882 lines
149 KiB
XML
882 lines
149 KiB
XML
<document ID-DOI="10.1016/j.cub.2017.09.047" ID-GBIF-Dataset="5229b2b3-ff60-40cf-878e-d570f65cf83f" ID-GBIF-Taxon="137239044" ID-Zenodo-Dep="1041345" LSID="urn:lsid:zoobank.org:act:A02FD225-ACFB-4CBE-A408-325CE2062E83" checkinTime="1509703394621" checkinUser="plazi" docAuthor="Alexander Nater, Maja P. Mattle-Greminger, Anton Nurcahyo, Matthew G. Nowak, Marc de Manuel, Tariq Desai, Colin Groves, Marc Pybus, Tugce Bilgin Sonay, Christian Roos, Adriano R. Lameira, Serge A. Wich, James Askew, Marina Davila-Ross, Gabriella Fredriksson, Guillem de Valles, Ferran Casals, avier Prado-Martinez, Benoit Goossens, Ernst J. Verschoor, Kristin S. Warren, Ian Singleton, David A. Marques, Joko Pamungkas, Dyah Perwitasari-Farajallah, Puji Rianti, Augustine Tuuga, Ivo G. Gut, Marta Gut, Pablo Orozco-terWengel, Carel P. van Schaik, Jaume Bertranpetit, Maria Anisimova, Aylwyn Scally, Tomas Marques-Bonet, Erik Meijaard & Michael Krüzen" docDate="2017" docId="03D987EAFFB0C332FF6212BFFCD3BB98" docLanguage="en" docName="currentBiology.27.1-12.pdf" docOrigin="Current Biology 27" docStyle="DocumentStyle{}" docTitle="Pongo tapanuliensis Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton 2017, sp. nov." docType="treatment" docUuid="A02FD225-ACFB-4CBE-A408-325CE2062E83" docUuidSource="ZooBank" docVersion="9" lastPageId="6" lastPageNumber="7" masterDocId="FFE0FF92FFB1C334FFFD171FFFD8BD4E" masterDocTitle="Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species" masterLastPageNumber="40" masterPageNumber="1" pageId="1" pageNumber="2" updateTime="1635897119265" updateUser="ExternalLinkService">
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<mods:mods xmlns:mods="http://www.loc.gov/mods/v3">
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<mods:titleInfo>
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<mods:title>Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species</mods:title>
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</mods:titleInfo>
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||
<mods:name type="personal">
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||
<mods:role>
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||
<mods:roleTerm>Author</mods:roleTerm>
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||
</mods:role>
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<mods:namePart>Alexander Nater</mods:namePart>
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||
</mods:name>
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<mods:name type="personal">
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||
<mods:role>
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||
<mods:roleTerm>Author</mods:roleTerm>
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||
</mods:role>
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||
<mods:namePart>Maja P. Mattle-Greminger</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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||
<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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||
</mods:role>
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<mods:namePart>Anton Nurcahyo</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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||
</mods:role>
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<mods:namePart>Matthew G. Nowak</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Marc de Manuel</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Tariq Desai</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Colin Groves</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Marc Pybus</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Tugce Bilgin Sonay</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Christian Roos</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Adriano R. Lameira</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Serge A. Wich</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>James Askew</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Marina Davila-Ross</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Gabriella Fredriksson</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Guillem de Valles</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Ferran Casals</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>avier Prado-Martinez</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Benoit Goossens</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Ernst J. Verschoor</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Kristin S. Warren</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Ian Singleton</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>David A. Marques</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Joko Pamungkas</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Dyah Perwitasari-Farajallah</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Puji Rianti</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Augustine Tuuga</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Ivo G. Gut</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Marta Gut</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Pablo Orozco-terWengel</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Carel P. van Schaik</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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||
</mods:role>
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<mods:namePart>Jaume Bertranpetit</mods:namePart>
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</mods:name>
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||
<mods:name type="personal">
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||
<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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||
</mods:role>
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<mods:namePart>Maria Anisimova</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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||
</mods:role>
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<mods:namePart>Aylwyn Scally</mods:namePart>
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||
</mods:name>
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<mods:name type="personal">
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<mods:role>
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||
<mods:roleTerm>Author</mods:roleTerm>
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||
</mods:role>
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||
<mods:namePart>Tomas Marques-Bonet</mods:namePart>
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||
</mods:name>
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<mods:name type="personal">
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||
<mods:role>
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||
<mods:roleTerm>Author</mods:roleTerm>
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||
</mods:role>
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||
<mods:namePart>Erik Meijaard</mods:namePart>
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||
</mods:name>
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||
<mods:name type="personal">
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||
<mods:role>
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||
<mods:roleTerm>Author</mods:roleTerm>
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||
</mods:role>
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||
<mods:namePart>Michael Krüzen</mods:namePart>
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||
</mods:name>
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<mods:typeOfResource>text</mods:typeOfResource>
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<mods:relatedItem type="host">
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<mods:titleInfo>
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||
<mods:title>Current Biology</mods:title>
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||
</mods:titleInfo>
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||
<mods:part>
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||
<mods:date>2017</mods:date>
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||
<mods:detail type="pubDate">
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||
<mods:number>2017-11-01</mods:number>
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||
</mods:detail>
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||
<mods:detail type="volume">
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||
<mods:number>27</mods:number>
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||
</mods:detail>
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||
<mods:extent unit="page">
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||
<mods:start>1</mods:start>
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<mods:end>40</mods:end>
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</mods:extent>
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||
</mods:part>
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||
</mods:relatedItem>
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||
<mods:classification>journal article</mods:classification>
|
||
<mods:identifier type="DOI">10.1016/j.cub.2017.09.047</mods:identifier>
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||
<mods:identifier type="GBIF-Dataset">5229b2b3-ff60-40cf-878e-d570f65cf83f</mods:identifier>
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||
<mods:identifier type="Zenodo-Dep">1041345</mods:identifier>
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||
<mods:identifier type="ZooBank">68FBFE28-103C-4E95-89BD-974A70D026F7</mods:identifier>
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</mods:mods>
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<treatment ID-GBIF-Taxon="137239044" LSID="urn:lsid:zoobank.org:act:A02FD225-ACFB-4CBE-A408-325CE2062E83" httpUri="http://treatment.plazi.org/id/03D987EAFFB0C332FF6212BFFCD3BB98" lastPageId="6" lastPageNumber="7" pageId="1" pageNumber="2">
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<subSubSection pageId="1" pageNumber="2" type="nomenclature">
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||
<paragraph blockId="1.[159,797,1382,1520]" pageId="1" pageNumber="2">
|
||
<taxonomicName authority="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton, 2017" authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[159,363,1440,1461]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="1" pageNumber="2" phylum="Chordata" rank="species" species="tapanuliensis" status="sp. nov.">
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<emphasis box="[159,363,1440,1461]" italics="true" pageId="1" pageNumber="2">Pongo tapanuliensis</emphasis>
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||
</taxonomicName>
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<taxonomicNameLabel box="[370,453,1440,1461]" pageId="1" pageNumber="2" rank="species">sp. nov.</taxonomicNameLabel>
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||
Nurcahyo, Meijaard, Nowak, Fredriksson & Groves.
|
||
</paragraph>
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||
</subSubSection>
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||
<subSubSection box="[159,366,1499,1520]" pageId="1" pageNumber="2" type="vernacular_names">
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||
<paragraph blockId="1.[159,797,1382,1520]" box="[159,366,1499,1520]" pageId="1" pageNumber="2">Tapanuli Orangutan.</paragraph>
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||
</subSubSection>
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||
<subSubSection pageId="1" pageNumber="2" type="etymology">
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||
<paragraph blockId="1.[159,797,1557,1666]" box="[159,277,1557,1578]" pageId="1" pageNumber="2">
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||
<heading bold="true" box="[159,277,1557,1578]" fontSize="8" level="10" pageId="1" pageNumber="2" reason="6">
|
||
<emphasis bold="true" box="[159,277,1557,1578]" pageId="1" pageNumber="2">Etymology</emphasis>
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||
</heading>
|
||
</paragraph>
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||
<paragraph blockId="1.[159,797,1557,1666]" pageId="1" pageNumber="2">
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||
The species name refers to three North Sumatran districts (North, Central, and South Tapanuli) to which
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||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[637,797,1616,1637]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="1" pageNumber="2" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[637,797,1616,1637]" italics="true" pageId="1" pageNumber="2">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
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||
is endemic.
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection pageId="1" pageNumber="2" type="materials_examined">
|
||
<materialsCitation ID-GBIF-Occurrence="3396424301" collectingDate="2013-11" collectionCode="Museum Zoologicum Bogoriense" country="Indonesia" httpUri="http://morphobank.org/permalink/?P2591" latitude="1.598361" location="near Sugi Tonga, Marancar, Tapanuli (Batang Toru) Forest Complex" longLatPrecision="1" longitude="99.27681" municipality="Indonesia" pageId="1" pageNumber="2" specimenCode="MZB39182" specimenCount="2" specimenCount-adult="1" specimenCount-male="1" stateProvince="South Tapanuli District" typeStatus="holotype">
|
||
<paragraph blockId="1.[159,798,1703,1987]" box="[159,259,1703,1724]" pageId="1" pageNumber="2">
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||
<heading bold="true" box="[159,259,1703,1724]" fontSize="8" level="10" pageId="1" pageNumber="2" reason="6">
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||
<emphasis bold="true" box="[159,259,1703,1724]" pageId="1" pageNumber="2">
|
||
<typeStatus box="[159,259,1703,1724]" pageId="1" pageNumber="2">Holotype</typeStatus>
|
||
</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="1.[159,798,1703,1987]" pageId="1" pageNumber="2">
|
||
The complete skeleton of an
|
||
<specimenCount box="[472,522,1733,1754]" pageId="1" pageNumber="2" type="adult">adult</specimenCount>
|
||
<specimenCount box="[532,581,1733,1754]" pageId="1" pageNumber="2" type="male">male</specimenCount>
|
||
orangutan that died from wounds sustained by local villagers in
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||
<date box="[631,797,1762,1783]" pageId="1" pageNumber="2" value="2013-11">
|
||
<collectingDate box="[631,797,1762,1783]" pageId="1" pageNumber="2" value="2013-11">November 2013</collectingDate>
|
||
</date>
|
||
<location LSID="urn:lsid:plazi:treatment:03D987EAFFB0C332FF6212BFFCD3BB98:8EAF6027FFB0C335FF6211E0FF22BA7F" country="Indonesia" latitude="1.598361" longLatPrecision="1" longitude="99.27681" municipality="Indonesia" name="near Sugi Tonga, Marancar, Tapanuli (Batang Toru) Forest Complex" pageId="1" pageNumber="2" stateProvince="South Tapanuli District">near Sugi Tonga, Marancar, Tapanuli (Batang Toru) Forest Complex</location>
|
||
(
|
||
<geoCoordinate box="[267,392,1820,1841]" degrees="1" direction="north" minutes="35" orientation="latitude" pageId="1" pageNumber="2" precision="1" seconds="54.1" value="1.598361">1 35’54.1’’N</geoCoordinate>
|
||
,
|
||
<geoCoordinate box="[403,541,1820,1841]" degrees="99" direction="east" minutes="16" orientation="longitude" pageId="1" pageNumber="2" precision="1" seconds="36.5" value="99.27681">99 16’36.5’’E</geoCoordinate>
|
||
),
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||
<collectingRegion box="[558,795,1820,1841]" pageId="1" pageNumber="2">South Tapanuli District</collectingRegion>
|
||
,
|
||
<collectingRegion box="[159,311,1849,1870]" country="Indonesia" name="Sumatera Utara" pageId="1" pageNumber="2">North Sumatra</collectingRegion>
|
||
,
|
||
<collectingMunicipality box="[321,423,1849,1870]" pageId="1" pageNumber="2">Indonesia</collectingMunicipality>
|
||
. Skull and postcranium are lodged in the
|
||
<collectionCode box="[199,540,1879,1900]" pageId="1" pageNumber="2">Museum Zoologicum Bogoriense</collectionCode>
|
||
,
|
||
<collectingCountry box="[550,652,1879,1900]" name="Indonesia" pageId="1" pageNumber="2">Indonesia</collectingCountry>
|
||
, under accession number
|
||
<specimenCode box="[303,418,1908,1929]" pageId="1" pageNumber="2">MZB39182</specimenCode>
|
||
. High-resolution 3D reconstructions of the skull and mandible are available from MorphoBank, http://morphobank.org/permalink/?P2591.
|
||
</paragraph>
|
||
</materialsCitation>
|
||
<materialsCitation ID-GBIF-Occurrence="3395934301" collectionCode="M, P" country="Indonesia" latitude="1.6858612" location="North Tapanuli District, North Sumatra" longLatPrecision="1" longitude="98.99391" pageId="1" pageNumber="2" specimenCode="(P2591, M435788, P2591, M435790" specimenCount="1" specimenCount-adult="1" stateProvince="North Tapanuli District, North Sumatra" typeStatus="paratype">
|
||
<paragraph blockId="1.[829,1467,1090,1257]" box="[829,942,1090,1111]" pageId="1" pageNumber="2">
|
||
<heading bold="true" box="[829,942,1090,1111]" fontSize="8" level="10" pageId="1" pageNumber="2" reason="6">
|
||
<emphasis bold="true" box="[829,942,1090,1111]" pageId="1" pageNumber="2">
|
||
<typeStatus box="[829,942,1090,1111]" pageId="1" pageNumber="2">Paratypes</typeStatus>
|
||
</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="1.[829,1467,1090,1257]" pageId="1" pageNumber="2">
|
||
<specimenCount box="[829,881,1119,1140]" pageId="1" pageNumber="2" type="adult">Adult</specimenCount>
|
||
individuals of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[1037,1198,1119,1140]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="1" pageNumber="2" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[1037,1198,1119,1140]" italics="true" pageId="1" pageNumber="2">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
<specimenCode box="[1208,1278,1119,1140]" pageId="1" pageNumber="2">(P2591</specimenCode>
|
||
-
|
||
<specimenCode box="[1284,1386,1119,1140]" pageId="1" pageNumber="2">M435788</specimenCode>
|
||
–
|
||
<specimenCode box="[1396,1461,1119,1140]" pageId="1" pageNumber="2">P2591</specimenCode>
|
||
-
|
||
<specimenCode box="[829,924,1148,1169]" pageId="1" pageNumber="2">M435790</specimenCode>
|
||
) photographed by Tim Laman in the Batang Toru Forest Complex (
|
||
<geoCoordinate box="[1002,1115,1177,1198]" degrees="1" direction="north" minutes="41" orientation="latitude" pageId="1" pageNumber="2" precision="1" seconds="9.1" value="1.6858612">1 41’9.1’’N</geoCoordinate>
|
||
,
|
||
<geoCoordinate box="[1122,1260,1177,1198]" degrees="98" direction="east" minutes="59" orientation="longitude" pageId="1" pageNumber="2" precision="1" seconds="38.1" value="98.99391">98 59’38.1’’E</geoCoordinate>
|
||
),
|
||
<collectingRegion pageId="1" pageNumber="2">North Tapanuli District, North Sumatra</collectingRegion>
|
||
,
|
||
<collectingCountry box="[1053,1155,1206,1227]" name="Indonesia" pageId="1" pageNumber="2">Indonesia</collectingCountry>
|
||
. Paratypes are available from MorphoBank at http://morphobank.org/permalink/?P2591.
|
||
</paragraph>
|
||
</materialsCitation>
|
||
</subSubSection>
|
||
<subSubSection lastPageId="2" lastPageNumber="3" pageId="1" pageNumber="2" type="diagnosis">
|
||
<paragraph blockId="1.[829,1468,1294,1987]" box="[829,1073,1294,1315]" pageId="1" pageNumber="2">
|
||
<heading bold="true" box="[829,1073,1294,1315]" fontSize="8" level="10" pageId="1" pageNumber="2" reason="6">
|
||
<emphasis bold="true" box="[829,1073,1294,1315]" pageId="1" pageNumber="2">Differential Diagnosis</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="1.[829,1468,1294,1987]" pageId="1" pageNumber="2">
|
||
We compared the holotype to a comprehensive comparative dataset of 33 adult male orangutans from ten institutions housing osteological specimens. Summary statistics for all measurements are listed in
|
||
<tableCitation box="[1092,1223,1411,1432]" captionStart="Table S" captionStartId="27.[189,261,542,568]" captionTargetBox="[189,2048,616,1570]" captionTargetPageId="27" captionText="Table S 1. Summary statistics for the cranio-mandibular variables utilized in this study [mm]. Related to Figure 1 B." httpUri="http://table.plazi.org/id/DF0F6674FFAAC32FFF401501F984BF79" pageId="1" pageNumber="2" tableUuid="DF0F6674FFAAC32FFF401501F984BF79">Tables S1–S</tableCitation>
|
||
<tableCitation box="[1224,1238,1411,1432]" captionStart="Table S" captionStartId="31.[192,264,200,226]" captionTargetBox="[192,1375,330,1544]" captionText="Table S 3. Summary statistics for the 15 long call variables utilized in this study. Related to STAR Methods." httpUri="http://table.plazi.org/id/DF0F6674FFAEC32BFF3D17D7FE52BC46" pageId="1" pageNumber="2" tableUuid="DF0F6674FFAEC32BFF3D17D7FE52BC46">3</tableCitation>
|
||
.
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[1257,1466,1411,1432]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="1" pageNumber="2" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[1257,1466,1411,1432]" italics="true" pageId="1" pageNumber="2">Pongo tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
differs from all extant orangutans in the breadth of the upper canine (21.5 versus <20.9 mm), the shallow face depth (6.0 versus>8.4 mm), the narrower interpterygoid distance (at posterior end of pterygoids 33.8 versus>43.9 mm; at anterior end of pterygoids, 33.7 versus>43.0 mm), the shorter tympanic tube (23.9 versus>28.4 mm, mostly>30 mm), the shorter temporomandibular joint (22.5 versus>24.7 mm), the narrower maxillary incisor row (28.3 versus>30.1 mm), the narrower distance across the palate at the first molars (62.7 versus>65.7 mm), the shorter horizontal length of the mandibular symphysis (49.3 versus>53.7 mm), the smaller inferior transverse torus (horizontal length from anterior surface of symphysis 31.8 compared to>36.0 mm), and the width of the ascending ramus of the mandible (55.9 versus>56.3 mm).
|
||
</paragraph>
|
||
<paragraph blockId="1.[829,1468,1294,1987]" lastBlockId="2.[142,780,1586,1987]" lastPageId="2" lastPageNumber="3" pageId="1" pageNumber="2">
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[851,1050,1849,1870]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="1" pageNumber="2" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[851,1050,1849,1870]" italics="true" pageId="1" pageNumber="2">Pongo tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
differs specifically from
|
||
<emphasis box="[1282,1358,1849,1870]" italics="true" pageId="1" pageNumber="2">P.abelii</emphasis>
|
||
by its deep suborbital fossa, triangular pyriform aperture, and angled facial profile; the longer nuchal surface (70.5 versus <64.7 mm); the wider rostrum, posterior to the canines (59.9 versus <59 mm); the narrower orbits (33.8 versus <34.6 mm); the shorter (29.2 versus>30.0 mm) and narrower (23.2 versus>23.3 mm) foramen magnum; the narrower bicondylar breadth (120.0 versus>127.2 mm); the narrower mandibular incisor row (24.4 versus>28.3 mm); and the greater mesio-distal length of the upper canine (19.4 versus <17.6 mm). The male long call has a higher maximum frequency range of the roar pulse type (>800 versus <747 Hz) with a higher ‘‘shape’’ (>952 versus <934 Hz/s).
|
||
</paragraph>
|
||
<caption httpUri="https://zenodo.org/record/1041353/files/figure.png" pageId="2" pageNumber="3" targetBox="[142,1608,0,1387]" targetPageId="2">
|
||
<paragraph blockId="2.[142,1450,1428,1547]" pageId="2" pageNumber="3">
|
||
Figure 1. Morphological Evidence Supporting a New Orangutan Species (A) Current distribution of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[353,519,1454,1471]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="2" pageNumber="3" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[353,519,1454,1471]" italics="true" pageId="2" pageNumber="3">Pongo tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
on Sumatra. The holotype locality is marked with a red star. The area shown in the map is indicated in
|
||
<figureCitation box="[1365,1446,1454,1471]" captionStart="Figure 2" captionStartId="4.[142,202,1189,1208]" captionTargetBox="[142,1608,0,1149]" captionTargetId="figure@4.[151,1439,271,1150]" captionTargetPageId="4" captionText="Figure 2. Distribution, Genomic Diversity, and Population Structure of the Genus Pongo (A) Sampling areas across the current distribution of orangutans. The contour indicates the extent of the exposed Sunda Shelf during the Last Glacial Maximum. The black rectangle delimits the area shown in Figure 1 A. n indicates the number of sequenced individuals. See also Table S 4. (B) PCA of genomic diversity in Pongo. Axis labels show the percentages of the total variance explained by the first two principal components. Colored bars in the insert represent the distribution of nucleotide diversity in genome-wide 1 - Mb windows across sampling areas. (C) Bayesian clustering analysis of population structure using the program ADMIXTURE. Each vertical bar depicts an individual, with colors representing the inferred ancestry proportions with different assumed numbers of genetic clusters (K, horizontal sections)." httpUri="https://zenodo.org/record/1041355/files/figure.png" pageId="2" pageNumber="3">Figure 2A</figureCitation>
|
||
. (B) Holotype skull and mandible of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[432,561,1479,1496]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="2" pageNumber="3" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[432,561,1479,1496]" italics="true" pageId="2" pageNumber="3">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
from a recently deceased individual from Batang Toru. See also
|
||
<figureCitation box="[1101,1181,1479,1496]" captionStart="Figure 1" captionStartId="2.[142,202,1428,1447]" captionTargetBox="[142,1608,0,1387]" captionTargetId="figure@2.[150,1441,271,1388]" captionTargetPageId="2" captionText="Figure 1. Morphological Evidence Supporting a New Orangutan Species (A) Current distribution of Pongo tapanuliensis on Sumatra. The holotype locality is marked with a red star. The area shown in the map is indicated in Figure 2 A. (B) Holotype skull and mandible of P. tapanuliensis from a recently deceased individual from Batang Toru. See also Figure S 1 and Tables S 1 and S 2. (C) Violin plots of the first seven principal components of 26 cranio-mandibular morphological variables of eight north Sumatran P. abelii and 19 Bornean P. pygmaeus individuals of similar developmental state as the P. tapanuliensis holotype skull (black horizontal lines). See also Figure S 2." httpUri="https://zenodo.org/record/1041353/files/figure.png" pageId="2" pageNumber="3">Figure S1</figureCitation>
|
||
and
|
||
<tableCitation box="[1222,1306,1479,1496]" captionStart="Table S" captionStartId="27.[189,261,542,568]" captionTargetBox="[189,2048,616,1570]" captionTargetPageId="27" captionText="Table S 1. Summary statistics for the cranio-mandibular variables utilized in this study [mm]. Related to Figure 1 B." httpUri="http://table.plazi.org/id/DF0F6674FFAAC32FFF401501F984BF79" pageId="2" pageNumber="3" tableUuid="DF0F6674FFAAC32FFF401501F984BF79">Tables S1</tableCitation>
|
||
and S
|
||
<tableCitation box="[1359,1369,1479,1496]" captionStart="Table S" captionStartId="30.[192,264,200,226]" captionTargetBox="[192,1375,311,1641]" captionText="Table S 2. Summary statistics for the dental variables utilized in this study [mm]. Related to Figure 1 B." httpUri="http://table.plazi.org/id/DF0F6674FFAFC32AFF3D17D7FE9CBC46" pageId="2" pageNumber="3" tableUuid="DF0F6674FFAFC32AFF3D17D7FE9CBC46">2</tableCitation>
|
||
. (C) Violin plots of the first seven principal components of 26 cranio-mandibular morphological variables of eight north Sumatran
|
||
<emphasis box="[1238,1305,1504,1521]" italics="true" pageId="2" pageNumber="3">P. abelii</emphasis>
|
||
and 19 Bornean
|
||
<emphasis box="[142,249,1530,1547]" italics="true" pageId="2" pageNumber="3">P. pygmaeus</emphasis>
|
||
individuals of similar developmental state as the
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[658,788,1530,1547]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="2" pageNumber="3" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[658,788,1530,1547]" italics="true" pageId="2" pageNumber="3">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
holotype skull (black horizontal lines). See also
|
||
<figureCitation box="[1184,1264,1530,1547]" captionStart="Figure 2" captionStartId="4.[142,202,1189,1208]" captionTargetBox="[142,1608,0,1149]" captionTargetId="figure@4.[151,1439,271,1150]" captionTargetPageId="4" captionText="Figure 2. Distribution, Genomic Diversity, and Population Structure of the Genus Pongo (A) Sampling areas across the current distribution of orangutans. The contour indicates the extent of the exposed Sunda Shelf during the Last Glacial Maximum. The black rectangle delimits the area shown in Figure 1 A. n indicates the number of sequenced individuals. See also Table S 4. (B) PCA of genomic diversity in Pongo. Axis labels show the percentages of the total variance explained by the first two principal components. Colored bars in the insert represent the distribution of nucleotide diversity in genome-wide 1 - Mb windows across sampling areas. (C) Bayesian clustering analysis of population structure using the program ADMIXTURE. Each vertical bar depicts an individual, with colors representing the inferred ancestry proportions with different assumed numbers of genetic clusters (K, horizontal sections)." httpUri="https://zenodo.org/record/1041355/files/figure.png" pageId="2" pageNumber="3">Figure S2</figureCitation>
|
||
.
|
||
</paragraph>
|
||
</caption>
|
||
<paragraph blockId="2.[142,780,1586,1987]" pageId="2" pageNumber="3">
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[164,364,1820,1841]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="2" pageNumber="3" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[164,364,1820,1841]" italics="true" pageId="2" pageNumber="3">Pongo tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
differs from
|
||
<emphasis box="[486,616,1820,1841]" italics="true" pageId="2" pageNumber="3">P. pygmaeus</emphasis>
|
||
by possessing a nearly straight zygomaxillary suture and lower orbit (orbit height 33.4 versus>35.3 mm); the male long call has a longer duration (>111 versus <90 s) with a greater number of pulses (>52 versus <45 pulses), and is delivered at a greater rate (>0.82 versus <0.79 pulses per 20 s).
|
||
</paragraph>
|
||
<paragraph blockId="2.[811,1449,1586,1724]" pageId="2" pageNumber="3">
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[834,1042,1586,1607]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="2" pageNumber="3" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[834,1042,1586,1607]" italics="true" pageId="2" pageNumber="3">Pongo tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
differs specifically from
|
||
<emphasis italics="true" pageId="2" pageNumber="3">
|
||
<taxonomicName authorityName="Lacepede" authorityYear="1799" box="[1313,1379,1586,1607]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="2" pageNumber="3" phylum="Chordata" rank="genus">Pongo</taxonomicName>
|
||
‘‘pygmaeus’’ palaeosumatrensis
|
||
</emphasis>
|
||
in the smaller size of the first upper molar (mesio-distal length 13.7 versus>14.0 mm, buccolingual breadth 11.4 versus>12.1 mm, crown area 155.2 versus>175.5 mm2;
|
||
<figureCitation box="[1020,1117,1703,1724]" captionStart="Figure 1" captionStartId="2.[142,202,1428,1447]" captionTargetBox="[142,1608,0,1387]" captionTargetId="figure@2.[150,1441,271,1388]" captionTargetPageId="2" captionText="Figure 1. Morphological Evidence Supporting a New Orangutan Species (A) Current distribution of Pongo tapanuliensis on Sumatra. The holotype locality is marked with a red star. The area shown in the map is indicated in Figure 2 A. (B) Holotype skull and mandible of P. tapanuliensis from a recently deceased individual from Batang Toru. See also Figure S 1 and Tables S 1 and S 2. (C) Violin plots of the first seven principal components of 26 cranio-mandibular morphological variables of eight north Sumatran P. abelii and 19 Bornean P. pygmaeus individuals of similar developmental state as the P. tapanuliensis holotype skull (black horizontal lines). See also Figure S 2." httpUri="https://zenodo.org/record/1041353/files/figure.png" pageId="2" pageNumber="3">Figure S1</figureCitation>
|
||
).
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection lastPageId="3" lastPageNumber="4" pageId="2" pageNumber="3" type="description">
|
||
<paragraph blockId="2.[811,1449,1762,1987]" box="[811,941,1762,1783]" pageId="2" pageNumber="3">
|
||
<heading bold="true" box="[811,941,1762,1783]" fontSize="8" level="10" pageId="2" pageNumber="3" reason="6">
|
||
<emphasis bold="true" box="[811,941,1762,1783]" pageId="2" pageNumber="3">Description</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="2.[811,1449,1762,1987]" lastBlockId="3.[159,798,271,555]" lastPageId="3" lastPageNumber="4" pageId="2" pageNumber="3">
|
||
Craniometrically, the type skull of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[1153,1310,1791,1812]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="2" pageNumber="3" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[1153,1310,1791,1812]" italics="true" pageId="2" pageNumber="3">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
(
|
||
<figureCitation box="[1323,1420,1791,1812]" captionStart="Figure 1" captionStartId="2.[142,202,1428,1447]" captionTargetBox="[142,1608,0,1387]" captionTargetId="figure@2.[150,1441,271,1388]" captionTargetPageId="2" captionText="Figure 1. Morphological Evidence Supporting a New Orangutan Species (A) Current distribution of Pongo tapanuliensis on Sumatra. The holotype locality is marked with a red star. The area shown in the map is indicated in Figure 2 A. (B) Holotype skull and mandible of P. tapanuliensis from a recently deceased individual from Batang Toru. See also Figure S 1 and Tables S 1 and S 2. (C) Violin plots of the first seven principal components of 26 cranio-mandibular morphological variables of eight north Sumatran P. abelii and 19 Bornean P. pygmaeus individuals of similar developmental state as the P. tapanuliensis holotype skull (black horizontal lines). See also Figure S 2." httpUri="https://zenodo.org/record/1041353/files/figure.png" pageId="2" pageNumber="3">Figure 1B</figureCitation>
|
||
) is significantly smaller than any skull of comparable developmental stage of other orangutans; it falls outside of the interquartile ranges of
|
||
<emphasis box="[910,989,1879,1900]" italics="true" pageId="2" pageNumber="3">P. abelii</emphasis>
|
||
and
|
||
<emphasis box="[1038,1169,1879,1900]" italics="true" pageId="2" pageNumber="3">P. pygmaeus</emphasis>
|
||
for 24 of 39 cranio-mandibular measurements (
|
||
<tableCitation box="[1019,1109,1908,1929]" captionStart="Table S" captionStartId="27.[189,261,542,568]" captionTargetBox="[189,2048,616,1570]" captionTargetPageId="27" captionText="Table S 1. Summary statistics for the cranio-mandibular variables utilized in this study [mm]. Related to Figure 1 B." httpUri="http://table.plazi.org/id/DF0F6674FFAAC32FFF401501F984BF79" pageId="2" pageNumber="3" tableUuid="DF0F6674FFAAC32FFF401501F984BF79">Table S1</tableCitation>
|
||
). A principal-component analysis (PCA) of 26 cranio-mandibular measurements commonly used in primate taxonomic classification [
|
||
<bibRefCitation author="Groves, C. P. & Westwood, C. & Shea, B. T." box="[1202,1217,1966,1987]" journalOrPublisher="J. Hum. Evol." pageId="2" pageNumber="3" pagination="327 - 340" part="22" refId="ref6550" refString="5. Groves, C. P., Westwood, C., and Shea, B. T. (1992). Unfinished business: Mahalanobis and a clockwork orang. J. Hum. Evol. 22, 327 - 340." title="Unfinished business: Mahalanobis and a clockwork orang" type="journal article" year="1992">5</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="Groves, C. P." box="[1234,1246,1966,1987]" journalOrPublisher="Systematics, Evolution, and Anatomy, D. R. Swindler, and J. Erwin, eds. (Alan R. Liss)" pageId="2" pageNumber="3" pagination="187 - 217" part="1" refId="ref6596" refString="6. Groves, C. P. (1986). Systematics of the great apes. In Comparative Primate Biology, Volume 1: Systematics, Evolution, and Anatomy, D. R. Swindler, and J. Erwin, eds. (Alan R. Liss), pp. 187 - 217." title="Systematics of the great apes. In Comparative Primate Biology" type="journal article" year="1986">6</bibRefCitation>
|
||
] shows consistent differences between
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[385,549,271,292]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[385,549,271,292]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
and the two currently recognized species (
|
||
<figureCitation box="[367,542,300,321]" captionStart="Figure 1" captionStartId="2.[142,202,1428,1447]" captionTargetBox="[142,1608,0,1387]" captionTargetId="figure@2.[150,1441,271,1388]" captionTargetPageId="2" captionText="Figure 1. Morphological Evidence Supporting a New Orangutan Species (A) Current distribution of Pongo tapanuliensis on Sumatra. The holotype locality is marked with a red star. The area shown in the map is indicated in Figure 2 A. (B) Holotype skull and mandible of P. tapanuliensis from a recently deceased individual from Batang Toru. See also Figure S 1 and Tables S 1 and S 2. (C) Violin plots of the first seven principal components of 26 cranio-mandibular morphological variables of eight north Sumatran P. abelii and 19 Bornean P. pygmaeus individuals of similar developmental state as the P. tapanuliensis holotype skull (black horizontal lines). See also Figure S 2." httpUri="https://zenodo.org/record/1041353/files/figure.png" pageId="3" pageNumber="4">Figures 1C and S</figureCitation>
|
||
<figureCitation box="[542,554,300,321]" captionStart="Figure 2" captionStartId="4.[142,202,1189,1208]" captionTargetBox="[142,1608,0,1149]" captionTargetId="figure@4.[151,1439,271,1150]" captionTargetPageId="4" captionText="Figure 2. Distribution, Genomic Diversity, and Population Structure of the Genus Pongo (A) Sampling areas across the current distribution of orangutans. The contour indicates the extent of the exposed Sunda Shelf during the Last Glacial Maximum. The black rectangle delimits the area shown in Figure 1 A. n indicates the number of sequenced individuals. See also Table S 4. (B) PCA of genomic diversity in Pongo. Axis labels show the percentages of the total variance explained by the first two principal components. Colored bars in the insert represent the distribution of nucleotide diversity in genome-wide 1 - Mb windows across sampling areas. (C) Bayesian clustering analysis of population structure using the program ADMIXTURE. Each vertical bar depicts an individual, with colors representing the inferred ancestry proportions with different assumed numbers of genetic clusters (K, horizontal sections)." httpUri="https://zenodo.org/record/1041355/files/figure.png" pageId="3" pageNumber="4">2</figureCitation>
|
||
).
|
||
</paragraph>
|
||
<paragraph blockId="3.[159,798,271,555]" pageId="3" pageNumber="4">
|
||
The external morphology of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[464,618,330,351]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[464,618,330,351]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
is more similar to that of
|
||
<emphasis box="[228,305,359,380]" italics="true" pageId="3" pageNumber="4">P. abelii</emphasis>
|
||
in its linear body build and more cinnamon pelage than that of
|
||
<emphasis box="[283,412,388,409]" italics="true" pageId="3" pageNumber="4">P. pygmaeus</emphasis>
|
||
. The hair texture of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[619,773,388,409]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[619,773,388,409]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
is frizzier, contrasting in particular with the long, loose body hair of
|
||
<emphasis box="[159,239,446,467]" italics="true" pageId="3" pageNumber="4">P. abelii</emphasis>
|
||
.
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[255,455,446,467]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[255,455,446,467]" italics="true" pageId="3" pageNumber="4">Pongo tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
has a prominent moustache and flat flanges covered in downy hair in dominant males, whereas flanges of older males resemble more those of Bornean males. Females of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[244,394,534,555]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[244,394,534,555]" italics="true" pageId="3" pageNumber="4">P.tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
have beards,unlike those of
|
||
<emphasis box="[666,791,534,555]" italics="true" pageId="3" pageNumber="4">P. pygmaeus</emphasis>
|
||
.
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection pageId="3" pageNumber="4" type="distribution">
|
||
<paragraph blockId="3.[159,799,593,964]" box="[159,292,593,614]" pageId="3" pageNumber="4">
|
||
<heading bold="true" box="[159,292,593,614]" fontSize="8" level="10" pageId="3" pageNumber="4" reason="6">
|
||
<emphasis bold="true" box="[159,292,593,614]" pageId="3" pageNumber="4">Distribution</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="3.[159,799,593,964]" pageId="3" pageNumber="4">
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[159,358,622,643]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[159,358,622,643]" italics="true" pageId="3" pageNumber="4">Pongo tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
occurs only in a small number of forest fragments in the districts of Central, North, and South Tapanuli, Indonesia (
|
||
<figureCitation box="[267,364,680,701]" captionStart="Figure 1" captionStartId="2.[142,202,1428,1447]" captionTargetBox="[142,1608,0,1387]" captionTargetId="figure@2.[150,1441,271,1388]" captionTargetPageId="2" captionText="Figure 1. Morphological Evidence Supporting a New Orangutan Species (A) Current distribution of Pongo tapanuliensis on Sumatra. The holotype locality is marked with a red star. The area shown in the map is indicated in Figure 2 A. (B) Holotype skull and mandible of P. tapanuliensis from a recently deceased individual from Batang Toru. See also Figure S 1 and Tables S 1 and S 2. (C) Violin plots of the first seven principal components of 26 cranio-mandibular morphological variables of eight north Sumatran P. abelii and 19 Bornean P. pygmaeus individuals of similar developmental state as the P. tapanuliensis holotype skull (black horizontal lines). See also Figure S 2." httpUri="https://zenodo.org/record/1041353/files/figure.png" pageId="3" pageNumber="4">Figure 1A</figureCitation>
|
||
). The total distribution covers approximately 1,000 km2, with an estimated population size of fewer than 800 individuals [
|
||
<bibRefCitation author="Wich, S. A. & Singleton, I & Nowak, M. G. & Utami Atmoko, S. S. & Nisam, G. & Arif, S. M. & Putra, R. H. & Ardi, R. & Fredriksson, G. & Usher, G." box="[258,270,739,760]" journalOrPublisher="Sci. Adv." pageId="3" pageNumber="4" pagination="1500789" part="2" refId="ref6655" refString="7. Wich, S. A., Singleton, I., Nowak, M. G., Utami Atmoko, S. S., Nisam, G., Arif, S. M., Putra, R. H., Ardi, R., Fredriksson, G., Usher, G., et al. (2016). Land-cover changes predict steep declines for the Sumatran orangutan (Pongo abelii). Sci. Adv. 2, e 1500789." title="Land-cover changes predict steep declines for the Sumatran orangutan (Pongo abelii)" type="journal article" year="2016">7</bibRefCitation>
|
||
]. The current distribution of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[548,703,739,760]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[548,703,739,760]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
is almost completely restricted to medium elevation hill and submontane forest (300–1300 m above sea level) [
|
||
<bibRefCitation author="Wich, S. A. & Singleton, I & Nowak, M. G. & Utami Atmoko, S. S. & Nisam, G. & Arif, S. M. & Putra, R. H. & Ardi, R. & Fredriksson, G. & Usher, G." box="[556,568,797,818]" journalOrPublisher="Sci. Adv." pageId="3" pageNumber="4" pagination="1500789" part="2" refId="ref6655" refString="7. Wich, S. A., Singleton, I., Nowak, M. G., Utami Atmoko, S. S., Nisam, G., Arif, S. M., Putra, R. H., Ardi, R., Fredriksson, G., Usher, G., et al. (2016). Land-cover changes predict steep declines for the Sumatran orangutan (Pongo abelii). Sci. Adv. 2, e 1500789." title="Land-cover changes predict steep declines for the Sumatran orangutan (Pongo abelii)" type="journal article" year="2016">7</bibRefCitation>
|
||
–
|
||
<bibRefCitation author="Wich, S. A. & Usher, G. & Peters, H. H. & Khakim, M. F. R. & Nowak, M. G. & Fredriksson, G. M." box="[580,592,797,818]" editor="B. N. Grow" journalOrPublisher="Springer" pageId="3" pageNumber="4" pagination="265 - 283" refId="ref6814" refString="9. Wich, S. A., Usher, G., Peters, H. H., Khakim, M. F. R., Nowak, M. G., and Fredriksson, G. M. (2014). Preliminary data on the highland Sumatran orangutans (Pongo abelii) of Batang Toru. In High Altitude Primates, B. N. Grow, S. Gursky-Doyen, and A. Krzton, eds. (Springer), pp. 265 - 283." title="Preliminary data on the highland Sumatran orangutans (Pongo abelii) of Batang Toru" type="book chapter" volumeTitle="High Altitude Primates" year="2014">9</bibRefCitation>
|
||
]. Although densities are highest in primary forest, it does occur at lower densities in mixed agroforest at the edge of primary forest areas [
|
||
<bibRefCitation author="Meijaard, E." box="[675,703,856,877]" journalOrPublisher="North Sumatra: New Chances for Orangutan Conservation (Tropenbos and the Golden Ark)" pageId="3" pageNumber="4" refId="ref6909" refString="10. Meijaard, E. (1997). A Survey of Some Forested Areas in South and Central Tapanuli, North Sumatra: New Chances for Orangutan Conservation (Tropenbos and the Golden Ark)." title="A Survey of Some Forested Areas in South and Central Tapanuli" type="book" year="1997">10</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="Wich, S. A. & Fredriksson, G. M. & Usher, G. & Peters, H. H. & Priatna, D. & Basalamah, F. & Susanto, W. & Kuhl, H." box="[711,736,856,877]" journalOrPublisher="Biol. Conserv." pageId="3" pageNumber="4" pagination="163 - 169" part="146" refId="ref6947" refString="11. Wich, S. A., Fredriksson, G. M., Usher, G., Peters, H. H., Priatna, D., Basalamah, F., Susanto, W., and Kuhl, H. (2012). Hunting of Sumatran orang-utans and its importance in determining distribution and density. Biol. Conserv. 146, 163 - 169." title="Hunting of Sumatran orang-utans and its importance in determining distribution and density" type="journal article" year="2012">11</bibRefCitation>
|
||
]. Until relatively recently,
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[346,502,885,906]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[346,502,885,906]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
was more widespread to the south and west of the current distribution, although evidence for this is largely anecdotal [
|
||
<bibRefCitation author="Kramm, W." box="[404,432,943,964]" journalOrPublisher="Sumatra-Courant" pageId="3" pageNumber="4" pagination="1 - 2" part="20" refId="ref7022" refString="12. Kramm, W. (1879). Tochtjes in Tapanoeli. Sumatra-Courant 20, 1 - 2." title="Tochtjes in Tapanoeli" type="journal article" year="1879">12</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="Miller, G. S." box="[441,466,943,964]" journalOrPublisher="Proc. U. S. Nat. Mus. Wash." pageId="3" pageNumber="4" pagination="437 - 484" part="26" refId="ref7043" refString="13. Miller, G. S. (1903). Mammals collected by Dr. W. L. Abbott on the coast and islands of northwest Sumatra. Proc. U. S. Nat. Mus. Wash. 26, 437 - 484." title="Mammals collected by Dr. W. L. Abbott on the coast and islands of northwest Sumatra" type="journal article" year="1903">13</bibRefCitation>
|
||
].
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection lastPageId="6" lastPageNumber="7" pageId="3" pageNumber="4" type="discussion">
|
||
<paragraph blockId="3.[159,304,1002,1023]" box="[159,304,1002,1023]" pageId="3" pageNumber="4">
|
||
<heading allCaps="true" bold="true" box="[159,304,1002,1023]" fontSize="8" level="4" pageId="3" pageNumber="4" reason="2">
|
||
<emphasis bold="true" box="[159,304,1002,1023]" pageId="3" pageNumber="4">DISCUSSION</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="3.[159,798,1060,1987]" pageId="3" pageNumber="4">
|
||
Other hominoid species and subspecies were previously described using standard univariate and multivariate techniques to quantify morphological character differences. The elevation of bonobos (
|
||
<emphasis box="[264,384,1148,1169]" italics="true" pageId="3" pageNumber="4">P. paniscus</emphasis>
|
||
) from a subspecies to a species dates back to Coolidge [
|
||
<bibRefCitation author="Coolidge, H. J." box="[347,372,1177,1198]" journalOrPublisher="Am. J. Phys. Anthropol." pageId="3" pageNumber="4" pagination="1 - 59" part="18" refId="ref7092" refString="14. Coolidge, H. J. (1933). Pan Paniscus. Pigmy chimpanzee from south of the Congo River. Am. J. Phys. Anthropol. 18, 1 - 59." title="Pan Paniscus. Pigmy chimpanzee from south of the Congo River" type="journal article" year="1933">14</bibRefCitation>
|
||
] and was based on summary statistics of primarily morphological data from a single female specimen of
|
||
<emphasis box="[159,277,1236,1257]" italics="true" pageId="3" pageNumber="4">P. paniscus</emphasis>
|
||
, five available
|
||
<emphasis box="[430,548,1236,1257]" italics="true" pageId="3" pageNumber="4">P. paniscus</emphasis>
|
||
skulls, and comparative data of what is now
|
||
<emphasis box="[373,515,1265,1286]" italics="true" pageId="3" pageNumber="4">P. troglodytes</emphasis>
|
||
. Groves and colleagues [
|
||
<bibRefCitation author="Groves, C. P. & Westwood, C. & Shea, B. T." box="[779,791,1265,1286]" journalOrPublisher="J. Hum. Evol." pageId="3" pageNumber="4" pagination="327 - 340" part="22" refId="ref6550" refString="5. Groves, C. P., Westwood, C., and Shea, B. T. (1992). Unfinished business: Mahalanobis and a clockwork orang. J. Hum. Evol. 22, 327 - 340." title="Unfinished business: Mahalanobis and a clockwork orang" type="journal article" year="1992">5</bibRefCitation>
|
||
] and Shea et al. [
|
||
<bibRefCitation author="Shea, B. T. & Leigh, S. R. & Groves, C. P." box="[323,348,1294,1315]" journalOrPublisher="Boston, eds. (Springer)" pageId="3" pageNumber="4" pagination="265 - 296" refId="ref7130" refString="15. Shea, B. T., Leigh, S. R., and Groves, C. P. (1993). Multivariate craniometric variation in chimpanzees. In Species, Species Concepts and Primate Evolution, W. H. Kimbel, L. B. Martin, and M. A. Boston, eds. (Springer), pp. 265 - 296." title="Multivariate craniometric variation in chimpanzees. In Species, Species Concepts and Primate Evolution, W. H. Kimbel, L. B. Martin, and M. A" type="book chapter" year="1993">15</bibRefCitation>
|
||
] supported Coolidge’s proposal using larger sample sizes and discriminant function analyses. Shea et al. [
|
||
<bibRefCitation author="Shea, B. T. & Leigh, S. R. & Groves, C. P." box="[766,791,1323,1344]" journalOrPublisher="Boston, eds. (Springer)" pageId="3" pageNumber="4" pagination="265 - 296" refId="ref7130" refString="15. Shea, B. T., Leigh, S. R., and Groves, C. P. (1993). Multivariate craniometric variation in chimpanzees. In Species, Species Concepts and Primate Evolution, W. H. Kimbel, L. B. Martin, and M. A. Boston, eds. (Springer), pp. 265 - 296." title="Multivariate craniometric variation in chimpanzees. In Species, Species Concepts and Primate Evolution, W. H. Kimbel, L. B. Martin, and M. A" type="book chapter" year="1993">15</bibRefCitation>
|
||
] remarked that the species designation for
|
||
<emphasis box="[603,722,1353,1374]" italics="true" pageId="3" pageNumber="4">P. paniscus</emphasis>
|
||
, which was largely based on morphological comparisons, was ultimately strengthened by genetic, ecological, and behavioral data, as we attempted here for
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[499,705,1440,1461]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[499,705,1440,1461]" italics="true" pageId="3" pageNumber="4">Pongo tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
. For the genus
|
||
<emphasis box="[229,293,1470,1491]" italics="true" pageId="3" pageNumber="4">Gorilla</emphasis>
|
||
, Stumpf et al. [
|
||
<bibRefCitation author="Stumpf, R. M. & Polk, J. D. & Oates, J. F. & Jungers, W. L. & Heesy, C. P. & Groves, C. P. & Fleagle, J. G." box="[456,481,1470,1491]" journalOrPublisher="Goldsmith, eds. (Cambridge University Press)" pageId="3" pageNumber="4" pagination="35 - 61" refId="ref7203" refString="16. Stumpf, R. M., Polk, J. D., Oates, J. F., Jungers, W. L., Heesy, C. P., Groves, C. P., and Fleagle, J. G. (2002). Patterns of diversity in gorilla cranial morphology. In Gorilla Biology: A Multidisciplinary Perspective, A. B. Taylor, and M. L. Goldsmith, eds. (Cambridge University Press), pp. 35 - 61." title="Patterns of diversity in gorilla cranial morphology. In Gorilla Biology: A Multidisciplinary Perspective, A. B. Taylor, and M. L" type="book chapter" year="2002">16</bibRefCitation>
|
||
] and Groves [
|
||
<bibRefCitation author="Groves, C. P." box="[629,654,1470,1491]" journalOrPublisher="Goldsmith, eds. (Cambridge University Press)" pageId="3" pageNumber="4" pagination="15 - 34" refId="ref7301" refString="17. Groves, C. P. (2002). A history of gorilla taxonomy. In Gorilla Biology: A Multidisciplinary Perspective, A. B. Taylor, and M. L. Goldsmith, eds. (Cambridge University Press), pp. 15 - 34." title="A history of gorilla taxonomy. In Gorilla Biology: A Multidisciplinary Perspective, A. B. Taylor, and M. L" type="book chapter" year="2002">17</bibRefCitation>
|
||
] used craniomandibular data from 747 individuals from 19 geographic regions, confirming a classification of the genus into two species (
|
||
<emphasis box="[165,257,1557,1578]" italics="true" pageId="3" pageNumber="4">G. gorilla</emphasis>
|
||
and
|
||
<emphasis box="[312,425,1557,1578]" italics="true" pageId="3" pageNumber="4">G. beringei</emphasis>
|
||
), as proposed earlier by Groves [
|
||
<bibRefCitation author="Groves, C. P." box="[772,784,1557,1578]" journalOrPublisher="Smithsonian Institution Press" pageId="3" pageNumber="4" refId="ref6366" refString="1. Groves, C. P. (2001). Primate Taxonomy (Smithsonian Institution Press)." title="Primate Taxonomy" type="book" year="2001">1</bibRefCitation>
|
||
]. Other recent
|
||
<taxonomicName box="[300,377,1586,1607]" class="Mammalia" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primate" pageId="3" pageNumber="10" phylum="Chordata" rank="order">primate</taxonomicName>
|
||
species descriptions primarily relied on an inconsistent mix of data on pelage color, ecology, morphology, and/or vocalizations [
|
||
<bibRefCitation author="Geissmann, T. & Lwin, N. & Aung, S. S. & Aung, T. N. & Aung, Z. M. & Hla, T. H. & Grindley, M. & Momberg, F." box="[512,536,1645,1666]" journalOrPublisher="Am. J. Primatol." pageId="3" pageNumber="4" pagination="96 - 107" part="73" refId="ref7354" refString="18. Geissmann, T., Lwin, N., Aung, S. S., Aung, T. N., Aung, Z. M., Hla, T. H., Grindley, M., and Momberg, F. (2011). A new species of snubnosed monkey, genus Rhinopithecus Milne-Edwards, 1872 (Primates, Colobinae), from northern Kachin state, northeastern Myanmar. Am. J. Primatol. 73, 96 - 107." title="A new species of snubnosed monkey, genus Rhinopithecus Milne-Edwards, 1872 (Primates, Colobinae), from northern Kachin state, northeastern Myanmar" type="journal article" year="2011">18</bibRefCitation>
|
||
–
|
||
<bibRefCitation author="Svensson, M. S. & Bersacola, E. & Mills, M. S. L. & Munds, R. A. & Nijman, V & Perkin, A. & Masters, J. C. & Couette, S. & Nekaris, K. A. & Bearder, S. K." box="[547,573,1645,1666]" journalOrPublisher="Am. J. Phys. Anthropol." pageId="3" pageNumber="4" pagination="30 - 43" part="163" refId="ref7695" refString="23. Svensson, M. S., Bersacola, E., Mills, M. S. L., Munds, R. A., Nijman, V., Perkin, A., Masters, J. C., Couette, S., Nekaris, K. A. I., and Bearder, S. K. (2017). A giant among dwarfs: a new species of galago (Primates: Galagidae) from Angola. Am. J. Phys. Anthropol. 163, 30 - 43." title="A giant among dwarfs: a new species of galago (Primates: Galagidae) from Angola" type="journal article" year="2017">23</bibRefCitation>
|
||
], with only a few also incorporating genetic analyses [
|
||
<bibRefCitation author="Davenport, T. R. B. & Stanley, W. T. & Sargis, E. J. & De Luca, D. W. & Mpunga, N. E. & Machaga, S. J. & Olson, L. E." box="[480,508,1674,1695]" journalOrPublisher="Science" pageId="3" pageNumber="4" pagination="1378 - 1381" part="312" refId="ref7799" refString="24. Davenport, T. R. B., Stanley, W. T., Sargis, E. J., De Luca, D. W., Mpunga, N. E., Machaga, S. J., and Olson, L. E. (2006). A new genus of African monkey, Rungwecebus: morphology, ecology, and molecular phylogenetics. Science 312, 1378 - 1381." title="A new genus of African monkey, Rungwecebus: morphology, ecology, and molecular phylogenetics" type="journal article" year="2006">24</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="Fan, P. F. & He, K. & Chen, X. & Ortiz, A. & Zhang, B. & Zhao, C. & Li, Y. Q. & Zhang, H. B. & Kimock, C. & Wang, W. Z." box="[518,543,1674,1695]" journalOrPublisher="Am. J. Primatol." pageId="3" pageNumber="4" pagination="22631" part="79" refId="ref7881" refString="25. Fan, P. F., He, K., Chen, X., Ortiz, A., Zhang, B., Zhao, C., Li, Y. Q., Zhang, H. B., Kimock, C., Wang, W. Z., et al. (2017). Description of a new species of Hoolock gibbon (Primates: Hylobatidae) based on integrative taxonomy. Am. J. Primatol. 79, e 22631." title="Description of a new species of Hoolock gibbon (Primates: Hylobatidae) based on integrative taxonomy" type="journal article" year="2017">25</bibRefCitation>
|
||
].
|
||
</paragraph>
|
||
<paragraph blockId="3.[159,798,1060,1987]" lastBlockId="3.[829,1468,271,1987]" pageId="3" pageNumber="4">
|
||
Here, we used an integrative approach by corroborating the morphological analysis and behavioral and ecological data with whole-genome data of 37 orangutans with known provenance, covering the entire range of extant orangutans including areas never sampled before (
|
||
<figureCitation box="[459,560,1820,1841]" captionStart="Figure 2" captionStartId="4.[142,202,1189,1208]" captionTargetBox="[142,1608,0,1149]" captionTargetId="figure@4.[151,1439,271,1150]" captionTargetPageId="4" captionText="Figure 2. Distribution, Genomic Diversity, and Population Structure of the Genus Pongo (A) Sampling areas across the current distribution of orangutans. The contour indicates the extent of the exposed Sunda Shelf during the Last Glacial Maximum. The black rectangle delimits the area shown in Figure 1 A. n indicates the number of sequenced individuals. See also Table S 4. (B) PCA of genomic diversity in Pongo. Axis labels show the percentages of the total variance explained by the first two principal components. Colored bars in the insert represent the distribution of nucleotide diversity in genome-wide 1 - Mb windows across sampling areas. (C) Bayesian clustering analysis of population structure using the program ADMIXTURE. Each vertical bar depicts an individual, with colors representing the inferred ancestry proportions with different assumed numbers of genetic clusters (K, horizontal sections)." httpUri="https://zenodo.org/record/1041355/files/figure.png" pageId="3" pageNumber="4">Figure 2A</figureCitation>
|
||
;
|
||
<tableCitation box="[571,661,1820,1841]" captionStart="Table S" captionStartId="34.[189,261,704,730]" captionTargetBox="[189,2054,776,1481]" captionTargetPageId="34" captionText="Table S 4. Details of study individuals. Related to Figure 2 A." httpUri="http://table.plazi.org/id/DF0F6674FF93C316FF4015DFFC71BF94" pageId="3" pageNumber="4" tableUuid="DF0F6674FF93C316FF4015DFFC71BF94">Table S4</tableCitation>
|
||
). We applied a model-based approach to statistically evaluate competing demographic models, identify independent evolutionary lineages and infer levels of gene flow and the timing of genetic isolation between lineages. This enabled us to directly compare complex and realistic models of speciation. We refrained from directly comparing genetic differentiation among the three species in the genus
|
||
<taxonomicName authorityName="Lacepede" authorityYear="1799" box="[943,1009,300,321]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="genus">
|
||
<emphasis box="[943,1009,300,321]" italics="true" pageId="3" pageNumber="4">Pongo</emphasis>
|
||
</taxonomicName>
|
||
with that of other hominoids, as we deem such comparisons problematic in order to evaluate whether
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[829,985,359,380]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[829,985,359,380]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
constitutes a new species. This is because estimates of genetic differentiation reflect a combination of divergence time, demographic history, and gene flow and are also influenced by the employed genetic marker system [
|
||
<bibRefCitation author="Jost, L." box="[1357,1385,447,468]" journalOrPublisher="Mol. Ecol." pageId="3" pageNumber="4" pagination="4015 - 4026" part="17" refId="ref7977" refString="26. Jost, L. (2008). GST and its relatives do not measure differentiation. Mol. Ecol. 17, 4015 - 4026." title="GST and its relatives do not measure differentiation" type="journal article" year="2008">26</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="Whitlock, M. C." box="[1394,1419,447,468]" journalOrPublisher="Mol. Ecol." pageId="3" pageNumber="4" pagination="1083 - 1091" part="20" refId="ref8006" refString="27. Whitlock, M. C. (2011). G'ST and D do not replace FST. Mol. Ecol. 20, 1083 - 1091." title="G'ST and D do not replace FST" type="journal article" year="2011">27</bibRefCitation>
|
||
].
|
||
</paragraph>
|
||
<paragraph blockId="3.[829,1468,271,1987]" pageId="3" pageNumber="4">
|
||
A PCA (
|
||
<figureCitation box="[931,1028,476,497]" captionStart="Figure 2" captionStartId="4.[142,202,1189,1208]" captionTargetBox="[142,1608,0,1149]" captionTargetId="figure@4.[151,1439,271,1150]" captionTargetPageId="4" captionText="Figure 2. Distribution, Genomic Diversity, and Population Structure of the Genus Pongo (A) Sampling areas across the current distribution of orangutans. The contour indicates the extent of the exposed Sunda Shelf during the Last Glacial Maximum. The black rectangle delimits the area shown in Figure 1 A. n indicates the number of sequenced individuals. See also Table S 4. (B) PCA of genomic diversity in Pongo. Axis labels show the percentages of the total variance explained by the first two principal components. Colored bars in the insert represent the distribution of nucleotide diversity in genome-wide 1 - Mb windows across sampling areas. (C) Bayesian clustering analysis of population structure using the program ADMIXTURE. Each vertical bar depicts an individual, with colors representing the inferred ancestry proportions with different assumed numbers of genetic clusters (K, horizontal sections)." httpUri="https://zenodo.org/record/1041355/files/figure.png" pageId="3" pageNumber="4">Figure 2B</figureCitation>
|
||
) of genomic diversity highlighted the divergence between individuals from Borneo and Sumatra (PC1) but also separated
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[988,1146,534,555]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[988,1146,534,555]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
from
|
||
<emphasis box="[1208,1289,534,555]" italics="true" pageId="3" pageNumber="4">P. abelii</emphasis>
|
||
(PC2). The same clustering pattern was also found in a model-based analysis of population structure (
|
||
<figureCitation box="[1043,1140,593,614]" captionStart="Figure 2" captionStartId="4.[142,202,1189,1208]" captionTargetBox="[142,1608,0,1149]" captionTargetId="figure@4.[151,1439,271,1150]" captionTargetPageId="4" captionText="Figure 2. Distribution, Genomic Diversity, and Population Structure of the Genus Pongo (A) Sampling areas across the current distribution of orangutans. The contour indicates the extent of the exposed Sunda Shelf during the Last Glacial Maximum. The black rectangle delimits the area shown in Figure 1 A. n indicates the number of sequenced individuals. See also Table S 4. (B) PCA of genomic diversity in Pongo. Axis labels show the percentages of the total variance explained by the first two principal components. Colored bars in the insert represent the distribution of nucleotide diversity in genome-wide 1 - Mb windows across sampling areas. (C) Bayesian clustering analysis of population structure using the program ADMIXTURE. Each vertical bar depicts an individual, with colors representing the inferred ancestry proportions with different assumed numbers of genetic clusters (K, horizontal sections)." httpUri="https://zenodo.org/record/1041355/files/figure.png" pageId="3" pageNumber="4">Figure 2C</figureCitation>
|
||
) and is consistent with an earlier genetic study analyzing a larger number of non-invasively collected samples using microsatellite markers [
|
||
<bibRefCitation author="Nater, A. & Arora, N. & Greminger, M. P. & van Schaik, C. P. & Singleton, I & Wich, S. A. & Fredriksson, G. & Perwitasari-Farajallah, D. & Pamungkas, J. & Krutzen, M." box="[1325,1350,651,672]" journalOrPublisher="J. Hered." pageId="3" pageNumber="4" pagination="2 - 13" part="104" refId="ref8036" refString="28. Nater, A., Arora, N., Greminger, M. P., van Schaik, C. P., Singleton, I., Wich, S. A., Fredriksson, G., Perwitasari-Farajallah, D., Pamungkas, J., and Krutzen, M. (2013). Marked population structure and recent migration in the critically endangered Sumatran orangutan (Pongo abelii). J. Hered. 104, 2 - 13." title="Marked population structure and recent migration in the critically endangered Sumatran orangutan (Pongo abelii)" type="journal article" year="2013">28</bibRefCitation>
|
||
]. However, although such clustering approaches are powerful in detecting extant population structure, population history and speciation cannot be inferred, as these methods are not suited to distinguish between old divergences with gene flow and cases of recent divergence with isolation [
|
||
<bibRefCitation author="Nielsen, R. & Wakeley, J." box="[1164,1192,797,818]" journalOrPublisher="Genetics" pageId="3" pageNumber="4" pagination="885 - 896" part="158" refId="ref8126" refString="29. Nielsen, R., and Wakeley, J. (2001). Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158, 885 - 896." title="Distinguishing migration from isolation: a Markov chain Monte Carlo approach" type="journal article" year="2001">29</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="Palsboll, P. J. & Berube, M. & Aguilar, A. & Notarbartolo-Di-Sciara, G. & Nielsen, R." box="[1202,1227,797,818]" journalOrPublisher="Evolution" pageId="3" pageNumber="4" pagination="670 - 675" part="58" refId="ref8161" refString="30. Palsboll, P. J., Berube, M., Aguilar, A., Notarbartolo-Di-Sciara, G., and Nielsen, R. (2004). Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations. Evolution 58, 670 - 675." title="Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations" type="journal article" year="2004">30</bibRefCitation>
|
||
]. To address this problem and further investigate the timing of population splits and gene flow, we therefore employed different complementary modeling and phylogenetic approaches.
|
||
</paragraph>
|
||
<paragraph blockId="3.[829,1468,271,1987]" pageId="3" pageNumber="4">
|
||
We applied an approximate Bayesian computation (ABC) approach, which allows inference and comparison of arbitrarily complex demographic modes based on the comparison of the observed genomic data to extensive population genetic simulations [
|
||
<bibRefCitation author="Beaumont, M. A. & Zhang, W. & Balding, D. J." box="[887,911,1031,1052]" journalOrPublisher="Genetics" pageId="3" pageNumber="4" pagination="2025 - 2035" part="162" refId="ref8229" refString="31. Beaumont, M. A., Zhang, W., and Balding, D. J. (2002). Approximate Bayesian computation in population genetics. Genetics 162, 2025 - 2035." title="Approximate Bayesian computation in population genetics" type="journal article" year="2002">31</bibRefCitation>
|
||
]. Our analyses revealed three deep evolutionary lineages in extant orangutans (
|
||
<figureCitation box="[1042,1227,1060,1081]" captionStart="Figure 3" captionStartId="5.[159,219,1181,1200]" captionTargetBox="[169,1455,274,1141]" captionTargetId="graphics@5.[170,741,774,1098]" captionTargetPageId="5" captionText="Figure 3. Demographic History and Gene Flow in Pongo (A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland. The ABC analyses are based on the comparison of 3,000 non-coding 2 - kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models. The numbers in the black boxes indicate the model’s posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A). Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also Table S 5. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species, and a ratio close to 0 indicates genetic isolation between species pairs. The x axis shows time scaled in years, assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also Figure S" httpUri="https://zenodo.org/record/1041357/files/figure.svg" pageId="3" pageNumber="4">Figures 3A and 3B</figureCitation>
|
||
). Colonization scenarios in which the earliest split within
|
||
<taxonomicName authorityName="Lacepede" authorityYear="1799" box="[1141,1206,1089,1110]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="genus">
|
||
<emphasis box="[1141,1206,1089,1110]" italics="true" pageId="3" pageNumber="4">Pongo</emphasis>
|
||
</taxonomicName>
|
||
occurred between the lineages leading to
|
||
<emphasis box="[1000,1078,1119,1140]" italics="true" pageId="3" pageNumber="4">P. abelii</emphasis>
|
||
and
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[1129,1284,1119,1140]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[1129,1284,1119,1140]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
were much better supported than scenarios in which the earliest split was between Bornean and Sumatran species (model 1 versus model 2, combined posterior probability: 99.91%;
|
||
<figureCitation box="[1196,1295,1206,1227]" captionStart="Figure 3" captionStartId="5.[159,219,1181,1200]" captionTargetBox="[169,1455,274,1141]" captionTargetId="graphics@5.[170,741,774,1098]" captionTargetPageId="5" captionText="Figure 3. Demographic History and Gene Flow in Pongo (A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland. The ABC analyses are based on the comparison of 3,000 non-coding 2 - kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models. The numbers in the black boxes indicate the model’s posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A). Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also Table S 5. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species, and a ratio close to 0 indicates genetic isolation between species pairs. The x axis shows time scaled in years, assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also Figure S" httpUri="https://zenodo.org/record/1041357/files/figure.svg" pageId="3" pageNumber="4">Figure 3A</figureCitation>
|
||
). Of the two best scenarios, a model postulating colonization of both northern Sumatra and Borneo from an ancestral population most likely situated south of Lake Toba on Sumatra had the highest support (model 1a versus model 1b, posterior probability: 97.56%; Figure 3A). Our results supported a scenario in which orangutans from mainland Asia first entered Sundaland south of what is now Lake Toba on Sumatra, the most likely entry point based on paleogeographic reconstructions [
|
||
<bibRefCitation author="Meijaard, E." box="[1201,1226,1440,1461]" journalOrPublisher="PhD thesis (Australian National University)" pageId="3" pageNumber="4" refId="ref8268" refString="32. Meijaard, E. (2004). Solving mammalian riddles: a reconstruction of the Tertiary and Quaternary distribution of mammals and their palaeoenvironments in island South-East Asia. PhD thesis (Australian National University)." title="Solving mammalian riddles: a reconstruction of the Tertiary and Quaternary distribution of mammals and their palaeoenvironments in island South-East Asia" type="book" year="2004">32</bibRefCitation>
|
||
]. This ancestral population, of which
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[964,1118,1469,1490]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[964,1118,1469,1490]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
is a direct descendant, then served as a source for the subsequent different colonization events of what is now Borneo, Java, and northern Sumatra.
|
||
</paragraph>
|
||
<paragraph blockId="3.[829,1468,271,1987]" lastBlockId="4.[142,780,1411,1987]" lastPageId="4" lastPageNumber="5" pageId="3" pageNumber="4">
|
||
We estimated the split time between populations north and south of Lake Toba at 3.4 Ma (
|
||
<figureCitation box="[1175,1278,1586,1607]" captionStart="Figure 3" captionStartId="5.[159,219,1181,1200]" captionTargetBox="[169,1455,274,1141]" captionTargetId="graphics@5.[170,741,774,1098]" captionTargetPageId="5" captionText="Figure 3. Demographic History and Gene Flow in Pongo (A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland. The ABC analyses are based on the comparison of 3,000 non-coding 2 - kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models. The numbers in the black boxes indicate the model’s posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A). Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also Table S 5. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species, and a ratio close to 0 indicates genetic isolation between species pairs. The x axis shows time scaled in years, assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also Figure S" httpUri="https://zenodo.org/record/1041357/files/figure.svg" pageId="3" pageNumber="4">Figure 3B</figureCitation>
|
||
;
|
||
<tableCitation box="[1291,1383,1586,1607]" captionStart="Table S" captionStartId="36.[143,215,474,500]" captionTargetBox="[143,1943,548,1522]" captionText="Table S 5. Parameter estimation of the best supported models in the ABC and G-PhoCS analyses. Related to Figure 3 B." httpUri="http://table.plazi.org/id/DF0F6674FF95C310FF7216C5F983BCBA" pageId="3" pageNumber="4" tableUuid="DF0F6674FF95C310FF7216C5F983BCBA">Table S5</tableCitation>
|
||
). Under our best-fitting model, we found evidence for post-split gene flow across Lake Toba (0.3–0.9 migrants per generation;
|
||
<tableCitation captionStart="Table S" captionStartId="36.[143,215,474,500]" captionTargetBox="[143,1943,548,1522]" captionText="Table S 5. Parameter estimation of the best supported models in the ABC and G-PhoCS analyses. Related to Figure 3 B." httpUri="http://table.plazi.org/id/DF0F6674FF95C310FF7216C5F983BCBA" pageId="3" pageNumber="4" tableUuid="DF0F6674FF95C310FF7216C5F983BCBA">Table S5</tableCitation>
|
||
), which is consistent with highly significant signatures of gene flow between
|
||
<emphasis box="[966,1044,1703,1724]" italics="true" pageId="3" pageNumber="4">P. abelii</emphasis>
|
||
and
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[1091,1246,1703,1724]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[1091,1246,1703,1724]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
using D statistics (CK, BT, WA,
|
||
<emphasis box="[917,1060,1732,1753]" italics="true" pageId="3" pageNumber="4">
|
||
<taxonomicName box="[917,978,1732,1753]" class="Mammalia" family="Hominidae" genus="Homo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="genus">Homo</taxonomicName>
|
||
sapiens
|
||
</emphasis>
|
||
: D = 0.2819, p <0.00001; WK, BT, LK,
|
||
<emphasis box="[829,977,1762,1783]" italics="true" pageId="3" pageNumber="4">
|
||
<taxonomicName box="[829,890,1762,1783]" class="Mammalia" family="Hominidae" genus="Homo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="genus">Homo</taxonomicName>
|
||
sapiens
|
||
</emphasis>
|
||
: D = 0.2967, p <0.00001). Such gene flow resulted in higher autosomal affinity of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[1267,1432,1791,1812]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[1267,1432,1791,1812]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
to
|
||
<emphasis box="[829,909,1820,1841]" italics="true" pageId="3" pageNumber="4">P. abelii</emphasis>
|
||
compared to
|
||
<emphasis box="[1054,1187,1820,1841]" italics="true" pageId="3" pageNumber="4">P. pygmaeus</emphasis>
|
||
in the PCA (
|
||
<figureCitation box="[1316,1416,1820,1841]" captionStart="Figure 2" captionStartId="4.[142,202,1189,1208]" captionTargetBox="[142,1608,0,1149]" captionTargetId="figure@4.[151,1439,271,1150]" captionTargetPageId="4" captionText="Figure 2. Distribution, Genomic Diversity, and Population Structure of the Genus Pongo (A) Sampling areas across the current distribution of orangutans. The contour indicates the extent of the exposed Sunda Shelf during the Last Glacial Maximum. The black rectangle delimits the area shown in Figure 1 A. n indicates the number of sequenced individuals. See also Table S 4. (B) PCA of genomic diversity in Pongo. Axis labels show the percentages of the total variance explained by the first two principal components. Colored bars in the insert represent the distribution of nucleotide diversity in genome-wide 1 - Mb windows across sampling areas. (C) Bayesian clustering analysis of population structure using the program ADMIXTURE. Each vertical bar depicts an individual, with colors representing the inferred ancestry proportions with different assumed numbers of genetic clusters (K, horizontal sections)." httpUri="https://zenodo.org/record/1041355/files/figure.png" pageId="3" pageNumber="4">Figure 2B</figureCitation>
|
||
), explaining the smaller amount of variance captured by PC2 (separating
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[894,1052,1878,1899]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="3" pageNumber="4" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[894,1052,1878,1899]" italics="true" pageId="3" pageNumber="4">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
from all other populations) compared to PC1 (separating
|
||
<emphasis box="[999,1131,1908,1929]" italics="true" pageId="3" pageNumber="4">P. pygmaeus</emphasis>
|
||
from the Sumatran populations). The parameter estimates from a Bayesian full-likelihood analysis implemented in the software G-PhoCS were in good agreement with those obtained by the ABC analysis, although the split time between populations north and south of Lake Toba was more recent (2.27 Ma; 95% highest posterior density [HPD]: 2.21– 2.35;
|
||
<tableCitation box="[200,292,1499,1520]" captionStart="Table S" captionStartId="36.[143,215,474,500]" captionTargetBox="[143,1943,548,1522]" captionText="Table S 5. Parameter estimation of the best supported models in the ABC and G-PhoCS analyses. Related to Figure 3 B." httpUri="http://table.plazi.org/id/DF0F6674FF95C310FF7216C5F983BCBA" pageId="4" pageNumber="5" tableUuid="DF0F6674FF95C310FF7216C5F983BCBA">Table S5</tableCitation>
|
||
). The G-PhoCS analysis revealed highly asymmetric gene flow between populations north and south of the Toba caldera, with much lower levels of gene flow into the Batang Toru population from the north than vice versa (
|
||
<tableCitation box="[672,761,1586,1607]" captionStart="Table S" captionStartId="36.[143,215,474,500]" captionTargetBox="[143,1943,548,1522]" captionText="Table S 5. Parameter estimation of the best supported models in the ABC and G-PhoCS analyses. Related to Figure 3 B." httpUri="http://table.plazi.org/id/DF0F6674FF95C310FF7216C5F983BCBA" pageId="4" pageNumber="5" tableUuid="DF0F6674FF95C310FF7216C5F983BCBA">Table S5</tableCitation>
|
||
).
|
||
</paragraph>
|
||
<caption httpUri="https://zenodo.org/record/1041355/files/figure.png" pageId="4" pageNumber="5" targetBox="[142,1608,0,1149]" targetPageId="4">
|
||
<paragraph blockId="4.[142,1450,1189,1359]" pageId="4" pageNumber="5">
|
||
Figure 2. Distribution, Genomic Diversity, and Population Structure of the Genus
|
||
<taxonomicName authorityName="Lacepede" authorityYear="1799" box="[912,973,1190,1208]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="4" pageNumber="5" phylum="Chordata" rank="genus">Pongo</taxonomicName>
|
||
(A) Sampling areas across the current distribution of orangutans. The contour indicates the extent of the exposed Sunda Shelf during the Last Glacial Maximum. The black rectangle delimits the area shown in
|
||
<figureCitation box="[533,633,1241,1258]" captionStart="Figure 1" captionStartId="2.[142,202,1428,1447]" captionTargetBox="[142,1608,0,1387]" captionTargetId="figure@2.[150,1441,271,1388]" captionTargetPageId="2" captionText="Figure 1. Morphological Evidence Supporting a New Orangutan Species (A) Current distribution of Pongo tapanuliensis on Sumatra. The holotype locality is marked with a red star. The area shown in the map is indicated in Figure 2 A. (B) Holotype skull and mandible of P. tapanuliensis from a recently deceased individual from Batang Toru. See also Figure S 1 and Tables S 1 and S 2. (C) Violin plots of the first seven principal components of 26 cranio-mandibular morphological variables of eight north Sumatran P. abelii and 19 Bornean P. pygmaeus individuals of similar developmental state as the P. tapanuliensis holotype skull (black horizontal lines). See also Figure S 2." httpUri="https://zenodo.org/record/1041353/files/figure.png" pageId="4" pageNumber="5">Figure 1A. n</figureCitation>
|
||
indicates the number of sequenced individuals. See also
|
||
<tableCitation box="[1113,1186,1241,1258]" captionStart="Table S" captionStartId="34.[189,261,704,730]" captionTargetBox="[189,2054,776,1481]" captionTargetPageId="34" captionText="Table S 4. Details of study individuals. Related to Figure 2 A." httpUri="http://table.plazi.org/id/DF0F6674FF93C316FF4015DFFC71BF94" pageId="4" pageNumber="5" tableUuid="DF0F6674FF93C316FF4015DFFC71BF94">Table S4</tableCitation>
|
||
. (B) PCA of genomic diversity in
|
||
<taxonomicName authorityName="Lacepede" authorityYear="1799" box="[395,449,1266,1283]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="4" pageNumber="5" phylum="Chordata" rank="genus">
|
||
<emphasis box="[395,449,1266,1283]" italics="true" pageId="4" pageNumber="5">Pongo</emphasis>
|
||
</taxonomicName>
|
||
. Axis labels show the percentages of the total variance explained by the first two principal components.Colored bars in the insert represent the distribution of nucleotide diversity in genome-wide 1-Mb windows across sampling areas. (C) Bayesian clustering analysis of population structure using the program ADMIXTURE. Each vertical bar depicts an individual, with colors representing the inferred ancestry proportions with different assumed numbers of genetic clusters (K, horizontal sections).
|
||
</paragraph>
|
||
</caption>
|
||
<paragraph blockId="4.[142,780,1411,1987]" pageId="4" pageNumber="5">
|
||
The existence of two deep evolutionary lineages among extant Sumatran orangutans was corroborated by phylogenetic analyses based on whole mitochondrial genomes (
|
||
<figureCitation box="[639,743,1674,1695]" captionStart="Figure 4" captionStartId="6.[142,202,831,850]" captionTargetBox="[142,1608,0,789]" captionTargetId="figure@6.[148,1442,271,790]" captionTargetPageId="6" captionText="Figure 4. Sex-Specific Evolutionary History of Orangutans Bayesian phylogenetic trees for (A) mitochondrial genomes and (B) Y chromosomes. The mitochondrial tree is rooted with a human and a central chimpanzee sequence and the Y chromosome tree with a human sequence (not shown). ** Posterior probability = 1.00. (C) Genotype-sharing matrix for mitogenomes (above the diagonal) and Y chromosomes (below the diagonal) for all analyzed male orangutans. A value of 1 indicates that two males have identical genotypes at all polymorphic sites; a value of 0 means that they have different genotypes at all variable positions" httpUri="https://zenodo.org/record/1041359/files/figure.png" pageId="4" pageNumber="5">Figure 4A</figureCitation>
|
||
), in which the deepest split occurred between populations north of Lake Toba and all other orangutans at 3.97 Ma (95% HPD: 2.35–5.57). Sumatran orangutans formed a paraphyletic group, with
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[190,348,1791,1812]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="4" pageNumber="5" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[190,348,1791,1812]" italics="true" pageId="4" pageNumber="5">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
being more closely related to the Bornean lineage from which it diverged 2.41 Ma (1.26–3.42 Ma). In contrast, Bornean populations formed a monophyletic group with a very recent mitochondrial coalescence at 160 ka (94–227 ka).
|
||
</paragraph>
|
||
<paragraph blockId="4.[142,780,1411,1987]" lastBlockId="4.[811,1449,1411,1987]" pageId="4" pageNumber="5">
|
||
Due to strong female philopatry [
|
||
<bibRefCitation author="Arora, N. & Van Noordwijk, M. A. & Ackermann, C. & Willems, E. P. & Nater, A. & Greminger, M. & Nietlisbach, P. & Dunkel, L. P. & Utami Atmoko, S. S. & Pamungkas, J." box="[494,519,1937,1958]" journalOrPublisher="Mol. Ecol." pageId="4" pageNumber="5" pagination="3352 - 3362" part="21" refId="ref8308" refString="33. Arora, N., Van Noordwijk, M. A., Ackermann, C., Willems, E. P., Nater, A., Greminger, M., Nietlisbach, P., Dunkel, L. P., Utami Atmoko, S. S., Pamungkas, J., et al. (2012). Parentage-based pedigree reconstruction reveals female matrilineal clusters and male-biased dispersal in nongregarious Asian great apes, the Bornean orang-utans (Pongo pygmaeus). Mol. Ecol. 21, 3352 - 3362." title="Parentage-based pedigree reconstruction reveals female matrilineal clusters and male-biased dispersal in nongregarious Asian great apes, the Bornean orang-utans (Pongo pygmaeus)" type="journal article" year="2012">33</bibRefCitation>
|
||
], gene flow in orangutans is almost exclusively male mediated [
|
||
<bibRefCitation author="Nater, A. & Nietlisbach, P. & Arora, N. & van Schaik, C. P. & van Noordwijk, M. A. & Willems, E. P. & Singleton, I & Wich, S. A. & Goossens, B. & Warren, K. S." box="[517,542,1966,1987]" journalOrPublisher="Mol. Biol. Evol." pageId="4" pageNumber="5" pagination="2275 - 2288" part="28" refId="ref8411" refString="34. Nater, A., Nietlisbach, P., Arora, N., van Schaik, C. P., van Noordwijk, M. A., Willems, E. P., Singleton, I., Wich, S. A., Goossens, B., Warren, K. S., et al. (2011). Sex-biased dispersal and volcanic activities shaped phylogeographic patterns of extant Orangutans (genus: Pongo). Mol. Biol. Evol. 28, 2275 - 2288." title="Sex-biased dispersal and volcanic activities shaped phylogeographic patterns of extant Orangutans (genus: Pongo)" type="journal article" year="2011">34</bibRefCitation>
|
||
]. Consistent with these pronounced differences in dispersal behavior, phylogenetic analysis of extensive Y chromosome sequencing data revealed a comparatively recent coalescence of Y chromosomes of all extant orangutans 430 kya (
|
||
<figureCitation box="[1122,1224,1499,1520]" captionStart="Figure 4" captionStartId="6.[142,202,831,850]" captionTargetBox="[142,1608,0,789]" captionTargetId="figure@6.[148,1442,271,790]" captionTargetPageId="6" captionText="Figure 4. Sex-Specific Evolutionary History of Orangutans Bayesian phylogenetic trees for (A) mitochondrial genomes and (B) Y chromosomes. The mitochondrial tree is rooted with a human and a central chimpanzee sequence and the Y chromosome tree with a human sequence (not shown). ** Posterior probability = 1.00. (C) Genotype-sharing matrix for mitogenomes (above the diagonal) and Y chromosomes (below the diagonal) for all analyzed male orangutans. A value of 1 indicates that two males have identical genotypes at all polymorphic sites; a value of 0 means that they have different genotypes at all variable positions" httpUri="https://zenodo.org/record/1041359/files/figure.png" pageId="4" pageNumber="5">Figure 4B</figureCitation>
|
||
). The single available Y-haplotype from
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[997,1156,1528,1549]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="4" pageNumber="5" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[997,1156,1528,1549]" italics="true" pageId="4" pageNumber="5">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
was nested within the other Sumatran sequences, pointing at the occurrence of male-mediated gene flow across the Toba divide. Thus, in combination with our modeling results, the sex-specific data highlighted the impact of extraordinarily strong male-biased dispersal in the speciation process of orangutans.
|
||
</paragraph>
|
||
<paragraph blockId="4.[811,1449,1411,1987]" lastBlockId="5.[159,797,1499,1987]" lastPageId="5" lastPageNumber="6" pageId="4" pageNumber="5">
|
||
Our analyses revealed significant divergence between
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[811,968,1733,1754]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="4" pageNumber="5" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[811,968,1733,1754]" italics="true" pageId="4" pageNumber="5">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<emphasis box="[1018,1097,1733,1754]" italics="true" pageId="4" pageNumber="5">P. abelii</emphasis>
|
||
(
|
||
<figureCitation box="[1109,1218,1733,1754]" captionStart="Figure 3" captionStartId="5.[159,219,1181,1200]" captionTargetBox="[169,1455,274,1141]" captionTargetId="graphics@5.[170,741,774,1098]" captionTargetPageId="5" captionText="Figure 3. Demographic History and Gene Flow in Pongo (A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland. The ABC analyses are based on the comparison of 3,000 non-coding 2 - kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models. The numbers in the black boxes indicate the model’s posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A). Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also Table S 5. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species, and a ratio close to 0 indicates genetic isolation between species pairs. The x axis shows time scaled in years, assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also Figure S" httpUri="https://zenodo.org/record/1041357/files/figure.svg" pageId="4" pageNumber="5">Figures 3B</figureCitation>
|
||
and
|
||
<figureCitation box="[1268,1295,1733,1754]" captionStart="Figure 4" captionStartId="6.[142,202,831,850]" captionTargetBox="[142,1608,0,789]" captionTargetId="figure@6.[148,1442,271,790]" captionTargetPageId="6" captionText="Figure 4. Sex-Specific Evolutionary History of Orangutans Bayesian phylogenetic trees for (A) mitochondrial genomes and (B) Y chromosomes. The mitochondrial tree is rooted with a human and a central chimpanzee sequence and the Y chromosome tree with a human sequence (not shown). ** Posterior probability = 1.00. (C) Genotype-sharing matrix for mitogenomes (above the diagonal) and Y chromosomes (below the diagonal) for all analyzed male orangutans. A value of 1 indicates that two males have identical genotypes at all polymorphic sites; a value of 0 means that they have different genotypes at all variable positions" httpUri="https://zenodo.org/record/1041359/files/figure.png" pageId="4" pageNumber="5">4A</figureCitation>
|
||
) and low levels of male-mediated gene flow (
|
||
<figureCitation box="[1112,1223,1762,1783]" captionStart="Figure 3" captionStartId="5.[159,219,1181,1200]" captionTargetBox="[169,1455,274,1141]" captionTargetId="graphics@5.[170,741,774,1098]" captionTargetPageId="5" captionText="Figure 3. Demographic History and Gene Flow in Pongo (A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland. The ABC analyses are based on the comparison of 3,000 non-coding 2 - kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models. The numbers in the black boxes indicate the model’s posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A). Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also Table S 5. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species, and a ratio close to 0 indicates genetic isolation between species pairs. The x axis shows time scaled in years, assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also Figure S" httpUri="https://zenodo.org/record/1041357/files/figure.svg" pageId="4" pageNumber="5">Figures 3B</figureCitation>
|
||
and
|
||
<figureCitation box="[1276,1305,1762,1783]" captionStart="Figure 4" captionStartId="6.[142,202,831,850]" captionTargetBox="[142,1608,0,789]" captionTargetId="figure@6.[148,1442,271,790]" captionTargetPageId="6" captionText="Figure 4. Sex-Specific Evolutionary History of Orangutans Bayesian phylogenetic trees for (A) mitochondrial genomes and (B) Y chromosomes. The mitochondrial tree is rooted with a human and a central chimpanzee sequence and the Y chromosome tree with a human sequence (not shown). ** Posterior probability = 1.00. (C) Genotype-sharing matrix for mitogenomes (above the diagonal) and Y chromosomes (below the diagonal) for all analyzed male orangutans. A value of 1 indicates that two males have identical genotypes at all polymorphic sites; a value of 0 means that they have different genotypes at all variable positions" httpUri="https://zenodo.org/record/1041359/files/figure.png" pageId="4" pageNumber="5">4B</figureCitation>
|
||
), which, however, completely ceased 10–20 kya (
|
||
<figureCitation box="[1203,1309,1791,1812]" captionStart="Figure 3" captionStartId="5.[159,219,1181,1200]" captionTargetBox="[169,1455,274,1141]" captionTargetId="graphics@5.[170,741,774,1098]" captionTargetPageId="5" captionText="Figure 3. Demographic History and Gene Flow in Pongo (A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland. The ABC analyses are based on the comparison of 3,000 non-coding 2 - kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models. The numbers in the black boxes indicate the model’s posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A). Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also Table S 5. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species, and a ratio close to 0 indicates genetic isolation between species pairs. The x axis shows time scaled in years, assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also Figure S" httpUri="https://zenodo.org/record/1041357/files/figure.svg" pageId="4" pageNumber="5">Figure 3C</figureCitation>
|
||
). Populations north and south of Lake Toba on Sumatra had been in genetic contact for most of the time since their split, but there was a marked reduction in gene flow after 100 ka (
|
||
<figureCitation box="[1261,1361,1879,1900]" captionStart="Figure 3" captionStartId="5.[159,219,1181,1200]" captionTargetBox="[169,1455,274,1141]" captionTargetId="graphics@5.[170,741,774,1098]" captionTargetPageId="5" captionText="Figure 3. Demographic History and Gene Flow in Pongo (A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland. The ABC analyses are based on the comparison of 3,000 non-coding 2 - kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models. The numbers in the black boxes indicate the model’s posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A). Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also Table S 5. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species, and a ratio close to 0 indicates genetic isolation between species pairs. The x axis shows time scaled in years, assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also Figure S" httpUri="https://zenodo.org/record/1041357/files/figure.svg" pageId="4" pageNumber="5">Figure 3C</figureCitation>
|
||
), consistent with habitat destruction caused by the Toba supereruption 73 kya [
|
||
<bibRefCitation author="Chesner, C. A. & Rose, W. & Deino, A. & Drake, R. & Westgate, J. A." box="[893,918,1937,1958]" journalOrPublisher="Geology" pageId="4" pageNumber="5" pagination="200 - 203" part="19" refId="ref8511" refString="35. Chesner, C. A., Rose, W. I., Deino, A., Drake, R., and Westgate, J. A. (1991). Eruptive history of earths largest Quaternary caldera (Toba, Indonesia) clarified. Geology 19, 200 - 203." title="Eruptive history of earths largest Quaternary caldera (Toba, Indonesia) clarified" type="journal article" year="1991">35</bibRefCitation>
|
||
]. However,
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[1041,1200,1937,1958]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="4" pageNumber="5" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[1041,1200,1937,1958]" italics="true" pageId="4" pageNumber="5">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<emphasis box="[1254,1334,1937,1958]" italics="true" pageId="4" pageNumber="5">P. abelii</emphasis>
|
||
have been on independent evolutionary trajectories at least since the late Pleistocene/early Holocene, as gene flow between these
|
||
</paragraph>
|
||
<caption httpUri="https://zenodo.org/record/1041357/files/figure.svg" pageId="5" pageNumber="6" targetBox="[169,1455,274,1141]" targetPageId="5">
|
||
<paragraph blockId="5.[159,1468,1181,1452]" pageId="5" pageNumber="6">
|
||
Figure 3. Demographic History and Gene Flow in
|
||
<taxonomicName authorityName="Lacepede" authorityYear="1799" box="[630,691,1182,1200]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="5" pageNumber="6" phylum="Chordata" rank="genus">Pongo</taxonomicName>
|
||
(A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland.The ABC analyses are based on the comparison of 3,000 non-coding 2-kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models.The numbers in the black boxes indicate the model’s posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A).Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also
|
||
<tableCitation box="[368,441,1359,1376]" captionStart="Table S" captionStartId="36.[143,215,474,500]" captionTargetBox="[143,1943,548,1522]" captionText="Table S 5. Parameter estimation of the best supported models in the ABC and G-PhoCS analyses. Related to Figure 3 B." httpUri="http://table.plazi.org/id/DF0F6674FF95C310FF7216C5F983BCBA" pageId="5" pageNumber="6" tableUuid="DF0F6674FF95C310FF7216C5F983BCBA">Table S5</tableCitation>
|
||
. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species,and a ratio close to 0 indicates genetic isolation between species pairs.The x axis shows time scaled in years,assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also
|
||
<figureCitation box="[919,998,1435,1452]" captionStart="Figure 3" captionStartId="5.[159,219,1181,1200]" captionTargetBox="[169,1455,274,1141]" captionTargetId="graphics@5.[170,741,774,1098]" captionTargetPageId="5" captionText="Figure 3. Demographic History and Gene Flow in Pongo (A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland. The ABC analyses are based on the comparison of 3,000 non-coding 2 - kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models. The numbers in the black boxes indicate the model’s posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A). Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also Table S 5. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species, and a ratio close to 0 indicates genetic isolation between species pairs. The x axis shows time scaled in years, assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also Figure S" httpUri="https://zenodo.org/record/1041357/files/figure.svg" pageId="5" pageNumber="6">Figure S3</figureCitation>
|
||
.
|
||
</paragraph>
|
||
</caption>
|
||
<paragraph blockId="5.[159,797,1499,1987]" box="[159,797,1528,1549]" pageId="5" pageNumber="6">
|
||
populations has ceased completely 10–20 kya (
|
||
<figureCitation box="[646,745,1528,1549]" captionStart="Figure 3" captionStartId="5.[159,219,1181,1200]" captionTargetBox="[169,1455,274,1141]" captionTargetId="graphics@5.[170,741,774,1098]" captionTargetPageId="5" captionText="Figure 3. Demographic History and Gene Flow in Pongo (A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland. The ABC analyses are based on the comparison of 3,000 non-coding 2 - kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models. The numbers in the black boxes indicate the model’s posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A). Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also Table S 5. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species, and a ratio close to 0 indicates genetic isolation between species pairs. The x axis shows time scaled in years, assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also Figure S" httpUri="https://zenodo.org/record/1041357/files/figure.svg" pageId="5" pageNumber="6">Figure 3C</figureCitation>
|
||
) and
|
||
</paragraph>
|
||
<paragraph blockId="5.[159,797,1499,1987]" box="[159,797,1557,1578]" pageId="5" pageNumber="6">is now impossible because of habitat loss in areas between</paragraph>
|
||
<paragraph blockId="5.[159,797,1499,1987]" box="[159,393,1586,1607]" pageId="5" pageNumber="6">
|
||
the species’ ranges [
|
||
<bibRefCitation author="Wich, S. A. & Singleton, I & Nowak, M. G. & Utami Atmoko, S. S. & Nisam, G. & Arif, S. M. & Putra, R. H. & Ardi, R. & Fredriksson, G. & Usher, G." box="[369,381,1586,1607]" journalOrPublisher="Sci. Adv." pageId="5" pageNumber="6" pagination="1500789" part="2" refId="ref6655" refString="7. Wich, S. A., Singleton, I., Nowak, M. G., Utami Atmoko, S. S., Nisam, G., Arif, S. M., Putra, R. H., Ardi, R., Fredriksson, G., Usher, G., et al. (2016). Land-cover changes predict steep declines for the Sumatran orangutan (Pongo abelii). Sci. Adv. 2, e 1500789." title="Land-cover changes predict steep declines for the Sumatran orangutan (Pongo abelii)" type="journal article" year="2016">7</bibRefCitation>
|
||
].
|
||
</paragraph>
|
||
<paragraph blockId="5.[159,797,1499,1987]" lastBlockId="5.[829,1468,1499,1987]" pageId="5" pageNumber="6">
|
||
Nowadays, most biologists would probably adopt an operational species definition such as ‘‘a species is a population (or group of populations) with fixed heritable differences from other such populations (or groups of populations)’’ [
|
||
<bibRefCitation author="Groves, C. P. & Grubb, P." box="[636,661,1703,1724]" journalOrPublisher="Johns Hopkins University Press" pageId="5" pageNumber="6" refId="ref8569" refString="36. Groves, C. P., and Grubb, P. (2011). Ungulate Taxonomy (Johns Hopkins University Press)." title="Ungulate Taxonomy" type="book" year="2011">36</bibRefCitation>
|
||
]. With totally allopatric populations, a ‘‘reproductive isolation’’ criterion, such as is still espoused by adherents of the biological species concept, is not possible [
|
||
<bibRefCitation author="Coyne, J. A. & Orr, H. A." box="[406,434,1791,1812]" journalOrPublisher="Sinauer Associates" pageId="5" pageNumber="6" refId="ref8596" refString="37. Coyne, J. A., and Orr, H. A. (2004). Speciation (Sinauer Associates)." title="Speciation" type="book" year="2004">37</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="Mayr, E." box="[442,467,1791,1812]" journalOrPublisher="Belknap Press of Harvard University Press" pageId="5" pageNumber="6" refId="ref8622" refString="38. Mayr, E. (1963). Animal Species and Evolution (Belknap Press of Harvard University Press)." title="Animal Species and Evolution" type="book" year="1963">38</bibRefCitation>
|
||
]. Notwithstanding a long-running debate about the role of gene flow during speciation and genetic interpretations of the species concept [
|
||
<bibRefCitation author="Arnold, M. L." box="[551,579,1849,1870]" journalOrPublisher="Oxford University Press" pageId="5" pageNumber="6" refId="ref8645" refString="39. Arnold, M. L. (2016). Divergence with Genetic Exchange (Oxford University Press)." title="Divergence with Genetic Exchange" type="book" year="2016">39</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="Reznick, D. N. & Ricklefs, R. E." box="[588,613,1849,1870]" journalOrPublisher="Nature" pageId="5" pageNumber="6" pagination="837 - 842" part="457" refId="ref8667" refString="40. Reznick, D. N., and Ricklefs, R. E. (2009). Darwin's bridge between microevolution and macroevolution. Nature 457, 837 - 842." title="Darwin's bridge between microevolution and macroevolution" type="journal article" year="2009">40</bibRefCitation>
|
||
], genomic studies have found evidence for many instances of recent or ongoing gene flow between taxa that are recognized as distinct and well-established species. This includes examples within each of the other three hominid genera. A recent genomic study using comparable methods to ours revealed extensive gene flow between
|
||
<emphasis box="[895,1024,1528,1549]" italics="true" pageId="5" pageNumber="6">Gorilla gorilla</emphasis>
|
||
and
|
||
<emphasis box="[1071,1181,1528,1549]" italics="true" pageId="5" pageNumber="6">G. beringei</emphasis>
|
||
until 20–30 ka [
|
||
<bibRefCitation author="Scally, A. & Dutheil, J. Y. & Hillier, L. W. & Jordan, G. E. & Goodhead, I & Herrero, J. & Hobolth, A. & Lappalainen, T. & Mailund, T. & Marques-Bonet, T." box="[1350,1375,1528,1549]" journalOrPublisher="Nature" pageId="5" pageNumber="6" pagination="169 - 175" part="483" refId="ref8701" refString="41. Scally, A., Dutheil, J. Y., Hillier, L. W., Jordan, G. E., Goodhead, I., Herrero, J., Hobolth, A., Lappalainen, T., Mailund, T., Marques-Bonet, T., et al. (2012). Insights into hominid evolution from the gorilla genome sequence. Nature 483, 169 - 175." title="Insights into hominid evolution from the gorilla genome sequence" type="journal article" year="2012">41</bibRefCitation>
|
||
]. Similar, albeit older and less extensive, admixture occurred between
|
||
<emphasis italics="true" pageId="5" pageNumber="6">
|
||
<taxonomicName box="[1428,1467,1557,1578]" class="Mammalia" family="Hominidae" genus="Pan" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="5" pageNumber="6" phylum="Chordata" rank="genus">Pan</taxonomicName>
|
||
troglodytes
|
||
</emphasis>
|
||
and
|
||
<emphasis box="[989,1103,1586,1607]" italics="true" pageId="5" pageNumber="6">P. paniscus</emphasis>
|
||
[
|
||
<bibRefCitation author="de Manuel, M. & Kuhlwilm, M. & Frandsen, P. & Sousa, V. C. & Desai, T. & Martinez, J. & Hernandez-Rodriguez, J. & Dupanloup, I & Lao, O. & Hallast, P." box="[1114,1139,1586,1607]" journalOrPublisher="Science" pageId="5" pageNumber="6" pagination="477 - 481" part="354" refId="ref8783" refString="42. de Manuel, M., Kuhlwilm, M., Frandsen, P., Sousa, V. C., Desai, T., Prado- Martinez, J., Hernandez-Rodriguez, J., Dupanloup, I., Lao, O., Hallast, P., et al. (2016). Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 354, 477 - 481." title="Chimpanzee genomic diversity reveals ancient admixture with bonobos" type="journal article" year="2016">42</bibRefCitation>
|
||
] and was also reported for
|
||
<emphasis italics="true" pageId="5" pageNumber="6">
|
||
<taxonomicName box="[1405,1466,1586,1607]" class="Mammalia" family="Hominidae" genus="Homo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="5" pageNumber="6" phylum="Chordata" rank="genus">Homo</taxonomicName>
|
||
sapiens
|
||
</emphasis>
|
||
and
|
||
<emphasis box="[959,1158,1616,1637]" italics="true" pageId="5" pageNumber="6">H. neanderthalensis</emphasis>
|
||
[
|
||
<bibRefCitation author="Kuhlwilm, M. & Gronau, I & Hubisz, M. J. & de Filippo, C. & Prado-Martinez, J. & Kircher, M. & Fu, Q. & Burbano, H. A. & Lalueza-Fox, C. & de la Rasilla, M." box="[1172,1197,1616,1637]" journalOrPublisher="Nature" pageId="5" pageNumber="6" pagination="429 - 433" part="530" refId="ref8862" refString="43. Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., et al. (2016). Ancient gene flow from early modern humans into Eastern Neanderthals. Nature 530, 429 - 433." title="Ancient gene flow from early modern humans into Eastern Neanderthals" type="journal article" year="2016">43</bibRefCitation>
|
||
].
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[1217,1421,1616,1637]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="5" pageNumber="6" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[1217,1421,1616,1637]" italics="true" pageId="5" pageNumber="6">Pongo tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<emphasis box="[829,913,1645,1666]" italics="true" pageId="5" pageNumber="6">P. abelii</emphasis>
|
||
appear to be further examples, showing diagnostic phenotypic and other distinctions that had persisted in the past despite gene flow between them.
|
||
</paragraph>
|
||
<paragraph blockId="5.[829,1468,1499,1987]" lastBlockId="6.[142,780,999,1750]" lastPageId="6" lastPageNumber="7" pageId="5" pageNumber="6">
|
||
Due to the challenges involved in collecting suitable specimens for morphological and genomic analyses from critically endangered great apes, our description of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[1237,1395,1791,1812]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="5" pageNumber="6" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[1237,1395,1791,1812]" italics="true" pageId="5" pageNumber="6">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
had to rely on a single skeleton and two individual genomes for our main lines of evidence. When further data become available, a more detailed picture of the morphological and genomic diversity within this species and of the differences to other
|
||
<taxonomicName authorityName="Lacepede" authorityYear="1799" box="[1401,1467,1908,1929]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="5" pageNumber="6" phylum="Chordata" rank="genus">
|
||
<emphasis box="[1401,1467,1908,1929]" italics="true" pageId="5" pageNumber="6">Pongo</emphasis>
|
||
</taxonomicName>
|
||
species might emerge, which may require further taxonomic revision. However, is not uncommon to describe species based on a single specimen (e.g., [
|
||
<bibRefCitation author="Alba, D. M. & Almecija, S. & DeMiguel, D & Fortuny, J & Perez de los Rios, M. & Pina, M. & Robles, J. M. & Moya-Sola, S." box="[416,442,999,1020]" journalOrPublisher="Science" pageId="6" pageNumber="7" pagination="2625" part="350" refId="ref8946" refString="44. Alba, D. M., Almecija, S., DeMiguel, D., Fortuny, J., Perez de los Rios, M., Pina, M., Robles, J. M., and Moya-Sola, S. (2015). Miocene small-bodied ape from Eurasia sheds light on hominoid evolution. Science 350, aab 2625." title="Miocene small-bodied ape from Eurasia sheds light on hominoid evolution" type="journal article" year="2015">44</bibRefCitation>
|
||
–
|
||
<bibRefCitation author="Zalmout, I. S & Sanders, W. J. & Maclatchy, L. M. & Gunnell, G. F & Al- Mufarreh, Y. A. & Ali, M. A. & Nasser, A. A. H. & Al-Masari, A. M. & Al-Sobhi, S. A. & Nadhra, A. O." box="[452,477,999,1020]" journalOrPublisher="Nature" pageId="6" pageNumber="7" pagination="360 - 364" part="466" refId="ref9104" refString="46. Zalmout, I. S., Sanders, W. J., Maclatchy, L. M., Gunnell, G. F., Al- Mufarreh, Y. A., Ali, M. A., Nasser, A. A. H., Al-Masari, A. M., Al-Sobhi, S. A., Nadhra, A. O., et al. (2010). New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys. Nature 466, 360 - 364." title="New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys" type="journal article" year="2010">46</bibRefCitation>
|
||
]), and, importantly, there were consistent differences among orangutan populations from multiple independent lines of evidence, warranting the designation of a new species with the limited data at hand.
|
||
</paragraph>
|
||
<caption httpUri="https://zenodo.org/record/1041359/files/figure.png" pageId="6" pageNumber="7" targetBox="[142,1608,0,789]" targetPageId="6">
|
||
<paragraph blockId="6.[142,1449,831,949]" pageId="6" pageNumber="7">Figure 4. Sex-Specific Evolutionary History of Orangutans Bayesian phylogenetic trees for (A) mitochondrial genomes and (B) Y chromosomes. The mitochondrial tree is rooted with a human and a central chimpanzee sequence and the Y chromosome tree with a human sequence (not shown). **Posterior probability = 1.00. (C) Genotype-sharing matrix for mitogenomes (above the diagonal) and Y chromosomes (below the diagonal) for all analyzed male orangutans. A value of 1 indicates that two males have identical genotypes at all polymorphic sites; a value of 0 means that they have different genotypes at all variable positions.</paragraph>
|
||
</caption>
|
||
<paragraph blockId="6.[142,780,999,1750]" pageId="6" pageNumber="7">
|
||
With a census size of fewer than 800 individuals [
|
||
<bibRefCitation author="Wich, S. A. & Singleton, I & Nowak, M. G. & Utami Atmoko, S. S. & Nisam, G. & Arif, S. M. & Putra, R. H. & Ardi, R. & Fredriksson, G. & Usher, G." box="[755,767,1116,1137]" journalOrPublisher="Sci. Adv." pageId="6" pageNumber="7" pagination="1500789" part="2" refId="ref6655" refString="7. Wich, S. A., Singleton, I., Nowak, M. G., Utami Atmoko, S. S., Nisam, G., Arif, S. M., Putra, R. H., Ardi, R., Fredriksson, G., Usher, G., et al. (2016). Land-cover changes predict steep declines for the Sumatran orangutan (Pongo abelii). Sci. Adv. 2, e 1500789." title="Land-cover changes predict steep declines for the Sumatran orangutan (Pongo abelii)" type="journal article" year="2016">7</bibRefCitation>
|
||
],
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[142,301,1145,1166]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[142,301,1145,1166]" italics="true" pageId="6" pageNumber="7">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
is the least numerous of all great ape species [
|
||
<bibRefCitation author="IUCN" box="[148,173,1174,1195]" journalOrPublisher="Nature" pageId="6" pageNumber="7" publicationUrl="http://www.iucnredlist.org" refId="ref9209" refString="47. IUCN (2016). IUCN Red List of Threatened Species, version 2016.2. http: // www. iucnredlist. org /." title="IUCN Red List of Threatened Species, version 2016.2" type="book" year="2016">47</bibRefCitation>
|
||
]. Its range is located around 100 km from the closest population of
|
||
<emphasis box="[227,305,1203,1224]" italics="true" pageId="6" pageNumber="7">P. abelii</emphasis>
|
||
to the north (
|
||
<figureCitation box="[438,537,1203,1224]" captionStart="Figure 2" captionStartId="4.[142,202,1189,1208]" captionTargetBox="[142,1608,0,1149]" captionTargetId="figure@4.[151,1439,271,1150]" captionTargetPageId="4" captionText="Figure 2. Distribution, Genomic Diversity, and Population Structure of the Genus Pongo (A) Sampling areas across the current distribution of orangutans. The contour indicates the extent of the exposed Sunda Shelf during the Last Glacial Maximum. The black rectangle delimits the area shown in Figure 1 A. n indicates the number of sequenced individuals. See also Table S 4. (B) PCA of genomic diversity in Pongo. Axis labels show the percentages of the total variance explained by the first two principal components. Colored bars in the insert represent the distribution of nucleotide diversity in genome-wide 1 - Mb windows across sampling areas. (C) Bayesian clustering analysis of population structure using the program ADMIXTURE. Each vertical bar depicts an individual, with colors representing the inferred ancestry proportions with different assumed numbers of genetic clusters (K, horizontal sections)." httpUri="https://zenodo.org/record/1041355/files/figure.png" pageId="6" pageNumber="7">Figure 2A</figureCitation>
|
||
). A combination of small population size and geographic isolation is of particularly high conservation concern, as it may lead to inbreeding depression [
|
||
<bibRefCitation author="Hedrick, P. W. & Kalinowski, S. T." box="[148,173,1291,1312]" journalOrPublisher="Annu. Rev. Ecol. Syst." pageId="6" pageNumber="7" pagination="139 - 162" part="31" refId="ref9236" refString="48. Hedrick, P. W., and Kalinowski, S. T. (2000). Inbreeding depression in conservation biology. Annu. Rev. Ecol. Syst. 31, 139 - 162." title="Inbreeding depression in conservation biology" type="journal article" year="2000">48</bibRefCitation>
|
||
] and threaten population persistence [
|
||
<bibRefCitation author="Allendorf, F. W. & Luikart, G. & Aitken, S. N." box="[566,591,1291,1312]" journalOrPublisher="Second Edition (John Wiley & Sons)" pageId="6" pageNumber="7" refId="ref9276" refString="49. Allendorf, F. W., Luikart, G., and Aitken, S. N. (2013). Conservation and the Genetics of Populations, Second Edition (John Wiley & Sons)." title="Conservation and the Genetics of Populations" type="book" year="2013">49</bibRefCitation>
|
||
]. Highlighting this, we discovered extensive runs of homozygosity in the genomes of both
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[224,383,1349,1370]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[224,383,1349,1370]" italics="true" pageId="6" pageNumber="7">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
individuals (
|
||
<figureCitation box="[512,610,1349,1370]" captionStart="Figure 3" captionStartId="5.[159,219,1181,1200]" captionTargetBox="[169,1455,274,1141]" captionTargetId="graphics@5.[170,741,774,1098]" captionTargetPageId="5" captionText="Figure 3. Demographic History and Gene Flow in Pongo (A) Model selection by ABC of plausible colonization histories of orangutans on Sundaland. The ABC analyses are based on the comparison of 3,000 non-coding 2 - kb loci randomly distributed across the genome with corresponding data simulated under the different demographic models. The numbers in the black boxes indicate the model’s posterior probability. NT, Sumatran populations north of Lake Toba; ST, the Sumatran population of Batang Toru south of Lake Toba; BO, Bornean populations. (B) ABC parameter estimates based on the full demographic model with colonization pattern inferred in (A). Numbers in gray rectangles represent point estimates of effective population size (Ne). Arrows indicate gene flow among populations, and numbers above the arrows represent point estimates of numbers of migrants per generation. See also Table S 5. (C) Relative cross-coalescent rate (RCCR) analysis for between-species pairs of phased high-coverage genomes. A RCCR close to 1 indicates extensive gene flow between species, and a ratio close to 0 indicates genetic isolation between species pairs. The x axis shows time scaled in years, assuming a generation time of 25 years and an autosomal mutation rate of 1.5 3 10 8 per site per generation. See also Figure S" httpUri="https://zenodo.org/record/1041357/files/figure.svg" pageId="6" pageNumber="7">Figure S3</figureCitation>
|
||
), pointing at the occurrence of recent inbreeding.
|
||
</paragraph>
|
||
<paragraph blockId="6.[142,780,999,1750]" pageId="6" pageNumber="7">
|
||
To ensure long-term survival of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[483,638,1408,1429]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[483,638,1408,1429]" italics="true" pageId="6" pageNumber="7">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
, conservation measures need to be implemented swiftly. Due to the rugged terrain, external threats have been primarily limited to road construction, illegal clearing of forests, hunting, killings during crop conflict, and trade in orangutans [
|
||
<bibRefCitation author="Wich, S. A. & Singleton, I & Nowak, M. G. & Utami Atmoko, S. S. & Nisam, G. & Arif, S. M. & Putra, R. H. & Ardi, R. & Fredriksson, G. & Usher, G." box="[550,565,1525,1546]" journalOrPublisher="Sci. Adv." pageId="6" pageNumber="7" pagination="1500789" part="2" refId="ref6655" refString="7. Wich, S. A., Singleton, I., Nowak, M. G., Utami Atmoko, S. S., Nisam, G., Arif, S. M., Putra, R. H., Ardi, R., Fredriksson, G., Usher, G., et al. (2016). Land-cover changes predict steep declines for the Sumatran orangutan (Pongo abelii). Sci. Adv. 2, e 1500789." title="Land-cover changes predict steep declines for the Sumatran orangutan (Pongo abelii)" type="journal article" year="2016">7</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="Wich, S. A. & Fredriksson, G. M. & Usher, G. & Peters, H. H. & Priatna, D. & Basalamah, F. & Susanto, W. & Kuhl, H." box="[579,603,1525,1546]" journalOrPublisher="Biol. Conserv." pageId="6" pageNumber="7" pagination="163 - 169" part="146" refId="ref6947" refString="11. Wich, S. A., Fredriksson, G. M., Usher, G., Peters, H. H., Priatna, D., Basalamah, F., Susanto, W., and Kuhl, H. (2012). Hunting of Sumatran orang-utans and its importance in determining distribution and density. Biol. Conserv. 146, 163 - 169." title="Hunting of Sumatran orang-utans and its importance in determining distribution and density" type="journal article" year="2012">11</bibRefCitation>
|
||
]. A hydroelectric development has been proposed recently in the area of highest orangutan density, which could impact up to 8% of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[142,303,1613,1634]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[142,303,1613,1634]" italics="true" pageId="6" pageNumber="7">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
’s habitat. This project might lead to further genetic impoverishment and inbreeding, as it would jeopardize chances of maintaining habitat corridors between the western and eastern range (
|
||
<figureCitation box="[378,476,1700,1721]" captionStart="Figure 1" captionStartId="2.[142,202,1428,1447]" captionTargetBox="[142,1608,0,1387]" captionTargetId="figure@2.[150,1441,271,1388]" captionTargetPageId="2" captionText="Figure 1. Morphological Evidence Supporting a New Orangutan Species (A) Current distribution of Pongo tapanuliensis on Sumatra. The holotype locality is marked with a red star. The area shown in the map is indicated in Figure 2 A. (B) Holotype skull and mandible of P. tapanuliensis from a recently deceased individual from Batang Toru. See also Figure S 1 and Tables S 1 and S 2. (C) Violin plots of the first seven principal components of 26 cranio-mandibular morphological variables of eight north Sumatran P. abelii and 19 Bornean P. pygmaeus individuals of similar developmental state as the P. tapanuliensis holotype skull (black horizontal lines). See also Figure S 2." httpUri="https://zenodo.org/record/1041353/files/figure.png" pageId="6" pageNumber="7">Figure 1A</figureCitation>
|
||
), as well as smaller nature reserves, all of which maintain small populations of
|
||
<taxonomicName authorityName="Alexander Nater & Maja P. Mattle-Greminger & nton Nurcahyo & Matthew G. Nowak & Marc de Manuel & Tariq Desai & Colin Groves & Marc Pybus & Tugce Bilgin Sonay & Christian Roos & Adriano R. Lameira & Serge A. Wich & James Askew & Marina Davila-Ross & Gabriella Fredriksson & Guillem de Valles & Ferran Casals & avier Prado-Martinez & Benoit Goossens & Ernst J. Verschoor & Kristin S. Warren & Ian Singleton" authorityYear="2017" box="[620,773,1729,1750]" class="Mammalia" family="Hominidae" genus="Pongo" higherTaxonomySource="GBIF" kingdom="Animalia" order="Primates" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="tapanuliensis">
|
||
<emphasis box="[620,773,1729,1750]" italics="true" pageId="6" pageNumber="7">P. tapanuliensis</emphasis>
|
||
</taxonomicName>
|
||
.
|
||
</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |