chimpanzees never experienced a severe population bottleneck. The existence of ILS is validated with simulations, site pattern analysis, and analysis of rare genomic events. The existence of ILS allows us to disentangle the time of isolation of humans and orangutans (the speciation time) from the genetic divergence time, and we find speciation to be as recent as 9⑴3 mya (contingent on the calibration point). The analyses provide further support fo电工套管压力实验机r a recent speciation of human and chimpanzee at ~4 mya and a diverse ancestor of human and chimpanzee with an effective population size of ~50,000 individuals. Posterior decoding infers ILS for each nucleotide in the genome and we use this塑料悬臂梁冲击实验机 to deduce patterns of selection ijb300b摆锤式冲击实验机n the ancestral species. We demonstrate the effect of background selection in the common ancestor of humans and chimpanzees. In agreement with predictions from population genetics, ILS found to be reduced in exons and gene dense小型高低温实验机 regions when we control for confounding factors such as GC content and recombination rate. Finally, we find the broad scale recombination rate to be conserved through the complete ape phylogeny.