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Previous studies limited to mtDNA suggest that the swimming crab Callinectes ornatus Ordway, 1863 exists as two distinct genetic clusters separated by the AOP. However, questions concerning migration, diversification time, and species delimitation are unresolved. Densely sampling markers across the genome (SNPs) could elucidate the evolutionary processes within this species. Here, we combined mtDNA data and ddRAD-seq to explore the diversification patterns and processes within the swimming crab C. ornatus. We show great genetic differentiation between groups on the north and south sides of the plume but also signs of hybridization. Demographic modeling indicates the divergence between groups starting around 8 Mya following the AOP\u2019s formation. After a period of isolation, we detect two incidences of secondary contact with stronger migration in concordance with the North Brazil Current flow. Our results suggest speciation with gene flow explained by the interplay among the AOP, oceanographic currents, and long larval dispersal. This work represents the first investigation employing ddRAD-seq in a marine invertebrate species with distribution encompassing the north and south Atlantic and sheds light on the role of the AOP in the diversification of a marine species.<\/jats:p>","DOI":"10.3390\/genes13122263","type":"journal-article","created":{"date-parts":[[2022,12,1]],"date-time":"2022-12-01T05:30:46Z","timestamp":1669872646000},"page":"2263","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Genomic Analyses Implicate the Amazon\u2013Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab"],"prefix":"10.3390","volume":"13","author":[{"given":"Pedro A.","family":"Peres","sequence":"first","affiliation":[{"name":"Department of Biology, Institute of Environment, Florida International University (FIU), Miami, FL 33199, USA"},{"name":"Laboratory of Bioecology and Systematics of Crustaceans (LBSC), Faculty of Philosophy, Sciences and Letters at Ribeir\u00e3o Preto (FFCLRP), University of S\u00e3o Paulo (USP), Ribeir\u00e3o Preto 14040-901, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4919-6679","authenticated-orcid":false,"given":"Heather","family":"Bracken-Grissom","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute of Environment, Florida International University (FIU), Miami, FL 33199, USA"},{"name":"Department of Invertebrate Zoology, National Museum of Natural History-Smithsonian, Washington, WA 20013-7012, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura E.","family":"Timm","sequence":"additional","affiliation":[{"name":"College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK 99775, USA"},{"name":"Auke Bay Laboratories, Alaska Fisheries Science Center, NOAA National Marine Fisheries Service, Juneau, AK 99801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8497-187X","authenticated-orcid":false,"given":"Fernando L.","family":"Mantelatto","sequence":"additional","affiliation":[{"name":"Laboratory of Bioecology and Systematics of Crustaceans (LBSC), Faculty of Philosophy, Sciences and Letters at Ribeir\u00e3o Preto (FFCLRP), University of S\u00e3o Paulo (USP), Ribeir\u00e3o Preto 14040-901, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"13","DOI":"10.5343\/bms.2013.1007","article-title":"Phylogeography unplugged: Comparative surveys in the genomic era","volume":"90","author":"Bowen","year":"2014","journal-title":"Bull. 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