Comparative and demographic analysis of orang-utan genomes

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Standard

Comparative and demographic analysis of orang-utan genomes. / Locke, Devin P.; Hillier, LaDeana W.; Warren, Wesley C.; Yang, Shiaw-Pyng; Wang, Zhengyuan; Chinwalla, Asif T.; Minx, Pat; Mitreva, Makedonka; Cook, Lisa; Delehaunty, Kim D.; Fronick, Catrina; Schmidt, Heather; Fulton, Lucinda A.; Fulton, Robert S.; Nelson, Joanne O.; Magrini, Vincent; Pohl, Craig; Graves, Tina A.; Markovic, Chris; Weinstock, George M.; Mardis, Elaine R.; Wilson, Richard K.; Worley, Kim C.; Nazareth, Lynne V.; Muzny, Donna M.; Cree, Andy; Dinh, Huyen H.; Hume, Jennifer; Kovar, Christie L.; Fowler, Gerald R.; Rogers, Jeffrey; Gibbs, Richard A.; Lunter, Gerton; Meader, Stephen; Heger, Andreas; Ponting, Chris P.; Marques-Bonet, Tomas; Alkan, Can; Cheng, Lin; Cheng, Ze; Kidd, Jeffrey M.; Eichler, Evan E.; Faria, Rui; Fernando, Olga; Darré, Fleur; Farré, Domèmec; Gazave, Elodie; Oliva, Meritxell; Navarro, Arcadi; White, Simon; Searle, Stephen; Vilella, Albert J.; Chen, Yuan; Flicek, Paul; Herrero, Javier; Ma, Jian; Raney, Brian; Suh, Bernard; Haussler, David; Burhans, Richard; Ratan, Aakrosh; Harris, Robert S.; Miller, Webb; Roberto, Roberta; Capozzi, Oronzo; Archidiacono, Nicoletta; Rocchi, Mariano; Della Valle, Giuliano; Purgato, Stefania; Konkel, Miriam K.; Walker, Jerilyn A.; Batzer, Mark A.; Ullmer, Brygg; Smit, Adrian F. A.; Hubley, Robert; Casola, Claudio; Schrider, Daniel R.; Hahn, Matthew W.; Quesada, Victor; Puente, Xose S.; Ordoñez, Gonzalo R.; López-Otín, Carlos; Vinar, Tomas; Brejova, Brona; Kosiol, Carolin; Lawson, Heather A.; Taliwal, Vikas; Martins, André L.; Siepel, Adam; Ma, Xin; Degenhardt, Jeremiah; RoyChoudhury, Arindam; Bustamante, Carlos D.; Gutenkunst, Ryan N.; Mailund, Thomas; Dutheil, Julien; Hobolth, Asger; Schierup, Mikkel Heide; Ryder, Oliver A.; Yoshinaga, Yuko; de Jong, Pieter J.

In: Nature, Vol. 469, 2011, p. 529-533.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Harvard

Locke, DP, Hillier, LW, Warren, WC, Yang, S-P, Wang, Z, Chinwalla, AT, Minx, P, Mitreva, M, Cook, L, Delehaunty, KD, Fronick, C, Schmidt, H, Fulton, LA, Fulton, RS, Nelson, JO, Magrini, V, Pohl, C, Graves, TA, Markovic, C, Weinstock, GM, Mardis, ER, Wilson, RK, Worley, KC, Nazareth, LV, Muzny, DM, Cree, A, Dinh, HH, Hume, J, Kovar, CL, Fowler, GR, Rogers, J, Gibbs, RA, Lunter, G, Meader, S, Heger, A, Ponting, CP, Marques-Bonet, T, Alkan, C, Cheng, L, Cheng, Z, Kidd, JM, Eichler, EE, Faria, R, Fernando, O, Darré, F, Farré, D, Gazave, E, Oliva, M, Navarro, A, White, S, Searle, S, Vilella, AJ, Chen, Y, Flicek, P, Herrero, J, Ma, J, Raney, B, Suh, B, Haussler, D, Burhans, R, Ratan, A, Harris, RS, Miller, W, Roberto, R, Capozzi, O, Archidiacono, N, Rocchi, M, Della Valle, G, Purgato, S, Konkel, MK, Walker, JA, Batzer, MA, Ullmer, B, Smit, AFA, Hubley, R, Casola, C, Schrider, DR, Hahn, MW, Quesada, V, Puente, XS, Ordoñez, GR, López-Otín, C, Vinar, T, Brejova, B, Kosiol, C, Lawson, HA, Taliwal, V, Martins, AL, Siepel, A, Ma, X, Degenhardt, J, RoyChoudhury, A, Bustamante, CD, Gutenkunst, RN, Mailund, T, Dutheil, J, Hobolth, A, Schierup, MH, Ryder, OA, Yoshinaga, Y & de Jong, PJ 2011, 'Comparative and demographic analysis of orang-utan genomes', Nature, vol. 469, pp. 529-533. https://doi.org/10.1038/nature09687

APA

Locke, D. P., Hillier, L. W., Warren, W. C., Yang, S-P., Wang, Z., Chinwalla, A. T., ... de Jong, P. J. (2011). Comparative and demographic analysis of orang-utan genomes. Nature, 469, 529-533. https://doi.org/10.1038/nature09687

CBE

Locke DP, Hillier LW, Warren WC, Yang S-P, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Weinstock GM, Mardis ER, Wilson RK, Worley KC, Nazareth LV, Muzny DM, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Rogers J, Gibbs RA, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Cheng L, Cheng Z, Kidd JM, Eichler EE, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Herrero J, Ma J, Raney B, Suh B, Haussler D, Burhans R, Ratan A, Harris RS, Miller W, Roberto R, Capozzi O, Archidiacono N, Rocchi M, Della Valle G, Purgato S, Konkel MK, Walker JA, Batzer MA, Ullmer B, Smit AFA, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Ma X, Degenhardt J, RoyChoudhury A, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil J, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ. 2011. Comparative and demographic analysis of orang-utan genomes. Nature. 469:529-533. https://doi.org/10.1038/nature09687

MLA

Vancouver

Locke DP, Hillier LW, Warren WC, Yang S-P, Wang Z, Chinwalla AT et al. Comparative and demographic analysis of orang-utan genomes. Nature. 2011;469:529-533. https://doi.org/10.1038/nature09687

Author

Locke, Devin P. ; Hillier, LaDeana W. ; Warren, Wesley C. ; Yang, Shiaw-Pyng ; Wang, Zhengyuan ; Chinwalla, Asif T. ; Minx, Pat ; Mitreva, Makedonka ; Cook, Lisa ; Delehaunty, Kim D. ; Fronick, Catrina ; Schmidt, Heather ; Fulton, Lucinda A. ; Fulton, Robert S. ; Nelson, Joanne O. ; Magrini, Vincent ; Pohl, Craig ; Graves, Tina A. ; Markovic, Chris ; Weinstock, George M. ; Mardis, Elaine R. ; Wilson, Richard K. ; Worley, Kim C. ; Nazareth, Lynne V. ; Muzny, Donna M. ; Cree, Andy ; Dinh, Huyen H. ; Hume, Jennifer ; Kovar, Christie L. ; Fowler, Gerald R. ; Rogers, Jeffrey ; Gibbs, Richard A. ; Lunter, Gerton ; Meader, Stephen ; Heger, Andreas ; Ponting, Chris P. ; Marques-Bonet, Tomas ; Alkan, Can ; Cheng, Lin ; Cheng, Ze ; Kidd, Jeffrey M. ; Eichler, Evan E. ; Faria, Rui ; Fernando, Olga ; Darré, Fleur ; Farré, Domèmec ; Gazave, Elodie ; Oliva, Meritxell ; Navarro, Arcadi ; White, Simon ; Searle, Stephen ; Vilella, Albert J. ; Chen, Yuan ; Flicek, Paul ; Herrero, Javier ; Ma, Jian ; Raney, Brian ; Suh, Bernard ; Haussler, David ; Burhans, Richard ; Ratan, Aakrosh ; Harris, Robert S. ; Miller, Webb ; Roberto, Roberta ; Capozzi, Oronzo ; Archidiacono, Nicoletta ; Rocchi, Mariano ; Della Valle, Giuliano ; Purgato, Stefania ; Konkel, Miriam K. ; Walker, Jerilyn A. ; Batzer, Mark A. ; Ullmer, Brygg ; Smit, Adrian F. A. ; Hubley, Robert ; Casola, Claudio ; Schrider, Daniel R. ; Hahn, Matthew W. ; Quesada, Victor ; Puente, Xose S. ; Ordoñez, Gonzalo R. ; López-Otín, Carlos ; Vinar, Tomas ; Brejova, Brona ; Kosiol, Carolin ; Lawson, Heather A. ; Taliwal, Vikas ; Martins, André L. ; Siepel, Adam ; Ma, Xin ; Degenhardt, Jeremiah ; RoyChoudhury, Arindam ; Bustamante, Carlos D. ; Gutenkunst, Ryan N. ; Mailund, Thomas ; Dutheil, Julien ; Hobolth, Asger ; Schierup, Mikkel Heide ; Ryder, Oliver A. ; Yoshinaga, Yuko ; de Jong, Pieter J. / Comparative and demographic analysis of orang-utan genomes. In: Nature. 2011 ; Vol. 469. pp. 529-533.

Bibtex

@article{bb9310c2a4d94184aa4547a5a3fb3656,
title = "Comparative and demographic analysis of orang-utan genomes",
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. ‘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.",
author = "Locke, {Devin P.} and Hillier, {LaDeana W.} and Warren, {Wesley C.} and Shiaw-Pyng Yang and Zhengyuan Wang and Chinwalla, {Asif T.} and Pat Minx and Makedonka Mitreva and Lisa Cook and Delehaunty, {Kim D.} and Catrina Fronick and Heather Schmidt and Fulton, {Lucinda A.} and Fulton, {Robert S.} and Nelson, {Joanne O.} and Vincent Magrini and Craig Pohl and Graves, {Tina A.} and Chris Markovic and Weinstock, {George M.} and Mardis, {Elaine R.} and Wilson, {Richard K.} and Worley, {Kim C.} and Nazareth, {Lynne V.} and Muzny, {Donna M.} and Andy Cree and Dinh, {Huyen H.} and Jennifer Hume and Kovar, {Christie L.} and Fowler, {Gerald R.} and Jeffrey Rogers and Gibbs, {Richard A.} and Gerton Lunter and Stephen Meader and Andreas Heger and Ponting, {Chris P.} and Tomas Marques-Bonet and Can Alkan and Lin Cheng and Ze Cheng and Kidd, {Jeffrey M.} and Eichler, {Evan E.} and Rui Faria and Olga Fernando and Fleur Darr{\'e} and Dom{\`e}mec Farr{\'e} and Elodie Gazave and Meritxell Oliva and Arcadi Navarro and Simon White and Stephen Searle and Vilella, {Albert J.} and Yuan Chen and Paul Flicek and Javier Herrero and Jian Ma and Brian Raney and Bernard Suh and David Haussler and Richard Burhans and Aakrosh Ratan and Harris, {Robert S.} and Webb Miller and Roberta Roberto and Oronzo Capozzi and Nicoletta Archidiacono and Mariano Rocchi and {Della Valle}, Giuliano and Stefania Purgato and Konkel, {Miriam K.} and Walker, {Jerilyn A.} and Batzer, {Mark A.} and Brygg Ullmer and Smit, {Adrian F. A.} and Robert Hubley and Claudio Casola and Schrider, {Daniel R.} and Hahn, {Matthew W.} and Victor Quesada and Puente, {Xose S.} and Ordo{\~n}ez, {Gonzalo R.} and Carlos L{\'o}pez-Ot{\'i}n and Tomas Vinar and Brona Brejova and Carolin Kosiol and Lawson, {Heather A.} and Vikas Taliwal and Martins, {Andr{\'e} L.} and Adam Siepel and Xin Ma and Jeremiah Degenhardt and Arindam RoyChoudhury and Bustamante, {Carlos D.} and Gutenkunst, {Ryan N.} and Thomas Mailund and Julien Dutheil and Asger Hobolth and Schierup, {Mikkel Heide} and Ryder, {Oliver A.} and Yuko Yoshinaga and {de Jong}, {Pieter J.}",
year = "2011",
doi = "10.1038/nature09687",
language = "English",
volume = "469",
pages = "529--533",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",

}

RIS

TY - JOUR

T1 - Comparative and demographic analysis of orang-utan genomes

AU - Locke, Devin P.

AU - Hillier, LaDeana W.

AU - Warren, Wesley C.

AU - Yang, Shiaw-Pyng

AU - Wang, Zhengyuan

AU - Chinwalla, Asif T.

AU - Minx, Pat

AU - Mitreva, Makedonka

AU - Cook, Lisa

AU - Delehaunty, Kim D.

AU - Fronick, Catrina

AU - Schmidt, Heather

AU - Fulton, Lucinda A.

AU - Fulton, Robert S.

AU - Nelson, Joanne O.

AU - Magrini, Vincent

AU - Pohl, Craig

AU - Graves, Tina A.

AU - Markovic, Chris

AU - Weinstock, George M.

AU - Mardis, Elaine R.

AU - Wilson, Richard K.

AU - Worley, Kim C.

AU - Nazareth, Lynne V.

AU - Muzny, Donna M.

AU - Cree, Andy

AU - Dinh, Huyen H.

AU - Hume, Jennifer

AU - Kovar, Christie L.

AU - Fowler, Gerald R.

AU - Rogers, Jeffrey

AU - Gibbs, Richard A.

AU - Lunter, Gerton

AU - Meader, Stephen

AU - Heger, Andreas

AU - Ponting, Chris P.

AU - Marques-Bonet, Tomas

AU - Alkan, Can

AU - Cheng, Lin

AU - Cheng, Ze

AU - Kidd, Jeffrey M.

AU - Eichler, Evan E.

AU - Faria, Rui

AU - Fernando, Olga

AU - Darré, Fleur

AU - Farré, Domèmec

AU - Gazave, Elodie

AU - Oliva, Meritxell

AU - Navarro, Arcadi

AU - White, Simon

AU - Searle, Stephen

AU - Vilella, Albert J.

AU - Chen, Yuan

AU - Flicek, Paul

AU - Herrero, Javier

AU - Ma, Jian

AU - Raney, Brian

AU - Suh, Bernard

AU - Haussler, David

AU - Burhans, Richard

AU - Ratan, Aakrosh

AU - Harris, Robert S.

AU - Miller, Webb

AU - Roberto, Roberta

AU - Capozzi, Oronzo

AU - Archidiacono, Nicoletta

AU - Rocchi, Mariano

AU - Della Valle, Giuliano

AU - Purgato, Stefania

AU - Konkel, Miriam K.

AU - Walker, Jerilyn A.

AU - Batzer, Mark A.

AU - Ullmer, Brygg

AU - Smit, Adrian F. A.

AU - Hubley, Robert

AU - Casola, Claudio

AU - Schrider, Daniel R.

AU - Hahn, Matthew W.

AU - Quesada, Victor

AU - Puente, Xose S.

AU - Ordoñez, Gonzalo R.

AU - López-Otín, Carlos

AU - Vinar, Tomas

AU - Brejova, Brona

AU - Kosiol, Carolin

AU - Lawson, Heather A.

AU - Taliwal, Vikas

AU - Martins, André L.

AU - Siepel, Adam

AU - Ma, Xin

AU - Degenhardt, Jeremiah

AU - RoyChoudhury, Arindam

AU - Bustamante, Carlos D.

AU - Gutenkunst, Ryan N.

AU - Mailund, Thomas

AU - Dutheil, Julien

AU - Hobolth, Asger

AU - Schierup, Mikkel Heide

AU - Ryder, Oliver A.

AU - Yoshinaga, Yuko

AU - de Jong, Pieter J.

PY - 2011

Y1 - 2011

N2 - ‘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. ‘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.

AB - ‘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. ‘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.

U2 - 10.1038/nature09687

DO - 10.1038/nature09687

M3 - Journal article

VL - 469

SP - 529

EP - 533

JO - Nature

JF - Nature

SN - 0028-0836

ER -