The bonobo genome compared with the chimpanzee and human genomes

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The chimpanzee and the bonobo are our species' two closest living relatives. This paper reports the genome sequence of the bonobo, the last ape to be sequenced. Comparative genomic analyses reveal that more than 3% of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. The results shed light on the ancestry of the two ape species and might eventually help us to understand the genetic basis of phenotypes that humans share with one or the other ape species. Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours1,2,3,4, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. 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class="c-context-bar__container u-container" data-track-context="sticky banner"> <div class="c-context-bar__title"> The bonobo genome compared with the chimpanzee and human genomes </div> <div class="c-pdf-download u-clear-both js-pdf-download"> <a href="/articles/nature11128.pdf" class="u-button u-button--full-width u-button--primary u-justify-content-space-between c-pdf-download__link" data-article-pdf="true" data-readcube-pdf-url="true" data-test="download-pdf" data-draft-ignore="true" data-track="content_download" data-track-type="article pdf download" data-track-action="download pdf" data-track-label="link" data-track-external download> <span class="c-pdf-download__text">Download PDF</span> <svg aria-hidden="true" focusable="false" width="16" height="16" class="u-icon"><use xlink:href="#icon-download"/></svg> </a> </div> </div> </div> <article lang="en"> <div class="c-pdf-button__container u-mb-16 u-hide-at-lg js-context-bar-sticky-point-mobile"> <div class="c-pdf-container" 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href="https://www.springernature.com/gp/open-research/about/the-fundamentals-of-open-access-and-open-research" data-track="click" data-track-action="open access" data-track-label="link" class="u-color-open-access" data-test="open-access">Open access</a> </li> <li class="c-article-identifiers__item">Published: <time datetime="2012-06-13">13 June 2012</time></li> </ul> <h1 class="c-article-title" data-test="article-title" data-article-title="">The bonobo genome compared with the chimpanzee and human genomes</h1> <ul class="c-article-author-list c-article-author-list--long" data-test="authors-list" data-component-authors-activator="authors-list"><li class="c-article-author-list__item"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Kay-Pr_fer-Aff1" data-author-popup="auth-Kay-Pr_fer-Aff1" data-author-search="Prüfer, Kay" data-corresp-id="c1">Kay Prüfer<svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-mail-medium"></use></svg></a><sup class="u-js-hide"><a href="#Aff1">1</a></sup>, </li><li class="c-article-author-list__item"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Kasper-Munch-Aff2" data-author-popup="auth-Kasper-Munch-Aff2" data-author-search="Munch, Kasper">Kasper Munch</a><sup class="u-js-hide"><a href="#Aff2">2</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Ines-Hellmann-Aff3" data-author-popup="auth-Ines-Hellmann-Aff3" data-author-search="Hellmann, Ines">Ines Hellmann</a><sup class="u-js-hide"><a href="#Aff3">3</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Keiko-Akagi-Aff4" data-author-popup="auth-Keiko-Akagi-Aff4" data-author-search="Akagi, Keiko">Keiko Akagi</a><sup class="u-js-hide"><a href="#Aff4">4</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Jason_R_-Miller-Aff5" data-author-popup="auth-Jason_R_-Miller-Aff5" data-author-search="Miller, Jason R.">Jason R. Miller</a><sup class="u-js-hide"><a href="#Aff5">5</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Brian-Walenz-Aff5" data-author-popup="auth-Brian-Walenz-Aff5" data-author-search="Walenz, Brian">Brian Walenz</a><sup class="u-js-hide"><a href="#Aff5">5</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Sergey-Koren-Aff6" data-author-popup="auth-Sergey-Koren-Aff6" data-author-search="Koren, Sergey">Sergey Koren</a><sup class="u-js-hide"><a href="#Aff6">6</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Granger-Sutton-Aff5" data-author-popup="auth-Granger-Sutton-Aff5" data-author-search="Sutton, Granger">Granger Sutton</a><sup class="u-js-hide"><a href="#Aff5">5</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Chinnappa-Kodira-Aff7" data-author-popup="auth-Chinnappa-Kodira-Aff7" data-author-search="Kodira, Chinnappa">Chinnappa Kodira</a><sup class="u-js-hide"><a href="#Aff7">7</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Roger-Winer-Aff7" data-author-popup="auth-Roger-Winer-Aff7" data-author-search="Winer, Roger">Roger Winer</a><sup class="u-js-hide"><a href="#Aff7">7</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-James_R_-Knight-Aff7" data-author-popup="auth-James_R_-Knight-Aff7" data-author-search="Knight, James R.">James R. Knight</a><sup class="u-js-hide"><a href="#Aff7">7</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-James_C_-Mullikin-Aff8" data-author-popup="auth-James_C_-Mullikin-Aff8" data-author-search="Mullikin, James C.">James C. Mullikin</a><sup class="u-js-hide"><a href="#Aff8">8</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Stephen_J_-Meader-Aff9" data-author-popup="auth-Stephen_J_-Meader-Aff9" data-author-search="Meader, Stephen J.">Stephen J. Meader</a><sup class="u-js-hide"><a href="#Aff9">9</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Chris_P_-Ponting-Aff9" data-author-popup="auth-Chris_P_-Ponting-Aff9" data-author-search="Ponting, Chris P.">Chris P. Ponting</a><sup class="u-js-hide"><a href="#Aff9">9</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Gerton-Lunter-Aff10" data-author-popup="auth-Gerton-Lunter-Aff10" data-author-search="Lunter, Gerton">Gerton Lunter</a><sup class="u-js-hide"><a href="#Aff10">10</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Saneyuki-Higashino-Aff11" data-author-popup="auth-Saneyuki-Higashino-Aff11" data-author-search="Higashino, Saneyuki">Saneyuki Higashino</a><sup class="u-js-hide"><a href="#Aff11">11</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Asger-Hobolth-Aff2" data-author-popup="auth-Asger-Hobolth-Aff2" data-author-search="Hobolth, Asger">Asger Hobolth</a><sup class="u-js-hide"><a href="#Aff2">2</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Julien-Dutheil-Aff2" data-author-popup="auth-Julien-Dutheil-Aff2" data-author-search="Dutheil, Julien">Julien Dutheil</a><sup class="u-js-hide"><a href="#Aff2">2</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Emre-Karako_-Aff12" data-author-popup="auth-Emre-Karako_-Aff12" data-author-search="Karakoç, Emre">Emre Karakoç</a><sup class="u-js-hide"><a href="#Aff12">12</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Can-Alkan-Aff12-Aff23" data-author-popup="auth-Can-Alkan-Aff12-Aff23" data-author-search="Alkan, Can">Can Alkan</a><sup class="u-js-hide"><a href="#Aff12">12</a></sup><sup class="u-js-hide"> <a href="#nAff23">nAff23</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Saba-Sajjadian-Aff12" data-author-popup="auth-Saba-Sajjadian-Aff12" data-author-search="Sajjadian, Saba">Saba Sajjadian</a><sup class="u-js-hide"><a href="#Aff12">12</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Claudia_Rita-Catacchio-Aff13" data-author-popup="auth-Claudia_Rita-Catacchio-Aff13" data-author-search="Catacchio, Claudia Rita">Claudia Rita Catacchio</a><sup class="u-js-hide"><a href="#Aff13">13</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Mario-Ventura-Aff12-Aff13" data-author-popup="auth-Mario-Ventura-Aff12-Aff13" data-author-search="Ventura, Mario">Mario Ventura</a><sup class="u-js-hide"><a href="#Aff12">12</a>,<a href="#Aff13">13</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Tomas-Marques_Bonet-Aff12-Aff14" data-author-popup="auth-Tomas-Marques_Bonet-Aff12-Aff14" data-author-search="Marques-Bonet, Tomas">Tomas Marques-Bonet</a><sup class="u-js-hide"><a href="#Aff12">12</a>,<a href="#Aff14">14</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Evan_E_-Eichler-Aff12" data-author-popup="auth-Evan_E_-Eichler-Aff12" data-author-search="Eichler, Evan E.">Evan E. Eichler</a><sup class="u-js-hide"><a href="#Aff12">12</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Claudine-Andr_-Aff15" data-author-popup="auth-Claudine-Andr_-Aff15" data-author-search="André, Claudine">Claudine André</a><sup class="u-js-hide"><a href="#Aff15">15</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Rebeca-Atencia-Aff16" data-author-popup="auth-Rebeca-Atencia-Aff16" data-author-search="Atencia, Rebeca">Rebeca Atencia</a><sup class="u-js-hide"><a href="#Aff16">16</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Lawrence-Mugisha-Aff17" data-author-popup="auth-Lawrence-Mugisha-Aff17" data-author-search="Mugisha, Lawrence">Lawrence Mugisha</a><sup class="u-js-hide"><a href="#Aff17">17</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-J_rg-Junhold-Aff18" data-author-popup="auth-J_rg-Junhold-Aff18" data-author-search="Junhold, Jörg">Jörg Junhold</a><sup class="u-js-hide"><a href="#Aff18">18</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Nick-Patterson-Aff19" data-author-popup="auth-Nick-Patterson-Aff19" data-author-search="Patterson, Nick">Nick Patterson</a><sup class="u-js-hide"><a href="#Aff19">19</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Michael-Siebauer-Aff1" data-author-popup="auth-Michael-Siebauer-Aff1" data-author-search="Siebauer, Michael">Michael Siebauer</a><sup class="u-js-hide"><a href="#Aff1">1</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Jeffrey_M_-Good-Aff1-Aff20" data-author-popup="auth-Jeffrey_M_-Good-Aff1-Aff20" data-author-search="Good, Jeffrey M.">Jeffrey M. Good</a><sup class="u-js-hide"><a href="#Aff1">1</a>,<a href="#Aff20">20</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Anne-Fischer-Aff1-Aff21" data-author-popup="auth-Anne-Fischer-Aff1-Aff21" data-author-search="Fischer, Anne">Anne Fischer</a><sup class="u-js-hide"><a href="#Aff1">1</a>,<a href="#Aff21">21</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Susan_E_-Ptak-Aff1" data-author-popup="auth-Susan_E_-Ptak-Aff1" data-author-search="Ptak, Susan E.">Susan E. Ptak</a><sup class="u-js-hide"><a href="#Aff1">1</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Michael-Lachmann-Aff1" data-author-popup="auth-Michael-Lachmann-Aff1" data-author-search="Lachmann, Michael">Michael Lachmann</a><sup class="u-js-hide"><a href="#Aff1">1</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-David_E_-Symer-Aff4" data-author-popup="auth-David_E_-Symer-Aff4" data-author-search="Symer, David E.">David E. Symer</a><sup class="u-js-hide"><a href="#Aff4">4</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Thomas-Mailund-Aff2" data-author-popup="auth-Thomas-Mailund-Aff2" data-author-search="Mailund, Thomas">Thomas Mailund</a><sup class="u-js-hide"><a href="#Aff2">2</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Mikkel_H_-Schierup-Aff2-Aff22" data-author-popup="auth-Mikkel_H_-Schierup-Aff2-Aff22" data-author-search="Schierup, Mikkel H.">Mikkel H. Schierup</a><sup class="u-js-hide"><a href="#Aff2">2</a>,<a href="#Aff22">22</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Aida_M_-Andr_s-Aff1" data-author-popup="auth-Aida_M_-Andr_s-Aff1" data-author-search="Andrés, Aida M.">Aida M. Andrés</a><sup class="u-js-hide"><a href="#Aff1">1</a></sup>, </li><li class="c-article-author-list__item c-article-author-list__item--hide c-article-author-list__item--hide-small-screen"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Janet-Kelso-Aff1" data-author-popup="auth-Janet-Kelso-Aff1" data-author-search="Kelso, Janet">Janet Kelso</a><sup class="u-js-hide"><a href="#Aff1">1</a></sup> & </li><li class="c-article-author-list__show-more" aria-label="Show all 41 authors for this article" title="Show all 41 authors for this article">…</li><li class="c-article-author-list__item"><a data-test="author-name" data-track="click" data-track-action="open author" data-track-label="link" href="#auth-Svante-P__bo-Aff1" data-author-popup="auth-Svante-P__bo-Aff1" data-author-search="Pääbo, Svante" data-corresp-id="c2">Svante Pääbo<svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-mail-medium"></use></svg></a><sup class="u-js-hide"><a href="#Aff1">1</a></sup> </li></ul><button aria-expanded="false" class="c-article-author-list__button"><svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-chevron-down-medium"></use></svg><span>Show authors</span></button> <p class="c-article-info-details" data-container-section="info"> <a data-test="journal-link" href="/" data-track="click" data-track-action="journal homepage" data-track-category="article body" data-track-label="link"><i data-test="journal-title">Nature</i></a> <b data-test="journal-volume"><span class="u-visually-hidden">volume</span> 486</b>, <span class="u-visually-hidden">pages </span>527–531 (<span data-test="article-publication-year">2012</span>)<a href="#citeas" class="c-article-info-details__cite-as u-hide-print" data-track="click" data-track-action="cite this article" data-track-label="link">Cite this article</a> </p> <div class="c-article-metrics-bar__wrapper u-clear-both"> <ul class="c-article-metrics-bar u-list-reset"> <li class=" c-article-metrics-bar__item" data-test="access-count"> <p class="c-article-metrics-bar__count">216k <span class="c-article-metrics-bar__label">Accesses</span></p> </li> <li class="c-article-metrics-bar__item" data-test="altmetric-score"> <p class="c-article-metrics-bar__count">1205 <span class="c-article-metrics-bar__label">Altmetric</span></p> </li> <li class="c-article-metrics-bar__item"> <p class="c-article-metrics-bar__details"><a href="/articles/nature11128/metrics" data-track="click" data-track-action="view metrics" data-track-label="link" rel="nofollow">Metrics <span class="u-visually-hidden">details</span></a></p> </li> </ul> </div> </header> <div class="u-js-hide" data-component="article-subject-links"> <h3 class="c-article__sub-heading">Subjects</h3> <ul class="c-article-subject-list"> <li class="c-article-subject-list__subject"><a href="/subjects/comparative-genomics" data-track="click" data-track-action="view subject" data-track-label="link">Comparative genomics</a></li><li class="c-article-subject-list__subject"><a href="/subjects/evolutionary-biology" data-track="click" data-track-action="view subject" data-track-label="link">Evolutionary biology</a></li> </ul> </div> </div> <div class="c-article-body"> <section aria-labelledby="Abs3" data-title="Abstract" lang="en"><div class="c-article-section" id="Abs3-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="Abs3">Abstract</h2><div class="c-article-section__content" id="Abs3-content"><p>Two African apes are the closest living relatives of humans: the chimpanzee (<i>Pan troglodytes</i>) and the bonobo (<i>Pan paniscus</i>). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Boesch, C., Hohmann, G. & Marchant, L. Behavioural Diversity in Chimpanzees and Bonobos (Cambridge Univ. Press, 2002)" href="/articles/nature11128#ref-CR1" id="ref-link-section-d557811183e1111">1</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 2" title="de Waal, F. & Lanting, F. Bonobo: the Forgotten Ape (Univ. California Press, 1997)" href="/articles/nature11128#ref-CR2" id="ref-link-section-d557811183e1114">2</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 3" title="Hare, B., Wobber, V. & Wrangham, R. The self-domestication hypothesis: evolution of bonobo psychology is due to selection against aggression. Anim. Behav. 83, 573–585 (2012)" href="/articles/nature11128#ref-CR3" id="ref-link-section-d557811183e1117">3</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 4" title="Kano, T. The Last Ape: Pygmy Chimpanzee Behavior and Ecology (Stanford Univ. Press, 1992)" href="/articles/nature11128#ref-CR4" id="ref-link-section-d557811183e1120">4</a></sup>, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other.</p></div></div></section> <section aria-labelledby="inline-recommendations" data-title="Inline Recommendations" class="c-article-recommendations" data-track-component="inline-recommendations"> <h3 class="c-article-recommendations-title" id="inline-recommendations">Similar content being viewed by others</h3> <div class="c-article-recommendations-list"> <div class="c-article-recommendations-list__item"> <article class="c-article-recommendations-card" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-article-recommendations-card__img"><img src="https://media.springernature.com/w215h120/springer-static/image/art%3A10.1038%2Fs41586-021-03519-x/MediaObjects/41586_2021_3519_Fig1_HTML.png" loading="lazy" alt=""></div> <div class="c-article-recommendations-card__main"> <h3 class="c-article-recommendations-card__heading" itemprop="name headline"> <a class="c-article-recommendations-card__link" itemprop="url" href="https://www.nature.com/articles/s41586-021-03519-x?fromPaywallRec=false" data-track="select_recommendations_1" data-track-context="inline recommendations" data-track-action="click recommendations inline - 1" data-track-label="10.1038/s41586-021-03519-x">A high-quality bonobo genome refines the analysis of hominid evolution </a> </h3> <div class="c-article-meta-recommendations" data-test="recommendation-info"> <span class="c-article-meta-recommendations__item-type">Article</span> <span class="c-article-meta-recommendations__access-type">Open access</span> <span class="c-article-meta-recommendations__date">05 May 2021</span> </div> </div> </article> </div> <div class="c-article-recommendations-list__item"> <article class="c-article-recommendations-card" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-article-recommendations-card__img"><img src="https://media.springernature.com/w215h120/springer-static/image/art%3A10.1038%2Fs41586-021-03535-x/MediaObjects/41586_2021_3535_Fig1_HTML.png" loading="lazy" alt=""></div> <div class="c-article-recommendations-card__main"> <h3 class="c-article-recommendations-card__heading" itemprop="name headline"> <a class="c-article-recommendations-card__link" itemprop="url" href="https://www.nature.com/articles/s41586-021-03535-x?fromPaywallRec=false" data-track="select_recommendations_2" data-track-context="inline recommendations" data-track-action="click recommendations inline - 2" data-track-label="10.1038/s41586-021-03535-x">Evolutionary and biomedical insights from a marmoset diploid genome assembly </a> </h3> <div class="c-article-meta-recommendations" data-test="recommendation-info"> <span class="c-article-meta-recommendations__item-type">Article</span> <span class="c-article-meta-recommendations__access-type">Open access</span> <span class="c-article-meta-recommendations__date">28 April 2021</span> </div> </div> </article> </div> <div class="c-article-recommendations-list__item"> <article class="c-article-recommendations-card" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-article-recommendations-card__img"><img src="https://media.springernature.com/w215h120/springer-static/image/art%3A10.1038%2Fs41576-022-00554-w/MediaObjects/41576_2022_554_Fig1_HTML.png" loading="lazy" alt=""></div> <div class="c-article-recommendations-card__main"> <h3 class="c-article-recommendations-card__heading" itemprop="name headline"> <a class="c-article-recommendations-card__link" itemprop="url" href="https://www.nature.com/articles/s41576-022-00554-w?fromPaywallRec=false" data-track="select_recommendations_3" data-track-context="inline recommendations" data-track-action="click recommendations inline - 3" data-track-label="10.1038/s41576-022-00554-w">Current advances in primate genomics: novel approaches for understanding evolution and disease </a> </h3> <div class="c-article-meta-recommendations" data-test="recommendation-info"> <span class="c-article-meta-recommendations__item-type">Article</span> <span class="c-article-meta-recommendations__date">04 January 2023</span> </div> </div> </article> </div> </div> </section> <script> window.dataLayer = window.dataLayer || []; window.dataLayer.push({ recommendations: { recommender: 'semantic', model: 'specter', policy_id: 'NA', timestamp: 1739839804, embedded_user: 'null' } }); </script> <div class="main-content"> <section data-title="Main"><div class="c-article-section" id="Sec1-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="Sec1">Main</h2><div class="c-article-section__content" id="Sec1-content"><p>Whereas chimpanzees are widespread across equatorial Africa, bonobos live only south of the Congo River in the Democratic Republic of Congo (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig1">Fig. 1a</a>). As a result of their relatively small and remote habitat, bonobos were the last ape species to be described<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 2" title="de Waal, F. & Lanting, F. Bonobo: the Forgotten Ape (Univ. California Press, 1997)" href="/articles/nature11128#ref-CR2" id="ref-link-section-d557811183e1153">2</a></sup> and are the rarest of all apes in captivity. As a consequence, they have, until recently, been little studied<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 2" title="de Waal, F. & Lanting, F. Bonobo: the Forgotten Ape (Univ. California Press, 1997)" href="/articles/nature11128#ref-CR2" id="ref-link-section-d557811183e1157">2</a></sup>. It is known that whereas DNA sequences in humans diverged from those in bonobos and chimpanzees five to seven million years ago, DNA sequences in bonobos diverged from those in chimpanzees around two million years ago. Bonobos are thus closely related to chimpanzees. Moreover, comparison of a small number of autosomal DNA sequences has shown that bonobo DNA sequences often fall within the variation of chimpanzees<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 5" title="Fischer, A. et al. Bonobos fall within the genomic variation of chimpanzees. PLoS ONE 6, e21605 (2011)" href="/articles/nature11128#ref-CR5" id="ref-link-section-d557811183e1161">5</a></sup>.</p><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-1" data-title=" Geographical distribution and test for admixture between chimpanzees and bonobos. "><figure><figcaption><b id="Fig1" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 1: <b>Geographical distribution and test for admixture between chimpanzees and bonobos.</b> </b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><a class="c-article-section__figure-link" data-test="img-link" data-track="click" data-track-label="image" data-track-action="view figure" href="/articles/nature11128/figures/1" rel="nofollow"><picture><source type="image/webp" srcset="//media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnature11128/MediaObjects/41586_2012_Article_BFnature11128_Fig1_HTML.jpg?as=webp"><img aria-describedby="Fig1" src="//media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnature11128/MediaObjects/41586_2012_Article_BFnature11128_Fig1_HTML.jpg" alt="figure 1" loading="lazy" width="685" height="363"></picture></a></div><div class="c-article-section__figure-description" data-test="bottom-caption" id="figure-1-desc"><p><b>a</b>, Geographical distribution of bonobos and chimpanzees. <b>b</b>, <i>D</i> statistics for the admixture test between bonobos and three chimpanzee groups. Each pairwise comparison between one bonobo and two chimpanzee groups is depicted as one panel. Each point in a panel represents one bonobo individual compared with two chimpanzee individuals from different groups. Admixture between bonobo and chimpanzee is indicated by a <i>Z</i>-score greater than 4.4 or less than −4.4.</p><p> <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM235">PowerPoint slide</a> </p></div></div><div class="u-text-right u-hide-print"><a class="c-article__pill-button" data-test="article-link" data-track="click" data-track-label="button" data-track-action="view figure" href="/articles/nature11128/figures/1" data-track-dest="link:Figure1 Full size image" aria-label="Full size image figure 1" rel="nofollow"><span>Full size image</span><svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-chevron-right-small"></use></svg></a></div></figure></div><p>Bonobos and chimpanzees are highly similar to each other in many respects. However, the behaviour of the two species differs in important ways<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Boesch, C., Hohmann, G. & Marchant, L. Behavioural Diversity in Chimpanzees and Bonobos (Cambridge Univ. Press, 2002)" href="/articles/nature11128#ref-CR1" id="ref-link-section-d557811183e1209">1</a></sup>. For example, male chimpanzees use aggression to compete for dominance rank and obtain sex, and they cooperate to defend their home range and attack other groups<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 3" title="Hare, B., Wobber, V. & Wrangham, R. The self-domestication hypothesis: evolution of bonobo psychology is due to selection against aggression. Anim. Behav. 83, 573–585 (2012)" href="/articles/nature11128#ref-CR3" id="ref-link-section-d557811183e1213">3</a></sup>. By contrast, bonobo males are commonly subordinate to females and do not compete intensely for dominance rank<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Boesch, C., Hohmann, G. & Marchant, L. Behavioural Diversity in Chimpanzees and Bonobos (Cambridge Univ. Press, 2002)" href="/articles/nature11128#ref-CR1" id="ref-link-section-d557811183e1217">1</a></sup>. They do not form alliances with one another and there is no evidence of lethal aggression between groups<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 3" title="Hare, B., Wobber, V. & Wrangham, R. The self-domestication hypothesis: evolution of bonobo psychology is due to selection against aggression. Anim. Behav. 83, 573–585 (2012)" href="/articles/nature11128#ref-CR3" id="ref-link-section-d557811183e1221">3</a></sup>. Compared with chimpanzees, bonobos are playful throughout their lives and show intense sexual behaviour<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 3" title="Hare, B., Wobber, V. & Wrangham, R. The self-domestication hypothesis: evolution of bonobo psychology is due to selection against aggression. Anim. Behav. 83, 573–585 (2012)" href="/articles/nature11128#ref-CR3" id="ref-link-section-d557811183e1225">3</a></sup> that serves non-conceptive functions and often involves same-sex partners<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 4" title="Kano, T. The Last Ape: Pygmy Chimpanzee Behavior and Ecology (Stanford Univ. Press, 1992)" href="/articles/nature11128#ref-CR4" id="ref-link-section-d557811183e1230">4</a></sup>. Thus, chimpanzees and bonobos each possess certain characteristics that are more similar to human traits than they are to one another’s. No parsimonious reconstruction of the social structure and behavioural patterns of the common ancestor of humans, chimpanzees and bonobos is therefore possible. That ancestor may in fact have possessed a mosaic of features, including those now seen in bonobo, chimpanzee and human.</p><p>To understand the evolutionary relationships of bonobos, chimpanzees and humans better, we sequenced and assembled the genome of a female bonobo individual (Ulindi) and compared it to those of chimpanzees and humans. Compared with the 6× Sanger-sequenced chimpanzee genome<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 6" title="The. Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87 (2005)" href="/articles/nature11128#ref-CR6" id="ref-link-section-d557811183e1237">6</a></sup> (panTro2), the bonobo genome assembly has a similar number of bases in alignment with the human genome, a similar number of lineage-specific substitutions and similar indel error rates (<a data-track="click" data-track-label="link" data-track-action="table anchor" href="/articles/nature11128#Tab1">Table 1</a> and <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, sections 2 and 3), suggesting that the two ape genomes are of similar quality. Segmental duplications affect at least 80 Mb of the bonobo genome, according to excess sequence read-depth predictions. Owing to over-collapsing of duplications, only 14.6 Mb are present in the final assembly (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 4), a common error seen in assemblies from shorter-read technologies<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 7" title="Alkan, C., Sajjadian, S. & Eichler, E. E. Limitations of next-generation genome sequence assembly. Nature Methods 8, 61–65 (2011)" href="/articles/nature11128#ref-CR7" id="ref-link-section-d557811183e1250">7</a></sup>. We used the finished chimpanzee sequence of chromosome 21 together with the human genome sequence to estimate an error rate of approximately two errors per 10 kb in the bonobo genome, with comparable qualities for the X chromosome and autosomes. The bonobo genome can therefore serve as a high-quality sequence for comparative genome analyses.</p><div class="c-article-table" data-test="inline-table" data-container-section="table" id="table-1"><figure><figcaption class="c-article-table__figcaption"><b id="Tab1" data-test="table-caption">Table 1 Bonobo genome assembly characteristics and genomic features compared with the chimpanzee genome (panTro2)</b></figcaption><div class="u-text-right u-hide-print"><a class="c-article__pill-button" data-test="table-link" data-track="click" data-track-action="view table" data-track-label="button" rel="nofollow" href="/articles/nature11128/tables/1" aria-label="Full size table 1"><span>Full size table</span><svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-chevron-right-small"></use></svg></a></div></figure></div><p>On average, the two alleles in single-copy, autosomal regions in the Ulindi genome are approximately 99.9% identical to each other, 99.6% identical to corresponding sequences in the chimpanzee genome and 98.7% identical to corresponding sequences in the human genome. A comprehensive analysis of the bonobo genome is presented in <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>. Here we summarize the most interesting results.</p><p>We identified and validated experimentally a total of 704 kb of DNA sequences that occur in bonobo-specific segmental duplications. They contain three partially duplicated genes (<i>CFHR2</i>, <i>DUS2L</i> and <i>CACNA1B</i>) and two completely duplicated genes (<i>CFHR4</i> and <i>DDX28</i>). However, bonobos and chimpanzees share the majority of segmental duplications, and they carry approximately similar numbers of bases in lineage-specific duplications (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig2">Fig. 2a</a>).</p><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-2" data-title=" Segmental duplications and transposon accumulation. "><figure><figcaption><b id="Fig2" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 2: <b>Segmental duplications and transposon accumulation.</b> </b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><a class="c-article-section__figure-link" data-test="img-link" data-track="click" data-track-label="image" data-track-action="view figure" href="/articles/nature11128/figures/2" rel="nofollow"><picture><source type="image/webp" srcset="//media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnature11128/MediaObjects/41586_2012_Article_BFnature11128_Fig2_HTML.jpg?as=webp"><img aria-describedby="Fig2" src="//media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnature11128/MediaObjects/41586_2012_Article_BFnature11128_Fig2_HTML.jpg" alt="figure 2" loading="lazy" width="685" height="302"></picture></a></div><div class="c-article-section__figure-description" data-test="bottom-caption" id="figure-2-desc"><p><b>a</b>, Venn diagram showing segmental duplications in the human (H), chimpanzee (C) and bonobo (B) genomes. Each number of megabases refers to the total amount of sequence that occurs in segmental duplications (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 4). <b>b</b>, Accumulation of different retrotransposon classes on each lineage.</p><p> <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM236">PowerPoint slide</a> </p></div></div><div class="u-text-right u-hide-print"><a class="c-article__pill-button" data-test="article-link" data-track="click" data-track-label="button" data-track-action="view figure" href="/articles/nature11128/figures/2" data-track-dest="link:Figure2 Full size image" aria-label="Full size image figure 2" rel="nofollow"><span>Full size image</span><svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-chevron-right-small"></use></svg></a></div></figure></div><p>As in other mammals, transposons, that is, mobile genetic elements, make up approximately half of the bonobo genome (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 6). In agreement with previous results<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 6" title="The. Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87 (2005)" href="/articles/nature11128#ref-CR6" id="ref-link-section-d557811183e1528">6</a></sup>, we find that <i>Alu</i> insertions accumulated about twice as fast on the human lineage as on the bonobo and chimpanzee lineages (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig2">Fig. 2b</a>). We identified two previously unreported <i>Alu</i> subfamilies in bonobos and chimpanzees, designated <i>Alu</i>Yp1, which is present in 5 copies in the human genome and in 54 and 114 copies in the bonobo and chimpanzee genomes, respectively, and <i>Alu</i>Yp2, which is absent from humans and present in 24 and 37 copies, respectively, in the two apes. We found that, as in mice<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 8" title="Akagi, K., Li, J., Stephens, R. M., Volfovsky, N. & Symer, D. E. Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Genome Res. 18, 869–880 (2008)" href="/articles/nature11128#ref-CR8" id="ref-link-section-d557811183e1548">8</a></sup>, African-ape-specific L1 insertions are enriched near genes involved in neuronal activities or cell adhesion and are depleted near genes encoding transcription factors or involved in nucleic-acid metabolism (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 6). In humans, L1 retrotransposition has been shown to occur preferentially in neuronal precursor cells and has been speculated to contribute to functional diversity in the brain<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 9" title="Baillie, J. K. et al. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479, 534–537 (2011)" href="/articles/nature11128#ref-CR9" id="ref-link-section-d557811183e1555">9</a></sup>. The tendency of new L1 integrants to accumulate near neuronal genes on evolutionary timescales may mimic the somatic variation found in the brain.</p><p>To investigate whether bonobos and chimpanzees exchanged genes subsequent to their separation, we used a test (the <i>D</i> statistic<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 10" title="Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010)" href="/articles/nature11128#ref-CR10" id="ref-link-section-d557811183e1565">10</a></sup>) to investigate the extent to which the bonobo genomes might be closer to some chimpanzees than to others (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 10). To this end, we generated Illumina shotgun sequences from two western, seven eastern, and seven central chimpanzees (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig1">Fig. 1a</a>) and from three bonobos (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 5). We then used alignments of sets of four genomes, each consisting of two chimpanzees, the bonobo and the human, and tested for an excess of shared derived alleles between bonobo and one chimpanzee as compared with the other chimpanzee. We observe no significant difference between the numbers of shared derived alleles (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig1">Fig. 1b</a>). There is thus no indication of preferential gene flow between bonobos and any of the chimpanzee groups tested. Such a complete separation contrasts with reports of hybridization between many other primates<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 11" title="Arnold, M. L. & Meyer, A. Natural hybridization in primates: one evolutionary mechanism. Zoology 109, 261–276 (2006)" href="/articles/nature11128#ref-CR11" id="ref-link-section-d557811183e1582">11</a></sup>. It is, however, consistent with the suggestion that the formation of the Congo River 1.5–2.5 million years ago created a barrier to gene flow that allowed bonobos and chimpanzees to evolve different phenotypes over a relatively short time.</p><p>Because the population split between bonobo and chimpanzee occurred relatively close in time to the split between the bonobo–chimpanzee ancestor (<i>Pan</i> ancestor) and humans, not all genomic regions are expected to show the pattern in which DNA sequences from bonobos and chimpanzees are more closely related to each other than to humans. Previous work using very low-coverage sequencing of ape genomes has suggested that less than 1% of the human genome may be more closely related to one of the two apes than the ape genomes are to one another<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 12" title="Caswell, J. L. et al. Analysis of chimpanzee history based on genome sequence alignments. PLoS Genet. 4, e1000057 (2008)" href="/articles/nature11128#ref-CR12" id="ref-link-section-d557811183e1592">12</a></sup>. To investigate the extent to which such so-called incomplete lineage sorting (ILS) exists between the three species, we used the bonobo genome and a coalescent hidden Markov model (HMM) approach<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 13" title="Hobolth, A., Christensen, O. F., Mailund, T. & Schierup, M. H. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet. 3, e7 (2007)" href="/articles/nature11128#ref-CR13" id="ref-link-section-d557811183e1596">13</a></sup> to analyse non-repetitive parts of the bonobo, chimpanzee<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 6" title="The. Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87 (2005)" href="/articles/nature11128#ref-CR6" id="ref-link-section-d557811183e1600">6</a></sup>, human<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 14" title="Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)" href="/articles/nature11128#ref-CR14" id="ref-link-section-d557811183e1604">14</a></sup> and orang-utan<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 15" title="Locke, D. P. et al. Comparative and demographic analysis of orang-utan genomes. Nature 469, 529–533 (2011)" href="/articles/nature11128#ref-CR15" id="ref-link-section-d557811183e1609">15</a></sup> genomes. This showed that 1.6% of the human genome is more closely related to the bonobo genome than to the chimpanzee genome, and that 1.7% of the human genome is more closely related to the chimpanzee than to the bonobo genome (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig3">Fig. 3a</a>).</p><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-3" data-title=" Incomplete lineage sorting. "><figure><figcaption><b id="Fig3" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 3: <b>Incomplete lineage sorting.</b> </b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><a class="c-article-section__figure-link" data-test="img-link" data-track="click" data-track-label="image" data-track-action="view figure" href="/articles/nature11128/figures/3" rel="nofollow"><picture><source type="image/webp" srcset="//media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnature11128/MediaObjects/41586_2012_Article_BFnature11128_Fig3_HTML.jpg?as=webp"><img aria-describedby="Fig3" src="//media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnature11128/MediaObjects/41586_2012_Article_BFnature11128_Fig3_HTML.jpg" alt="figure 3" loading="lazy" width="685" height="329"></picture></a></div><div class="c-article-section__figure-description" data-test="bottom-caption" id="figure-3-desc"><p><b>a</b>, Schematic description of ILS states and percentage of bases assigned to each state. <b>b</b>, Effective population sizes and split times inferred from ILS and based on a molecular clock with a mutation rate of 10<sup>−9</sup> yr<sup>−1</sup>. Myr, million years. We note that other estimates of mutation rates will correspondingly affect the estimates of the split times. <b>c</b>, Overlap between predicted ILS transposons and the closest HMM ILS assignments within 100 bp of a transposon insertion. <b>d</b>, Proportion of ILS in exons, introns and across the whole genome, counted within <span class="stix">∼</span>1-Mb segments of alignment (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 8). <b>e</b>, Proportion of ILS dependent on recombination rates. Errors, 95% confidence interval.</p><p> <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM237">PowerPoint slide</a> </p></div></div><div class="u-text-right u-hide-print"><a class="c-article__pill-button" data-test="article-link" data-track="click" data-track-label="button" data-track-action="view figure" href="/articles/nature11128/figures/3" data-track-dest="link:Figure3 Full size image" aria-label="Full size image figure 3" rel="nofollow"><span>Full size image</span><svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-chevron-right-small"></use></svg></a></div></figure></div><p>To test this result independently, we analysed transposon integrations, which occur so rarely in ape and human genomes that the chance of two independent insertions of the same type of transposon at the same position and in the same orientation in different species is exceedingly low. We identified 991 integrations of transposons absent from the orang-utan genome but present in two of the three species bonobo, chimpanzee and human. Of these, 27 are shared between the bonobo and human genomes but are absent from the chimpanzee genome, and 30 are shared between the chimpanzee and human genomes but are absent from the bonobo genome, suggesting that approximately 6% (95% confidence interval, 4.1–7.0%) of the genome is affected by ILS among the three species. The HMM estimation of ILS is further supported by the fact that the HMM tree topology assignments tend to match the ILS status of the neighbouring transposons (<i>P</i> = 7.2 × 10<sup>−6</sup> and 0.025 for bonobo–human and chimpanzee–human ILS, respectively; <a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig3">Fig. 3c</a> and <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 6). We conclude that more than 3% of the human genome is more closely related to either bonobos or chimpanzees than these are to each other.</p><p>Such regions of ILS may influence phenotypic similarities that humans share with one of the apes but not the other. In fact, about 25% of all genes contain regions of ILS (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 8), and genes encoding membrane proteins and proteins involved in cell adhesion have a higher fraction of bases assigned to ILS than do other genes. Amino-acid substitutions that are fixed in the apes and show ILS may be particularly informative about phenotypic differences. We identified 18 such amino-acid substitutions shared between humans and bonobos and 18 shared between chimpanzees and humans (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 12). These are candidates for further study. An interesting example is the gene encoding the trace amine associated receptor 8 (TAAR8), a member of a family of G-coupled protein receptors that in the mouse detect volatile amines in urine that may provide social cues<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 16" title="Liberles, S. D. & Buck, L. B. A second class of chemosensory receptors in the olfactory epithelium. Nature 442, 645–650 (2006)" href="/articles/nature11128#ref-CR16" id="ref-link-section-d557811183e1691">16</a></sup>. Although this gene seems to be pseudogenized independently on multiple ape lineages, humans and bonobos share a single amino-acid change in the first extracellular domain and carry the longest open reading frames (of 342 and 256 amino acids, respectively; open reading frames in all other apes, <180 amino acids) (SI 12). Further work is needed to clarify if TAAR8 is functional in humans and apes.</p><p>The ILS among bonobos, chimpanzees and humans opens the possibility of gauging the genetic diversity and, hence, the population history of the <i>Pan</i> ancestor. We used the HMM to estimate the effective population size of the <i>Pan</i> ancestor to 27,000 individuals (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig3">Fig. 3b</a>), which is almost three times larger than that of present-day bonobos (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 9) and humans<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 17" title="Takahata, N. Allelic genealogy and human evolution. Mol. Biol. Evol. 10, 2–22 (1993)" href="/articles/nature11128#ref-CR17" id="ref-link-section-d557811183e1711">17</a></sup> but is similar to that of central chimpanzees<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 5" title="Fischer, A. et al. Bonobos fall within the genomic variation of chimpanzees. PLoS ONE 6, e21605 (2011)" href="/articles/nature11128#ref-CR5" id="ref-link-section-d557811183e1716">5</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 18" title="Hey, J. The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses. Mol. Biol. Evol. 27, 921–933 (2010)" href="/articles/nature11128#ref-CR18" id="ref-link-section-d557811183e1719">18</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 19" title="Wegmann, D. & Excoffier, L. Bayesian inference of the demographic history of chimpanzees. Mol. Biol. Evol. 27, 1425–1435 (2010)" href="/articles/nature11128#ref-CR19" id="ref-link-section-d557811183e1722">19</a></sup>. We also estimated a population split time between bonobos and chimpanzees of one million years, which is in agreement with most previous estimates<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 18" title="Hey, J. The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses. Mol. Biol. Evol. 27, 921–933 (2010)" href="/articles/nature11128#ref-CR18" id="ref-link-section-d557811183e1726">18</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 19" title="Wegmann, D. & Excoffier, L. Bayesian inference of the demographic history of chimpanzees. Mol. Biol. Evol. 27, 1425–1435 (2010)" href="/articles/nature11128#ref-CR19" id="ref-link-section-d557811183e1729">19</a></sup>.</p><p>Differences in female and male population history, for example, with respect to reproductive success and migration rates, are of special interest in understanding the evolution of social structure. To approach this question in the <i>Pan</i> ancestor, we compared the inferred ancestral population sizes of the X chromosome and the autosomes. Because two-thirds of X chromosomes are found in females whereas autosomes are split equally between the two sexes, a ratio between their effective population sizes (X/A ratio) of 0.75 is expected under random mating. The X/A ratio in the <i>Pan</i> ancestor, corrected for the higher mutation rate in males, is 0.83 (0.75–0.91) (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig4">Fig. 4</a> and <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 8). Similarly, we estimated an X/A ratio of 0.85 (0.79–0.93) for present-day bonobos using Ulindi single nucleotide polymorphisms in 200-kb windows (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 9). Under the assumption of random mating, this would mean that on average two females reproduce for each reproducing male. The difference in the variance of reproductive success between the sexes certainly contributes to this observation, as does the fact that whereas bonobo females often move to new groups upon maturation, males tend to stay within their natal group<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 20" title="Eriksson, J. et al. Y-chromosome analysis confirms highly sex-biased dispersal and suggests a low male effective population size in bonobos (Pan paniscus). Mol. Ecol. 15, 939–949 (2006)" href="/articles/nature11128#ref-CR20" id="ref-link-section-d557811183e1752">20</a></sup>. Because both current and ancestral X/A ratios are similar to each other and also to some human groups (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig4">Fig. 4</a>), this suggests that they may also have been typical for the ancestor shared with humans.</p><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-4" data-title=" X/A ratios. "><figure><figcaption><b id="Fig4" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 4: <b>X/A ratios.</b> </b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><a class="c-article-section__figure-link" data-test="img-link" data-track="click" data-track-label="image" data-track-action="view figure" href="/articles/nature11128/figures/4" rel="nofollow"><picture><source type="image/webp" srcset="//media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnature11128/MediaObjects/41586_2012_Article_BFnature11128_Fig4_HTML.jpg?as=webp"><img aria-describedby="Fig4" src="//media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnature11128/MediaObjects/41586_2012_Article_BFnature11128_Fig4_HTML.jpg" alt="figure 4" loading="lazy" width="685" height="480"></picture></a></div><div class="c-article-section__figure-description" data-test="bottom-caption" id="figure-4-desc"><p>The X/A ratios for Ulindi (bonobo), an African human and a European human were inferred from heterozygosity, and that for the <i>Pan</i> ancestor was inferred from ILS. The low X/A ratio for the European has been suggested to be due to demographic effects connected to migrating out of Africa<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 30" title="Gottipati, S., Arbiza, L., Siepel, A., Clark, A. G. & Keinan, A. Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing. Nature Genet. 43, 741–743 (2011)" href="/articles/nature11128#ref-CR30" id="ref-link-section-d557811183e1778">30</a></sup>. Errors, 95% confidence interval (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, sections 8 and 9).</p><p> <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM238">PowerPoint slide</a> </p></div></div><div class="u-text-right u-hide-print"><a class="c-article__pill-button" data-test="article-link" data-track="click" data-track-label="button" data-track-action="view figure" href="/articles/nature11128/figures/4" data-track-dest="link:Figure4 Full size image" aria-label="Full size image figure 4" rel="nofollow"><span>Full size image</span><svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-chevron-right-small"></use></svg></a></div></figure></div><p>Because factors that reduce the effective population size, in particular positive and negative selection, will decrease the extent of ILS, the distribution of ILS across the genome allows regions affected by selection in the <i>Pan</i> ancestor to be identified. In agreement with this, we find that exons show less ILS than introns (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig3">Fig. 3d</a> and <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 8). We also find that recombination rates are positively correlated with ILS (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig3">Fig. 3e</a>), probably because recombination uncouples regions from neighbouring selective events. Unlike positive and negative selection, balancing selection is expected to increase ILS. In agreement with this, we find that ILS is most frequent in the major histocompatibility complex (MHC), which encodes cell-surface proteins that present antigens to immune cells (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 10) and is known to contain genes that evolve under balancing selection<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 21" title="Gyllensten, U. B. & Erlich, H. A. Ancient roots for polymorphism at the HLA-DQ alpha locus in primates. Proc. Natl Acad. Sci. USA 86, 9986–9990 (1989)" href="/articles/nature11128#ref-CR21" id="ref-link-section-d557811183e1818">21</a></sup>.</p><p>To identify regions affected by selective sweeps in the <i>Pan</i> ancestor, we isolated long genomic regions devoid of ILS. The largest such region is 6.1 Mb long and is located on human chromosome 3. This region contains a cluster of tumour suppressor genes<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 22" title="Hesson, L. B., Cooper, W. N. & Latif, F. Evaluation of the 3p21.3 tumour-suppressor gene cluster. Oncogene 26, 7283–7301 (2007)" href="/articles/nature11128#ref-CR22" id="ref-link-section-d557811183e1828">22</a></sup>, has an estimated recombination rate of 10% of the human genome average<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 23" title="Kong, A. et al. Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467, 1099–1103 (2010)" href="/articles/nature11128#ref-CR23" id="ref-link-section-d557811183e1832">23</a></sup> and has been found to evolve under strong purifying selection in humans<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 24" title="McVicker, G., Gordon, D., Davis, C. & Green, P. Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet. 5, e1000471 (2009)" href="/articles/nature11128#ref-CR24" id="ref-link-section-d557811183e1836">24</a></sup>. The diversity in the region, corrected for mutation rate, is lower than in neighbouring regions in chimpanzee but not in bonobos (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig5">Fig. 5a</a>), and parts of the region show signatures of positive selection in humans<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 10" title="Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010)" href="/articles/nature11128#ref-CR10" id="ref-link-section-d557811183e1844">10</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 25" title="Voight, B. F., Kudaravalli, S., Wen, X. & Pritchard, J. K. A map of recent positive selection in the human genome. PLoS Biol. 4, e72 (2006)" href="/articles/nature11128#ref-CR25" id="ref-link-section-d557811183e1847">25</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 26" title="Wang, E. T., Kodama, G., Baldi, P. & Moyzis, R. K. Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc. Natl Acad. Sci. USA 103, 135–140 (2006)" href="/articles/nature11128#ref-CR26" id="ref-link-section-d557811183e1850">26</a></sup>. Apparently this region evolves in unique ways that may involve both strong background selection and several independent events of positive selection among apes and humans.</p><div class="c-article-section__figure js-c-reading-companion-figures-item" data-test="figure" data-container-section="figure" id="figure-5" data-title=" Selection in the bonobo–chimpanzee common ancestor and chimpanzees. "><figure><figcaption><b id="Fig5" class="c-article-section__figure-caption" data-test="figure-caption-text">Figure 5: <b>Selection in the bonobo–chimpanzee common ancestor and chimpanzees.</b> </b></figcaption><div class="c-article-section__figure-content"><div class="c-article-section__figure-item"><a class="c-article-section__figure-link" data-test="img-link" data-track="click" data-track-label="image" data-track-action="view figure" href="/articles/nature11128/figures/5" rel="nofollow"><picture><source type="image/webp" srcset="//media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnature11128/MediaObjects/41586_2012_Article_BFnature11128_Fig5_HTML.jpg?as=webp"><img aria-describedby="Fig5" src="//media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnature11128/MediaObjects/41586_2012_Article_BFnature11128_Fig5_HTML.jpg" alt="figure 5" loading="lazy" width="685" height="733"></picture></a></div><div class="c-article-section__figure-description" data-test="bottom-caption" id="figure-5-desc"><p><b>a</b>, Diversity in chimpanzee and bonobo around the region on chromosome 3 devoid of ILS. <b>b</b>, Regions where bonobos fall outside the variation of chimpanzee upstream of the MHC. The MHC region is not plotted because the SNP density is sparse there as a result of duplications. Five regions among the 50 longest regions are shown in yellow. Red points show posterior probabilities >0.8.</p><p> <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM239">PowerPoint slide</a> </p></div></div><div class="u-text-right u-hide-print"><a class="c-article__pill-button" data-test="article-link" data-track="click" data-track-label="button" data-track-action="view figure" href="/articles/nature11128/figures/5" data-track-dest="link:Figure5 Full size image" aria-label="Full size image figure 5" rel="nofollow"><span>Full size image</span><svg width="16" height="16" focusable="false" role="img" aria-hidden="true" class="u-icon"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#icon-eds-i-chevron-right-small"></use></svg></a></div></figure></div><p>The fact that the chimpanzee diversity encompasses bonobos for most regions of the genome can be exploited to identify regions that have been positively selected in chimpanzees after their separation from bonobos, because in such regions bonobos will fall outside the chimpanzee variation. We implemented a search for such regions, which is similar to a test previously applied to humans to detect selective sweeps since their split from Neanderthals<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 10" title="Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010)" href="/articles/nature11128#ref-CR10" id="ref-link-section-d557811183e1892">10</a></sup> (<i>Homo neanderthalensis</i>), in an HMM that uses coalescent simulations for parameter training, the chimpanzee resequencing data and the megabase-wide average of the human recombination rates (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 7). Because the size of a region affected by a selective sweep will be larger the faster fixation was reached, the intensity of selection will correlate positively with genetic length. We therefore ranked the regions according to genetic length and further corrected for the effect of background selection<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 24" title="McVicker, G., Gordon, D., Davis, C. & Green, P. Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet. 5, e1000471 (2009)" href="/articles/nature11128#ref-CR24" id="ref-link-section-d557811183e1902">24</a></sup>. The highest-ranking region contains an miRNA, miR-4465, that has not yet been functionally characterized. Four of the ten highest-ranking regions contain no protein- or RNA-coding genes, and may thus contain structural or regulatory features that have been subject to selection. Notably, four of these ten regions are on chromosome 6, and two of these four are within 2 Mb of the MHC (<a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig5">Fig. 5b</a>). This suggests that the MHC and surrounding genomic regions have been a major target of positive selection in chimpanzees, presumably as a result of infectious diseases. Indeed, chimpanzees have experienced a selective sweep that targeted MHC class-I genes and reduced allelic diversity across a wide region surrounding the MHC<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 27" title="de Groot, N. G. et al. AIDS-protective HLA-B*27/B*57 and chimpanzee MHC class I molecules target analogous conserved areas of HIV-1/SIVcpz. Proc. Natl Acad. Sci. USA 107, 15175–15180 (2010)" href="/articles/nature11128#ref-CR27" id="ref-link-section-d557811183e1910">27</a></sup>, perhaps caused by the HIV-1/SIV<sub>CPZ</sub> retrovirus<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 27" title="de Groot, N. G. et al. AIDS-protective HLA-B*27/B*57 and chimpanzee MHC class I molecules target analogous conserved areas of HIV-1/SIVcpz. Proc. Natl Acad. Sci. USA 107, 15175–15180 (2010)" href="/articles/nature11128#ref-CR27" id="ref-link-section-d557811183e1916">27</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 28" title="Yohn, C. T. et al. Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biol. 3, e110 (2005)" href="/articles/nature11128#ref-CR28" id="ref-link-section-d557811183e1919">28</a></sup>.</p><p>The bonobo genome shows that more than 3% of the human genome is more closely related to either bonobos or chimpanzees than these are to each other. This can be used to illuminate the population history and selective events that affected the ancestor of bonobos and chimpanzees. In addition, about 25% of human genes contain parts that are more closely related to one of the two apes than the other. Such regions can now be identified and will hopefully contribute to the unravelling of the genetic background of phenotypic similarities among humans, bonobos and chimpanzees.</p></div></div></section><section data-title="Methods Summary"><div class="c-article-section" id="Sec2-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="Sec2">Methods Summary</h2><div class="c-article-section__content" id="Sec2-content"><p>We generated a total of 86 Gb of DNA sequence from Ulindi, a female bonobo who lives in Leipzig Zoo (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 1). All sequencing was done on the 454 sequencing platform and included 10 Gb of paired-end reads from clones of insert sizes of 3, 9 and 20 kb. The genome was assembled using the open-source Celera Assembler software<sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 29" title="Miller, J. R. et al. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24, 2818–2824 (2008)" href="/articles/nature11128#ref-CR29" id="ref-link-section-d557811183e1937">29</a></sup> (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 2). In addition, we sequenced 19 bonobo and chimpanzee individuals on the Illumina GAIIx platform to about one-fold genomic coverage per individual (<a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a>, section 5). <a data-track="click" data-track-label="link" data-track-action="supplementary material anchor" href="/articles/nature11128#MOESM240">Supplementary Information</a> provides a full description of our methods.</p></div></div></section> </div> <div class="u-mt-32"> <section data-title="Accession codes"><div class="c-article-section" id="accession-codes-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="accession-codes">Accession codes</h2><div class="c-article-section__content" id="accession-codes-content"> <h3 class="c-article__sub-heading">Primary accessions</h3> <h4 class="c-article__sub-heading c-article__sub-heading--small">Sequence Read Archive</h4><ul class="c-article-data-availability-list u-list-reset"> <li class="c-article-data-availability-list__item"> <p> <a href="http://www.ncbi.nlm.nih.gov/sra?term=ERP000601">ERP000601</a> </p> </li> <li class="c-article-data-availability-list__item"> <p> <a href="http://www.ncbi.nlm.nih.gov/sra?term=ERP000602">ERP000602</a> </p> </li> </ul> <h3 class="c-article__sub-heading">Data deposits</h3> <p>The bonobo genome assembly has been deposited with the International Nucleotide Sequence Database Collaboration (DDBJ/EMBL/GenBank) under the EMBL accession number AJFE01000000. 454 shotgun data of Ulindi have been made available through the NCBI Sequence Read Archive under study ID <a href="http://www.ncbi.nlm.nih.gov/sra?term=ERP000601">ERP000601</a>; Illumina sequences of 19 chimpanzee and bonobo individuals are available under study ID <a href="http://www.ncbi.nlm.nih.gov/sra?term=ERP000602">ERP000602</a>.</p> </div></div></section><div id="MagazineFulltextArticleBodySuffix"><section aria-labelledby="Bib1" data-title="References"><div class="c-article-section" id="Bib1-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="Bib1">References</h2><div class="c-article-section__content" id="Bib1-content"><div data-container-section="references"><ol class="c-article-references" data-track-component="outbound reference" data-track-context="references section"><li class="c-article-references__item js-c-reading-companion-references-item" data-counter="1"><p class="c-article-references__text" id="ref-CR1">Boesch, C., Hohmann, G. & Marchant, L. <i>Behavioural Diversity in Chimpanzees and Bonobos</i> (Cambridge Univ. 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We thank D. Reich and L. Vigilant for comments; the 454 Sequencing Center, the MPI-EVA sequencing group, M. Kircher, M. Rampp and M. Halbwax for technical support; the staff of Zoo Leipzig (Germany), the Ngamba Island Chimpanzee Sanctuary (Entebbe, Uganda), the Tchimpounga Chimpanzee Rehabilitation Center (Pointe-Noire, Republic of Congo) and the Lola ya Bonobo bonobo sanctuary (Kinshasa, Democratic Republic of Congo) for providing samples; and A. Navarro, E. Gazave and C. Baker for performing the ArrayCGH hybridizations. The ape distribution layers for <a data-track="click" data-track-label="link" data-track-action="figure anchor" href="/articles/nature11128#Fig1">Fig. 1a</a> were provided by UNEP-WCMC and IUCN.2008 (IUCN Red List of Threatened Species, Version 2011.2, <a href="http://www.iucnredlist.org">http://www.iucnredlist.org</a>). The National Institutes of Health provided funding for J.R.M., B.W., S.K., G.S. (2R01GM077117-04A1), J.C.M. (Intramural Research Program of the National Human Genome Research Institute) and E.E.E. (HG002385). E.E.E is an Investigator of the Howard Hughes Medical Institute. T.M.-B. was supported by a Ramón y Cajal grant (MICINN-RYC 2010) and an ERC Starting Grant (StG_20091118); D.E.S., K.A. and S.H. were supported by the Ohio State University Comprehensive Cancer Center, the Ohio Supercomputer Center (#PAS0425) and the Ohio Cancer Research Associates (GRT00024299); and G.L. was supported by a Wellcome Trust grant (090532/Z/09/Z). The US National Science Foundation provided an International Postdoctoral Fellowship (OISE-0754461) to J.M.G. The Danish Council for Independent Research | Natural Sciences (grant no. 09-062535) provided funding for K.M. and M.H.S.</p></div></div></section><section aria-labelledby="author-information" data-title="Author information"><div class="c-article-section" id="author-information-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="author-information">Author information</h2><div class="c-article-section__content" id="author-information-content"><span class="c-article-author-information__subtitle u-visually-hidden" id="author-notes">Author notes</span><ol class="c-article-author-information__list"><li class="c-article-author-information__item" id="nAff23"><p class="c-article-author-information__authors-list">Can Alkan</p><p class="js-present-address">Present address: Present address: Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey., </p></li></ol><h3 class="c-article__sub-heading" id="affiliations">Authors and Affiliations</h3><ol class="c-article-author-affiliation__list"><li id="Aff1"><p class="c-article-author-affiliation__address"> Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany , </p><p class="c-article-author-affiliation__authors-list">Kay Prüfer, Michael Siebauer, Jeffrey M. Good, Anne Fischer, Susan E. Ptak, Michael Lachmann, Aida M. Andrés, Janet Kelso & Svante Pääbo</p></li><li id="Aff2"><p class="c-article-author-affiliation__address"> Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark , </p><p class="c-article-author-affiliation__authors-list">Kasper Munch, Asger Hobolth, Julien Dutheil, Thomas Mailund & Mikkel H. Schierup</p></li><li id="Aff3"><p class="c-article-author-affiliation__address"> Max F. Perutz Laboratories, University Vienna, A-1030 Vienna, Austria , </p><p class="c-article-author-affiliation__authors-list">Ines Hellmann</p></li><li id="Aff4"><p class="c-article-author-affiliation__address">Human Cancer Genetics Program and Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, 43210, Ohio, USA</p><p class="c-article-author-affiliation__authors-list">Keiko Akagi & David E. Symer</p></li><li id="Aff5"><p class="c-article-author-affiliation__address">J. Craig Venter Institute, Rockville, 20850, Maryland, USA</p><p class="c-article-author-affiliation__authors-list">Jason R. Miller, Brian Walenz & Granger Sutton</p></li><li id="Aff6"><p class="c-article-author-affiliation__address">University of Maryland, College Park, Maryland, 20742, USA</p><p class="c-article-author-affiliation__authors-list">Sergey Koren</p></li><li id="Aff7"><p class="c-article-author-affiliation__address">454 Life Sciences, Branford, 06405, Connecticut, USA</p><p class="c-article-author-affiliation__authors-list">Chinnappa Kodira, Roger Winer & James R. Knight</p></li><li id="Aff8"><p class="c-article-author-affiliation__address">Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA</p><p class="c-article-author-affiliation__authors-list">James C. Mullikin</p></li><li id="Aff9"><p class="c-article-author-affiliation__address">Department of Physiology, MRC Functional Genomics Unit, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK, </p><p class="c-article-author-affiliation__authors-list">Stephen J. Meader & Chris P. Ponting</p></li><li id="Aff10"><p class="c-article-author-affiliation__address"> The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK , </p><p class="c-article-author-affiliation__authors-list">Gerton Lunter</p></li><li id="Aff11"><p class="c-article-author-affiliation__address"> Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa 226-8503, Japan , </p><p class="c-article-author-affiliation__authors-list">Saneyuki Higashino</p></li><li id="Aff12"><p class="c-article-author-affiliation__address">Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, 98195, Washington, USA</p><p class="c-article-author-affiliation__authors-list">Emre Karakoç, Can Alkan, Saba Sajjadian, Mario Ventura, Tomas Marques-Bonet & Evan E. Eichler</p></li><li id="Aff13"><p class="c-article-author-affiliation__address">Sezione di Genetica-Dipartimento di Anatomia Patologica e Genetica, University of Bari, I-70125 Bari, Italy, </p><p class="c-article-author-affiliation__authors-list">Claudia Rita Catacchio & Mario Ventura</p></li><li id="Aff14"><p class="c-article-author-affiliation__address"> ICREA, Institut de Biologia Evolutiva (UPF-CSIC), 08003 Barcelona, Catalonia, Spain , </p><p class="c-article-author-affiliation__authors-list">Tomas Marques-Bonet</p></li><li id="Aff15"><p class="c-article-author-affiliation__address"> Lola Ya Bonobo Bonobo Sanctuary, “Petites Chutes de la Lukaya”, Kinshasa, Democratic Republic of Congo , </p><p class="c-article-author-affiliation__authors-list">Claudine André</p></li><li id="Aff16"><p class="c-article-author-affiliation__address">Réserve Naturelle Sanctuaire à Chimpanzés de Tchimpounga, Jane Goodall Institute, Pointe-Noire, Republic of Congo</p><p class="c-article-author-affiliation__authors-list">Rebeca Atencia</p></li><li id="Aff17"><p class="c-article-author-affiliation__address">Chimpanzee Sanctuary and Wildlife Conservation Trust (CSWCT), Entebbe, Uganda</p><p class="c-article-author-affiliation__authors-list">Lawrence Mugisha</p></li><li id="Aff18"><p class="c-article-author-affiliation__address"> Zoo Leipzig, D-04105 Leipzig, Germany , </p><p class="c-article-author-affiliation__authors-list">Jörg Junhold</p></li><li id="Aff19"><p class="c-article-author-affiliation__address">Department of Genetics, Harvard Medical School, Boston, 02115, Massachusetts, USA</p><p class="c-article-author-affiliation__authors-list">Nick Patterson</p></li><li id="Aff20"><p class="c-article-author-affiliation__address">Division of Biological Sciences, University of Montana, Missoula, 59812, Montana, USA</p><p class="c-article-author-affiliation__authors-list">Jeffrey M. Good</p></li><li id="Aff21"><p class="c-article-author-affiliation__address"> International Center for Insect Physiology and Ecology, 00100 Nairobi, Kenya , </p><p class="c-article-author-affiliation__authors-list">Anne Fischer</p></li><li id="Aff22"><p class="c-article-author-affiliation__address">Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark, </p><p class="c-article-author-affiliation__authors-list">Mikkel H. 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Alkan, S.S., C.R.C., M.V., T.M.-B., E.E.E., N.P., M.S., J.M.G., A.F., S.E.P., M.L., D.E.S., T.M., M.H.S., A.M.A., J.K. and S.P. analysed genetic data. C. André, R.A., L.M. and J.J. provided samples. K.P., J.K. and S.P. wrote the manuscript.</p><h3 class="c-article__sub-heading" id="corresponding-author">Corresponding authors</h3><p id="corresponding-author-list">Correspondence to <a id="corresp-c1" href="mailto:pruefer@eva.mpg.de">Kay Prüfer</a> or <a id="corresp-c2" href="mailto:paabo@eva.mpg.de">Svante Pääbo</a>.</p></div></div></section><section data-title="Ethics declarations"><div class="c-article-section" id="ethics-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="ethics">Ethics declarations</h2><div class="c-article-section__content" id="ethics-content"> <h3 class="c-article__sub-heading">Competing interests</h3> <p>C.K., R.W. and J.R.K. are employees of Roche/454 Life sciences, which developed the technology used for the sequencing of the genome studied here.</p> </div></div></section><section data-title="Supplementary information"><div class="c-article-section" id="Sec3-section"><h2 class="c-article-section__title js-section-title js-c-reading-companion-sections-item" id="Sec3">Supplementary information</h2><div class="c-article-section__content" id="Sec3-content"><div data-test="supplementary-info"><div id="figshareContainer" class="c-article-figshare-container" data-test="figshare-container"></div><div class="c-article-supplementary__item" data-test="supp-item" id="MOESM240"><h3 class="c-article-supplementary__title u-h3"><a class="print-link" data-track="click" data-track-action="view supplementary info" data-test="supp-info-link" data-track-label="supplementary information" href="https://static-content.springer.com/esm/art%3A10.1038%2Fnature11128/MediaObjects/41586_2012_BFnature11128_MOESM240_ESM.pdf" data-supp-info-image="">Supplementary Information</a></h3><div class="c-article-supplementary__description" data-component="thumbnail-container"><p>This file contains Supplementary Text and Data sections 1-12, which include Supplementary Figures, Supplementary Tables and Supplementary References (see Contents for details). 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