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dc.contributor.authorLocke, Devin P.
dc.contributor.authorHillier, LaDeana W.
dc.contributor.authorWarren, Wesley C.
dc.contributor.authorWorley, Kim C.
dc.contributor.authorNazareth, Lynne V.
dc.contributor.authorMuzny, Donna M.
dc.contributor.authorYang, Shiaw-Pyng
dc.contributor.authorWang, Zhengyuan
dc.contributor.authorChinwalla, Asif T.
dc.contributor.authorMinx, Pat
dc.contributor.authorMitreva, Makedonka
dc.contributor.authorCook, Lisa
dc.contributor.authorDelehaunty, Kim D.
dc.contributor.authorFronick, Catrina
dc.contributor.authorSchmidt, Heather
dc.contributor.authorFulton, Lucinda A.
dc.contributor.authorFulton, Robert S.
dc.contributor.authorNelson, Joanne O.
dc.contributor.authorMagrini, Vincent
dc.contributor.authorPohl, Craig
dc.contributor.authorGraves, Tina A.
dc.contributor.authorMarkovic, Chris
dc.contributor.authorCree, Andy
dc.contributor.authorDinh, Huyen H.
dc.contributor.authorHume, Jennifer
dc.contributor.authorKovar, Christie L.
dc.contributor.authorFowler, Gerald R.
dc.contributor.authorLunter, Gerton
dc.contributor.authorMeader, Stephen
dc.contributor.authorHeger, Andreas
dc.contributor.authorPonting, Chris P.
dc.contributor.authorMarques-Bonet, Tomas
dc.contributor.authorAlkan, Can
dc.contributor.authorChen, Lin
dc.contributor.authorCheng, Ze
dc.contributor.authorKidd, Jeffrey M.
dc.contributor.authorEichler, Evan E.
dc.contributor.authorWhite, Simon
dc.contributor.authorSearle, Stephen
dc.contributor.authorVilella, Albert J.
dc.contributor.authorChen, Yuan
dc.contributor.authorFlicek, Paul
dc.contributor.authorMa, Jian
dc.contributor.authorRaney, Brian
dc.contributor.authorSuh, Bernard
dc.contributor.authorBurhans, Richard
dc.contributor.authorHerrero, Javier
dc.contributor.authorHaussler, David
dc.contributor.authorFaria, Rui
dc.contributor.authorFernando, Olga
dc.contributor.authorDarré, Fleur
dc.contributor.authorFarré, Domènec
dc.contributor.authorGazave, Elodie
dc.contributor.authorOliva, Meritxell
dc.contributor.authorNavarro, Arcadi
dc.contributor.authorRoberto, Roberta
dc.contributor.authorCapozzi, Oronzo
dc.contributor.authorArchidiacono, Nicoletta
dc.contributor.authorValle, Giuliano Della
dc.contributor.authorPurgato, Stefania
dc.contributor.authorRocchi, Mariano
dc.contributor.authorKonkel, Miriam K.
dc.contributor.authorWalker, Jerilyn A.
dc.contributor.authorUllmer, Brygg
dc.contributor.authorBatzer, Mark A.
dc.contributor.authorSmit, Arian F. A.
dc.contributor.authorHubley, Robert
dc.contributor.authorCasola, Claudio
dc.contributor.authorSchrider, Daniel R.
dc.contributor.authorHahn, Matthew W.
dc.contributor.authorQuesada, Victor
dc.contributor.authorPuente, Xose S.
dc.contributor.authorOrdoñez, Gonzalo R.
dc.contributor.authorLópez-Otín, Carlos
dc.contributor.authorVinar, Tomas
dc.contributor.authorBrejova, Brona
dc.contributor.authorRatan, Aakrosh
dc.contributor.authorHarris, Robert S.
dc.contributor.authorMiller, Webb
dc.contributor.authorKosiol, Carolin
dc.contributor.authorLawson, Heather A.
dc.contributor.authorTaliwal, Vikas
dc.contributor.authorMartins, André L.
dc.contributor.authorSiepel, Adam
dc.contributor.authorRoyChoudhury, Arindam
dc.contributor.authorMa, Xin
dc.contributor.authorDegenhardt, Jeremiah
dc.contributor.authorBustamante, Carlos D.
dc.contributor.authorGutenkunst, Ryan N.
dc.contributor.authorMailund, Thomas
dc.contributor.authorDutheil, Julien Y.
dc.contributor.authorHobolth, Asger
dc.contributor.authorSchierup, Mikkel H.
dc.contributor.authorRyder, Oliver A.
dc.contributor.authorYoshinaga, Yuko
dc.contributor.authorde Jong, Pieter J.
dc.contributor.authorWeinstock, George M.
dc.contributor.authorRogers, Jeffrey
dc.contributor.authorMardis, Elaine R.
dc.contributor.authorGibbs, Richard A.
dc.contributor.authorWilson, Richard K.
dc.date.accessioned2021-02-10T00:30:43Z
dc.date.available2021-02-10T00:30:43Z
dc.date.issued2011
dc.identifier.doihttps://doi.org/10.1038/nature09687
dc.identifier.urihttp://hdl.handle.net/20.500.12634/871
dc.description.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 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 relative to the ancestral Ne after the split, while Bornean Ne 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.
dc.description.sponsorship
dc.language.isoen
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/3.0/
dc.subjectORANGUTANS
dc.subjectSOUTHEAST ASIA
dc.subjectBORNEO
dc.subjectAPES
dc.subjectHUMANS
dc.subjectGENOMICS
dc.subjectTAXONOMIES
dc.subjectEVOLUTION
dc.subjectMETABOLISM
dc.subjectBIODIVERSITY
dc.subjectPOPULATIONS
dc.subjectWILDLIFE CONSERVATION
dc.subjectPRIMATOLOGY
dc.subjectRESEARCH
dc.titleComparative and demographic analysis of orang-utan genomes
dc.typeArticle
dc.source.journaltitleNature
dc.source.volume469
dc.source.issue7331
dc.source.beginpage529
dc.source.endpage533
refterms.dateFOA2021-02-10T01:41:23Z
html.description.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 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 relative to the ancestral Ne after the split, while Bornean Ne 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.


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This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.
Except where otherwise noted, this item's license is described as This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.