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This study investigates the patterns of divergence and discusses the processes that form and maintain divergent lineages of the tsetse fly<jats:italic>Glossina fuscipes fuscipes<\/jats:italic>in Uganda. We sampled 251 flies from 18 sites spanning known genetic lineages and the four admixture zones between them. We apply population genomics, hybrid zone and approximate Bayesian computation to the analysis of three types of genetic markers: 55,267 double\u2010digest restriction site\u2010associated DNA (ddRAD) SNPs to assess genome\u2010wide admixture, 16 microsatellites to provide continuity with published data and accurate biogeographic modelling, and a 491\u2010bp fragment of mitochondrial cytochrome oxidase I and II to infer maternal inheritance patterns. Admixture zones correspond with regions impacted by the reorganization of Uganda's river networks that occurred during the formation of the West African Rift system over the last several hundred thousand years. Because tsetse fly population distributions are defined by rivers, admixture zones likely represent both old and new regions of secondary contact. Our results indicate that older hybrid zones contain mostly parental types, while younger zones contain variable hybrid types resulting from multiple generations of interbreeding. These findings suggest that reproductive barriers are nearly complete in the older admixture zones, while nearly absent in the younger admixture zones. Findings are consistent with predictions of hybrid zone theory: Populations in zones of secondary contact transition rapidly from early to late stages of speciation or collapse all together.<\/jats:p>","DOI":"10.1111\/mec.14957","type":"journal-article","created":{"date-parts":[[2018,11,24]],"date-time":"2018-11-24T16:04:49Z","timestamp":1543075489000},"page":"66-85","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["The population genomics of multiple tsetse fly (<i>Glossina fuscipes fuscipes<\/i>) admixture zones in Uganda"],"prefix":"10.1111","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8974-0301","authenticated-orcid":false,"given":"Norah P.","family":"Saarman","sequence":"first","affiliation":[{"name":"Department of Ecology and Evolutionary Biology Yale University New Haven Connecticut"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Opiro","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Science Gulu University Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2567-8013","authenticated-orcid":false,"given":"Chaz","family":"Hyseni","sequence":"additional","affiliation":[{"name":"Department of Biology University of Mississippi Oxford Mississippi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Echodu","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Science Gulu University Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth A.","family":"Opiyo","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Science Gulu University Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kirstin","family":"Dion","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology Yale University New Haven Connecticut"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Johnson","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology Yale University New Haven Connecticut"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serap","family":"Aksoy","sequence":"additional","affiliation":[{"name":"Department of Epidemiology of Microbial Diseases Yale School of Public Health New Haven Connecticut"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adalgisa","family":"Caccone","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology Yale University New Haven Connecticut"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,1,23]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0000242"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.12158"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pt.2013.06.005"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00806-12"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-294x.2001.01216.x"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/hdy.1986.135"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.es.16.110185.000553"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1086\/661246"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0000636"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.2517-6161.1995.tb02031.x"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2003.2404"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.2011.05080.x"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.2011.05106.x"},{"key":"e_1_2_8_15_1","volume-title":"Pleistocene stratigraphy in Uganda","author":"Bishop W. 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