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One reason for this is the difficulty of distinguishing genetic admixture following secondary contact from incomplete lineage sorting, both of which can generate similar patterns of genetic variation. Using a combination of multilocus analyses and coalescent simulation, we explore how these two processes occurred in the <jats:styled-content style=\"fixed-case\">P<\/jats:styled-content>leistocene evolutionary history of a widespread <jats:styled-content style=\"fixed-case\">E<\/jats:styled-content>ast <jats:styled-content style=\"fixed-case\">A<\/jats:styled-content>sian bird, the <jats:styled-content style=\"fixed-case\">V<\/jats:styled-content>inous\u2010throated parrotbill, <jats:italic><jats:styled-content style=\"fixed-case\">P<\/jats:styled-content>aradoxornis webbianus<\/jats:italic>. Maximum likelihood (<jats:styled-content style=\"fixed-case\">ML<\/jats:styled-content>) tree identified two major mitochondrial lineages, which are geographically separated in most parts of its range, but are sympatric at a few sampling sites. <jats:styled-content style=\"fixed-case\">NJ<\/jats:styled-content> tree and <jats:styled-content style=\"fixed-case\">S<\/jats:styled-content>tructure analysis of microsatellite data set revealed an extensive level of admixture and little population structure, suggesting recent admixture between two formerly separated groups. Networks from nuclear <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> data sets, however, did not indicate any geographically isolated groups but rather a panmictic population, thus support incomplete lineage sorting. By using coalescent simulation approaches, we show that both processes did occur, although at different temporal scales. During the <jats:styled-content style=\"fixed-case\">P<\/jats:styled-content>leistocene glaciations, probably around 0.1\u20130.5\u00a0Ma (the <jats:styled-content style=\"fixed-case\">M<\/jats:styled-content>arine <jats:styled-content style=\"fixed-case\">I<\/jats:styled-content>sotope <jats:styled-content style=\"fixed-case\">S<\/jats:styled-content>tage 6, <jats:styled-content style=\"fixed-case\">MIS<\/jats:styled-content>6), <jats:italic><jats:styled-content style=\"fixed-case\">P<\/jats:styled-content>.\u00a0webbianus<\/jats:italic> contracted into two separate refugia, and subsequently accumulated genetic divergence. During the interglacial <jats:styled-content style=\"fixed-case\">MIS<\/jats:styled-content>5, the species expanded into previously glaciated areas allowing the once separated groups to come into contact and become admixed. Taken together, our results indicate the current genetic variation within <jats:italic><jats:styled-content style=\"fixed-case\">P<\/jats:styled-content>.\u00a0webbianus<\/jats:italic> is a combination pattern of widespread distribution in pre\u2010<jats:styled-content style=\"fixed-case\">P<\/jats:styled-content>leistocene, then contraction and fragmentation into separated refugia during glacial advance, followed by recently postglacial expansion and admixture.<\/jats:p>","DOI":"10.1111\/mec.12080","type":"journal-article","created":{"date-parts":[[2012,10,23]],"date-time":"2012-10-23T15:44:06Z","timestamp":1351007046000},"page":"6117-6133","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":68,"title":["Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the <scp>V<\/scp>inous\u2010throated parrotbill (<i><scp>P<\/scp>aradoxornis webbianus<\/i>)"],"prefix":"10.1111","volume":"21","author":[{"given":"Yanhua","family":"Qu","sequence":"first","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing 100101 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruiying","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing 100101 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qing","family":"Quan","sequence":"additional","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing 100101 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gang","family":"Song","sequence":"additional","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing 100101 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shou Hsien","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Life Science National Taiwan Normal University Taibei Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fumin","family":"Lei","sequence":"additional","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing 100101 China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2012,10,23]]},"reference":[{"key":"e_1_2_7_2_1","first-page":"267","volume-title":"Second International Symposium on Information Theory","author":"Akaike 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