{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T01:44:44Z","timestamp":1747187084416,"version":"3.40.5"},"reference-count":71,"publisher":"Wiley","issue":"19","license":[{"start":{"date-parts":[[2021,8,4]],"date-time":"2021-08-04T00:00:00Z","timestamp":1628035200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100006363","name":"National Geographic Society","doi-asserted-by":"publisher","award":["8753\u201010"],"award-info":[{"award-number":["8753\u201010"]}],"id":[{"id":"10.13039\/100006363","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005835","name":"American Museum of Natural History","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005835","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006405","name":"American Ornithologists' Union","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006405","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008294","name":"Louisiana State University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008294","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008175","name":"Coypu Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008175","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB\u20100228688","DEB\u20101241059"],"award-info":[{"award-number":["DEB\u20100228688","DEB\u20101241059"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology"],"published-print":{"date-parts":[[2021,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Intraspecific polymorphism in birds, especially plumage colour polymorphism, and the mechanisms that control it are an area of active research in evolutionary biology. The black\u2010headed bulbul (<jats:italic>Brachypodius atriceps<\/jats:italic>) is a polymorphic species with two distinct morphs, yellow and grey. This species inhabits the mainland and virtually all continental islands of Southeast Asia where yellow morphs predominate, but on two islands in the Sunda region, Bawean and Maratua, grey morphs are common or exclusive. Here, we generated a high\u2010quality reference genome of a yellow individual and resequenced genomes of multiple individuals of both yellow and grey morphs to study the genetic basis of coloration and population history of the species. Using PCA and STRUCTURE analysis, we found the Maratua Island population (which is exclusively grey) to be distinct from all other <jats:italic>B<\/jats:italic>. <jats:italic>atriceps<\/jats:italic> populations, having been isolated c. 1.9\u00a0million years ago (Ma). In contrast, Bawean grey individuals (a subset of yellow and grey individuals on that island) are embedded within an almost panmictic Sundaic clade of yellow birds. Using <jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub> and <jats:italic>d<\/jats:italic><jats:sub>xy<\/jats:sub> to compare variable genomic segments between Maratua and yellow individuals, we located peaks of divergence and identified candidate loci involved in the colour polymorphism. Tests of selection among coding\u2010proteins in high <jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub> regions, however, did not indicate selection on the candidate genes. Overall, we report on some loci that are potentially responsible for the grey\/yellow polymorphism in a species that otherwise shows little genetic diversification across most of its range.<\/jats:p>","DOI":"10.1111\/mec.16089","type":"journal-article","created":{"date-parts":[[2021,7,23]],"date-time":"2021-07-23T15:10:51Z","timestamp":1627053051000},"page":"4757-4770","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Genomic investigation of colour polymorphism and phylogeographic variation among populations of black\u2010headed bulbul (<i>Brachypodius atriceps<\/i>) in insular southeast Asia"],"prefix":"10.1111","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3561-2336","authenticated-orcid":false,"given":"Subir B.","family":"Shakya","sequence":"first","affiliation":[{"name":"Museum of Natural Science and Department of Biological Sciences Louisiana State University Baton Rouge Louisiana USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tri","family":"Haryoko","sequence":"additional","affiliation":[{"name":"Museum Zoologicum Bogoriense Research Centre for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammad","family":"Irham","sequence":"additional","affiliation":[{"name":"Museum Zoologicum Bogoriense Research Centre for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"family":"Suparno","sequence":"additional","affiliation":[{"name":"Museum Zoologicum Bogoriense Research Centre for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dewi M.","family":"Prawiradilaga","sequence":"additional","affiliation":[{"name":"Museum Zoologicum Bogoriense Research Centre for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frederick H.","family":"Sheldon","sequence":"additional","affiliation":[{"name":"Museum of Natural Science and Department of Biological Sciences Louisiana State University Baton Rouge Louisiana USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2021,8,4]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.101410.109"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010019\u201009579\u2010y"},{"key":"e_1_2_9_4_1","first-page":"235","article-title":"Birds from Maratua Island, off the east coast of Borneo","volume":"5","author":"Bangs O.","year":"1927","journal-title":"Occasional Papers of the Boston Society of Natural History"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.14862"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/0168\u20109525(96)10031\u20107"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.109.101741"},{"issue":"2","key":"e_1_2_9_8_1","first-page":"546","article-title":"Notices and Descriptions of various new or little known Species of Birds","volume":"14","author":"Blyth E.","year":"1845","journal-title":"Journal of the Asiatic Society of Bengal"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msy188"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0092233"},{"key":"e_1_2_9_11_1","doi-asserted-by":"crossref","first-page":"11","DOI":"10.14203\/treubia.v45i0.3445","article-title":"Ornithological observations from Maratua and Bawean Islands, Indonesia","volume":"45","author":"Burner R. C.","year":"2018","journal-title":"Treubia"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.1602404"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a026334"},{"key":"e_1_2_9_14_1","first-page":"259","article-title":"Phylogeography of three endemic birds of Maratua Island, a potential archive of Bornean biogeography","volume":"63","author":"Chua V. L.","year":"2015","journal-title":"Raffles Bulletin of Zoology"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12796"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/jbi.12662"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.73.1.262"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12686\u2010011\u20109548\u20107"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365\u2010294X.2005.02553.x"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv646"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2873-9"},{"key":"e_1_2_9_22_1","first-page":"1","article-title":"Systematic review of Southeast Asian longtail macaques, Macaca\n                  fascicularis (Raffles, [1821])","volume":"81","author":"Fooden J.","year":"1995","journal-title":"Fieldiana: Zoology New Series"},{"issue":"10","key":"e_1_2_9_23_1","first-page":"1","article-title":"Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage coloration","volume":"7","author":"Gao G.","year":"2018","journal-title":"GigaScience"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aba0803"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7755"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000695"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.2307\/j.ctv22jnscm"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.hdy.6800861"},{"key":"e_1_2_9_29_1","first-page":"313","article-title":"Notes on the Island of Bawean (Java Sea) with special reference to the birds","volume":"21","author":"Hoogerwerf A.","year":"1966","journal-title":"The Natural History Bulletin of the Siam Society"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn129"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09806-6"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.2307\/3211856"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1525\/auk.2011.11096"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10872\u2010008\u20100005\u20105"},{"issue":"1","key":"e_1_2_9_35_1","first-page":"79","article-title":"A supergene determines highly divergent male reproductive morphs in the ruff","volume":"48","author":"K\u00fcpper C.","year":"2015","journal-title":"Nature"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.abb.2010.08.006"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3430"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1111\/evo.13093"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.5964"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.12995"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr642"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2016.03.076"},{"volume-title":"The Theory of Island Biogeography","year":"1967","author":"MacArthur R. 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C.(1987).Biogeographic Evolution of the Malay Archipelago(vol.4).Oxford UK:Oxford University Press."},{"key":"e_1_2_9_72_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msm088"}],"container-title":["Molecular Ecology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/mec.16089","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/mec.16089","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/am-pdf\/10.1111\/mec.16089","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/mec.16089","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,12]],"date-time":"2024-03-12T08:30:48Z","timestamp":1710232248000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/mec.16089"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,4]]},"references-count":71,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2021,10]]}},"alternative-id":["10.1111\/mec.16089"],"URL":"https:\/\/doi.org\/10.1111\/mec.16089","archive":["Portico"],"relation":{},"ISSN":["0962-1083","1365-294X"],"issn-type":[{"type":"print","value":"0962-1083"},{"type":"electronic","value":"1365-294X"}],"subject":[],"published":{"date-parts":[[2021,8,4]]},"assertion":[{"value":"2020-08-04","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-07-19","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-08-04","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}