{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T16:36:04Z","timestamp":1762101364437},"reference-count":56,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2012,11,15]],"date-time":"2012-11-15T00:00:00Z","timestamp":1352937600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0049429","type":"journal-article","created":{"date-parts":[[2012,11,15]],"date-time":"2012-11-15T22:38:39Z","timestamp":1353019119000},"page":"e49429","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":22,"title":["Effective Population Size Dynamics and the Demographic Collapse of Bornean Orang-Utans"],"prefix":"10.1371","volume":"7","author":[{"given":"Reeta","family":"Sharma","sequence":"first","affiliation":[]},{"given":"Natasha","family":"Arora","sequence":"additional","affiliation":[]},{"given":"Benoit","family":"Goossens","sequence":"additional","affiliation":[]},{"given":"Alexander","family":"Nater","sequence":"additional","affiliation":[]},{"given":"Nadja","family":"Morf","sequence":"additional","affiliation":[]},{"given":"Jordi","family":"Salmona","sequence":"additional","affiliation":[]},{"given":"Michael W.","family":"Bruford","sequence":"additional","affiliation":[]},{"given":"Carel P.","family":"Van Schaik","sequence":"additional","affiliation":[]},{"given":"Michael","family":"Kr\u00fctzen","sequence":"additional","affiliation":[]},{"given":"Loun\u00e8s","family":"Chikhi","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2012,11,15]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","unstructured":"Qu\u00e9m\u00e9r\u00e9 E, Amelot X, Pierson J, Crouau-Roy B, Chikhi L (2012) Genetic data suggest a natural prehuman origin of open habitats in northern Madagascar and question the deforestation narrative in this region (in press). Proceedings of the National Academy of Sciences.","DOI":"10.1073\/pnas.1200153109"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1016\/j.biocon.2008.02.025","article-title":"From genetic diversity and structure to conservation:Genetic signature of recent population declines in three mouse lemur species (<italic>Microcebus<\/italic> spp.)","volume":"141","author":"GL Olivieri","year":"2008","journal-title":"Biol Conserv"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1007\/s10592-007-9399-7","article-title":"Genetic structure and signature of population decrease in the critically endangered freshwater cyprinid <italic>Chondrostoma lusitanicum<\/italic>","volume":"9","author":"VC Sousa","year":"2008","journal-title":"Conserv Genet"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/S0006-3207(97)00046-3","article-title":"Genetic effects of forest fragmentation on a rainforest restricted lizard (<italic>scincidae<\/italic>:<italic>gnypetoscincus queenslandiae<\/italic>)","volume":"83","author":"M Cunningham","year":"1998","journal-title":"Biol Conserv"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1111\/j.1365-294X.2006.03216.x","article-title":"Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera:Stenopelmatidae: Stenopelmatus)","volume":"16","author":"AG Vandergast","year":"2007","journal-title":"Mol Ecol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1111\/j.1365-294X.2007.03147.x","article-title":"Population fragmentation leads to spatial and temporal genetic structure in the endangered Spanish imperial eagle","volume":"16","author":"B Mart\u00ednez-Cruz","year":"2007","journal-title":"Mol Ecol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"e43524","DOI":"10.1371\/journal.pone.0043524","article-title":"Signature of a pre-human population decline in the critically endangered Reunion Island endemic forest bird <italic>Coracina newtoni<\/italic>","volume":"7","author":"J Salmona","year":"2012","journal-title":"Plos One"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1093\/genetics\/153.4.2013","article-title":"Detecting population expansion and decline using microsatellites","volume":"153","author":"MA Beaumont","year":"1999","journal-title":"Genetics"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.1007\/s10592-010-0076-x","article-title":"Genetic signatures of population change in the British golden eagle (<italic>Aquila chrysaetos<\/italic>)","volume":"11","author":"BP Bourke","year":"2010","journal-title":"Conserv Genet"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1111\/j.0014-3820.2002.tb00857.x","article-title":"Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical bayesian model","volume":"56","author":"JF Storz","year":"2002","journal-title":"Evolution"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"e25","DOI":"10.1371\/journal.pbio.0040025","article-title":"Genetic Signature of Anthropogenic Population Collapse in Orang-utans","volume":"4","author":"B Goossens","year":"2006","journal-title":"PLoS Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e193","DOI":"10.1371\/journal.pbio.0030193","article-title":"On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas","volume":"3","author":"J Hey","year":"2005","journal-title":"PLoS Biology"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1073\/pnas.0611164104","article-title":"Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics","volume":"104","author":"J Hey","year":"2007","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1534\/genetics.110.118661","article-title":"The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes","volume":"186","author":"L Chikhi","year":"2010","journal-title":"Genetics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"4648","DOI":"10.1111\/j.1365-294X.2010.04783.x","article-title":"Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure","volume":"19","author":"B Peter","year":"2010","journal-title":"Mol Ecol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1534\/genetics.108.094904","article-title":"The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations","volume":"182","author":"T St\u00e4dler","year":"2009","journal-title":"Genetics"},{"key":"ref17","doi-asserted-by":"crossref","unstructured":"Girod C, Vitalis R, Leblois R, Freville H (2010) Inferring Population Decline and Expansion from Microsatellite Data: a Simulation-Based Evaluation of the MSVAR Method. Genetics.","DOI":"10.1534\/genetics.110.121764"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1111\/j.1523-1739.2010.01556.x","article-title":"Genetic Bottlenecks Driven by Population Disconnection","volume":"24","author":"T Broquet","year":"2010","journal-title":"Conserv Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1002\/1520-6505(2000)9:5<201::AID-EVAN2>3.0.CO;2-Y","article-title":"The Behavioral Ecology and Conservation of the Orangutan (<italic>Pongo pygmaeus<\/italic>): A Tale of Two Islands","volume":"9","author":"RA Delgado","year":"2000","journal-title":"Evol Anthropol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e12042","DOI":"10.1371\/journal.pone.0012042","article-title":"Declining orangutan encounter rates from wallace to the present suggest the species was once more abundant","volume":"5","author":"E Meijaard","year":"2010","journal-title":"PLoS ONE"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"21376","DOI":"10.1073\/pnas.1010169107","article-title":"Effects of Pleistocene glaciations and rivers on the population structure of Bornean orangutans (<italic>Pongo pygmaeus<\/italic>)","volume":"107","author":"N Arora","year":"2010","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/nature09687","article-title":"Comparative and demographic analysis of orang-utan genomes","volume":"469","author":"DP Locke","year":"2011","journal-title":"Nature"},{"key":"ref23","first-page":"51","article-title":"The Niah excavations and an assessment of the impact of early man on mammals in Borneo","volume":"20","author":"L Medway","year":"1977","journal-title":"Asian Perspect"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1017\/S0003598X00067922","article-title":"The prehistory of a Friction Zone: first farmers and hunters-gatherers in Southeast Asia","volume":"85","author":"CFW Higham","year":"2011","journal-title":"Antiquity"},{"key":"ref25","first-page":"147","article-title":"Barker G. Prehistoric foragers and farmers in Southeast Asia: renewed investigations at Niah Cave, Sarawak","volume":"2002"},{"key":"ref26","doi-asserted-by":"crossref","unstructured":"Rijksen HD, Meijaard E (1999) Our Vanishing Relative:The Status of Wild Orang-utans at the Close of the Twentieth Century. Kluwer Academic Publishers, Dordrecht, The Netherlands.","DOI":"10.1007\/978-94-010-9020-9"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/S0006-3207(00)00087-2","article-title":"The population and distribution of Orang-utans (<italic>Pongo pygmaeus pygmaeus<\/italic>) in and around the Danau Sentarum Wildlife Reserve, West Kalimantan, Indonesia","volume":"97","author":"AE Russon","year":"2001","journal-title":"Biological Conservation"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1017\/S136794300400157X","article-title":"Determination of ape distribution and population size using ground and aerial surveys: a case study with orang-utans in lower Kinabatangan, Sabah, Malaysia","volume":"7","author":"M Ancrenaz","year":"2004","journal-title":"Anim Conserv"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1111\/j.1523-1739.2004.00018.x","article-title":"Loss of Forest Cover in Kalimantan, Indonesia, since the 1997\u20131998 El Ni\u00f1o","volume":"18","author":"DO Fuller","year":"2003","journal-title":"Conservation Biology"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/S0006-3207(02)00186-6","article-title":"Population status of the Bornean orang-utan (<italic>Pongo pygmaeus<\/italic>) in the Sebangau peat swamp forest, Central Kalimantan, Indonesia","volume":"110","author":"H Morrogh-Bernard","year":"2003","journal-title":"Biol Conserv"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1111\/j.1365-294X.2004.02421.x","article-title":"Patterns of genetic diversity and migration in increasingly fragmented and declining orang-utan (<italic>Pongo pygmaeus<\/italic>) populations from Sabah, Malaysia","volume":"14","author":"B Goossens","year":"2005","journal-title":"Mol Ecol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"249","DOI":"10.3354\/esr00295","article-title":"Projecting genetic diversity and population viability for the fragmented orang-utan population in the Kinabatangan floodplain, Sabah, Malaysia","volume":"12","author":"MW Bruford","year":"2010","journal-title":"Endangered Species Research"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1863","DOI":"10.1093\/genetics\/153.4.1863","article-title":"Nonequilibrium Migration in Human History","volume":"153","author":"J Wakeley","year":"1999","journal-title":"Genetics"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1093\/genetics\/89.3.583","article-title":"Estimation of average heterozygosity and genetic distance from a small sample of individuals","volume":"89","author":"M Nei","year":"1978","journal-title":"Genetics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.2307\/2408641","article-title":"Estimating F-statistics for the analysis of population structure","volume":"38","author":"BS Weir","year":"1984","journal-title":"Evolution"},{"key":"ref36","unstructured":"Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (1996\u20132004) GENETIX 4.05. <italic>Logiciel sous Windows Pour la G\u00e9n\u00e9tique des Populations<\/italic> (Universit\u00e9 de Montpellier II, Montpellier, France), vol 4.05."},{"key":"ref37","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1534\/genetics.110.121764","article-title":"Inferring Population Decline and Expansion from Microsatellite Data: a Simulation-Based Evaluation of the MSVAR Method","volume":"188","author":"C Girod","year":"2011","journal-title":"Genetics"},{"key":"ref38","doi-asserted-by":"crossref","unstructured":"Geweke J (1992) Evaluating the accuracy of sampling-based approaches to the calculation of posterior moments. In Proceedings of the Fourth Valencia International Meeting on Bayesian Statistics, edited by Bernado, J, J Berger, A Dawid, and A Smith, Oxford University Press. 169\u2013193.","DOI":"10.1093\/oso\/9780198522669.003.0010"},{"key":"ref39","doi-asserted-by":"crossref","unstructured":"Wich SA, Vries Hd, Ancrenaz M, Perkins L, Shumaker RW, <etal>et al<\/etal>.. (2009) Orangutan life history variation. In: Wich SA, Atmoko SSU, Setia TM, Schaik CPv, editors. Orangutans: Geographic Variation in Behavioral Ecology and Conservation: New York: Oxford University Press.","DOI":"10.1093\/acprof:oso\/9780199213276.003.0005"},{"key":"ref40","doi-asserted-by":"crossref","unstructured":"Langergraber KE, Pr\u00fcfer K, Rowney C, Boesch C, Crockford C, <etal>et al<\/etal>.. (2012) Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proceedings of the National Academy of Sciences.","DOI":"10.1073\/pnas.1211740109"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"90","DOI":"10.7152\/bippa.v14i0.11592","article-title":"The palaeoecological context at Niah cave, Saravak: evidence from the primate fauna","volume":"14","author":"T Harrison","year":"1996","journal-title":"Indo-Pacific Prehistory Association Bulletin"},{"key":"ref42","doi-asserted-by":"crossref","unstructured":"Cribb R (2000) Historical atlas of Indonesia. London: Curzon-New Asian Library. 256 p.","DOI":"10.4324\/9780203824610"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"2275","DOI":"10.1093\/molbev\/msr042","article-title":"Sex-biased Dispersal and Volcanic Activities Shaped Phylogeographic Patterns of Extant Orangutans (genus: <italic>Pongo<\/italic>)","volume":"28","author":"A Nater","year":"2011","journal-title":"Mol Biol Evol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1159\/000156681","article-title":"Quaternary environments and the evolution of primates in East Asia, with notes on two new specimens of fossil <italic>Cercopithecidae<\/italic> from China","volume":"60","author":"NG Jablonski","year":"1993","journal-title":"Folia Primatol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"2228","DOI":"10.1016\/j.quascirev.2005.04.004","article-title":"Paleoenvironments of insular Southeast Asia during the Last Glacial Period: a savanna corridor in Sundaland","volume":"24","author":"M Bird","year":"2005","journal-title":"Sci Rev"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/j.jhevol.2005.12.005","article-title":"Population history, biogeography, and taxonomy of orangutans (Genus: <italic>Pongo<\/italic>) based on a population genetic meta-analysis of multiple loci","volume":"50","author":"ME Steiper","year":"2006","journal-title":"Journal of Human Evolution"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1016\/j.ympev.2006.11.015","article-title":"Molecular phylogeny and evolutionary history of Southeast Asian macaques forming the <italic>M. silenus<\/italic> group","volume":"42","author":"T Ziegler","year":"2007","journal-title":"Mol Phylogenet Evol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1111\/j.1365-2699.2008.02071.x","article-title":"The Indochinese\u2013Sundaic zoogeographic transition: a description and analysis of terrestrial mammal species distributions","volume":"36","author":"DS Woodruff","year":"2009","journal-title":"J Biogeogr"},{"key":"ref49","doi-asserted-by":"crossref","unstructured":"Harrison T, Krigbaum J, Manser J (2006) Primate Biogeography and Ecology on the Sunda Shelf Islands: A Paleontological and Zooarchaeological Perspective. In: S M Lehman JGF, editor. Primate Biogeography: Springer, New York.","DOI":"10.1007\/0-387-31710-4_12"},{"key":"ref50","first-page":"1","article-title":"Quaternary gibbons from the Malay Archipelago","volume":"46","author":"DA Hooijer","year":"1960","journal-title":"Zool Verhand Leiden"},{"key":"ref51","first-page":"133","article-title":"Archaeological and ecological implications of the primate fauna from prehistoric sites in Borneo","volume":"20","author":"T Harrison","year":"2000","journal-title":"Bull Indo-Pacific Prehist Assoc"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"3788","DOI":"10.1111\/j.1365-294X.2008.03871.x","article-title":"Effective population size dynamics reveal impacts of historic climatic events and recent anthropogenic pressure in African elephants","volume":"17","author":"JBA Okello","year":"2008","journal-title":"Mol Ecol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"2898","DOI":"10.1111\/j.1365-294X.2008.03793.x","article-title":"Riverine effects on mitochondrial structure of Bornean orang-utans (<italic>Pongo pygmaeus<\/italic>) at two spatial scales","volume":"17","author":"M Jalil","year":"2008","journal-title":"Mol Ecol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"3352","DOI":"10.1111\/j.1365-294X.2012.05608.x","article-title":"Parentage-based pedigree reconstruction reveals female matrilineal clusters and male-biased dispersal in nongregarious Asian great apes, the Bornean orang-utans (<italic>Pongo pygmaeus<\/italic>)","volume":"21","author":"N Arora","year":"2012","journal-title":"Molecular Ecology"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"2025","DOI":"10.1093\/genetics\/162.4.2025","article-title":"Approximate Bayesian Computation in Population Genetics","volume":"162","author":"MA Beaumont","year":"2002","journal-title":"Genetics"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"2609","DOI":"10.1111\/j.1365-294X.2010.04690.x","article-title":"ABC as a flexible framework to estimate demography over space and time: some cons, many pros","volume":"19","author":"G Bertorelle","year":"2010","journal-title":"Mol Ecol"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0049429","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T11:54:41Z","timestamp":1714564481000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0049429"}},"subtitle":[],"editor":[{"given":"Wayne M.","family":"Getz","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2012,11,15]]},"references-count":56,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2012,11,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0049429","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,11,15]]}}}