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These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister\u2010taxa, <jats:italic>Daphnia pulicaria<\/jats:italic> and <jats:italic>Daphnia pulex<\/jats:italic>. First, we assembled a phased chromosome\u2010scale genome assembly using trio\u2010binning for <jats:italic>D<\/jats:italic>. <jats:italic>pulicaria<\/jats:italic> and constructed a genetic map using an F2\u2010intercross panel to understand sex\u2010specific recombination rate heterogeneity. Finally, we used a ddRADseq data set with broad geographic sampling of <jats:italic>D<\/jats:italic>. <jats:italic>pulicaria<\/jats:italic>, <jats:italic>D<\/jats:italic>. <jats:italic>pulex<\/jats:italic>, and their hybrids to understand the patterns of genome\u2010scale divergence and demographic parameters. Our study provides the first sex\u2010specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male\u2010biased heterochiasmy in <jats:italic>D<\/jats:italic>. <jats:italic>pulicaria<\/jats:italic>, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are probably driven by selection on <jats:italic>D<\/jats:italic>. <jats:italic>pulicaria<\/jats:italic>, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome\u2010wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty.<\/jats:p>","DOI":"10.1111\/mec.16383","type":"journal-article","created":{"date-parts":[[2022,2,4]],"date-time":"2022-02-04T12:33:51Z","timestamp":1643978031000},"page":"1478-1496","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex"],"prefix":"10.1111","volume":"32","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9973-6410","authenticated-orcid":false,"given":"Matthew J.","family":"Wersebe","sequence":"first","affiliation":[{"name":"Department of Biology Program in Ecology and Evolutionary Biology University of Oklahoma  Norman Oklahoma USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0745-3996","authenticated-orcid":false,"given":"Ryan E.","family":"Sherman","sequence":"additional","affiliation":[{"name":"Department of Integrative Biology Oklahoma State University  Stillwater Oklahoma USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5323-3217","authenticated-orcid":false,"given":"Punidan D.","family":"Jeyasingh","sequence":"additional","affiliation":[{"name":"Department of Integrative Biology Oklahoma State University  Stillwater Oklahoma USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1310-4418","authenticated-orcid":false,"given":"Lawrence J.","family":"Weider","sequence":"additional","affiliation":[{"name":"Department of Biology Program in Ecology and Evolutionary Biology University of Oklahoma  Norman Oklahoma USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2022,2,15]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1558\u20105646.2011.01488.x"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010019\u20101829\u20106"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.2004"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.88502"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.150.3692.28"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00442\u2010004\u20101657\u20105"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u201010\u2010421"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/biolinnean\/bly063"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.108.096826"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.2307\/1939878"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12354"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/0888\u20107543(91)90123\u2010V"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010020\u201001056\u20105"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12862\u2010019\u20101542\u20109"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.15824"},{"key":"e_1_2_9_17_1","volume-title":"Genomic and regulatory divergence between sister species of Daphnia","author":"Clifford B. 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