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Using genomic data, we investigated secondary contact between two pairs of\n                    <jats:italic>Copsychus<\/jats:italic>\n                    (Muscicapidae) lineages in Borneo: subspecies of magpie\u2010robins (\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C. saularis<\/jats:italic>\n                    <\/jats:styled-content>\n                    ) and two species of shamas (\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C. malabaricus<\/jats:italic>\n                    <\/jats:styled-content>\n                    and\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>C. stricklandii<\/jats:italic>\n                    <\/jats:styled-content>\n                    ). Although eastern and western lineages in both groups have similar divergence times, they show markedly different phenotypic and genomic outcomes following contact. Magpie\u2010robins exhibit extensive genomic introgression and weak population structure across Borneo, consistent with shallow plumage clines. In contrast, eastern and western shama lineages remain genetically distinct, with little apparent evidence of late\u2010generation hybrids or backcrosses, indicating strong postmating reproductive isolation. The genomic landscape of divergence in shamas contains pronounced peaks, including loci putatively associated with melanism and song learning and production. Mitogenomic data suggest repeated colonization of Borneo by western Sundaland magpie\u2010robin lineages, displacing older Bornean lineages eastward, likely reflecting their greater ability to exploit open habitats that expanded across the Sunda Shelf during glacial periods. In magpie\u2010robin, but not shama, absolute divergence (D\n                    <jats:sub>XY<\/jats:sub>\n                    ) is positively associated with recombination rate at the chromosomal level, suggesting a greater role for within\u2010population processes, such as reduced linked selection in high\u2010recombination regions, in shaping genetic diversity, whereas divergence in shama reflects greater accumulation of differences between populations. Elevated introgression of the Z chromosome in magpie\u2010robins suggests a role for sex\u2010biased processes such as dispersal. Our study highlights Sundaland as a natural laboratory for understanding genomic and evolutionary outcomes of secondary contact.\n                  <\/jats:p>","DOI":"10.1111\/mec.70444","type":"journal-article","created":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T09:22:33Z","timestamp":1782120153000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Contrasting Genomic Outcomes of Secondary Contact in Bornean Bird Lineages: Insights From Barrier Loci, Demographic History and Genomic Features"],"prefix":"10.1111","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6420-1667","authenticated-orcid":false,"given":"Haw Chuan","family":"Lim","sequence":"first","affiliation":[{"name":"Department of Biology George Mason University  Fairfax Virginia USA"},{"name":"Center for Conservation Genomics National Zoo and Conservation Biology Institute  Washington District of Columbia USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Subir B.","family":"Shakya","sequence":"additional","affiliation":[{"name":"Museum of Natural Science and Department of Biological Sciences Louisiana State University  Baton Rouge Louisiana USA"},{"name":"Division of Evolutionary Biology LMU Munich  Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dency F.","family":"Gawin","sequence":"additional","affiliation":[{"name":"Faculty of Resource Science and Technology Universiti Malaysia Sarawak  Kota Samarahan Sarawak Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,6,22]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1420\u20109101.2012.02599.x"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa038"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.094052.109"},{"key":"e_1_2_11_5_1","unstructured":"Alonge M. andA.Leonard.2021.\u201cRAGTAG v2.1 (Version 2.1.0) [Computer Software].\u201dhttps:\/\/doi.org\/10.5281\/zenodo.5634263."},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2008.1012"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.101410.109"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.16562"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-294x.2001.01216.x"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.es.16.110185.000553"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evad233"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.2008.03857.x"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1086\/648559"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2006.11.004"},{"key":"e_1_2_11_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/cobi.13486"},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.15501"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006650"},{"key":"e_1_2_11_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroscience.2012.09.023"},{"key":"e_1_2_11_20_1","doi-asserted-by":"publisher","DOI":"10.1002\/evl3.14"},{"key":"e_1_2_11_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/0169\u20105347(87)90193\u20105"},{"key":"e_1_2_11_22_1","doi-asserted-by":"publisher","DOI":"10.1155\/2012\/295463"},{"key":"e_1_2_11_23_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2014.1461"},{"key":"e_1_2_11_24_1","doi-asserted-by":"crossref","unstructured":"Cavill E. 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