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Here, we map two genetically divergent lineages of an obligate rocky shore fish,<jats:italic>Clinus cottoides<\/jats:italic>, and model sea-level change during the last 110 000 years to provide the first evidence of a vicariant event along the southern coastline of Africa. Results reveal that lowered sea levels during glacial periods drastically reduced rocky intertidal habitat, which may have isolated populations in two refugia for at least 40 000 years. Contemporary coastal dynamics and oceanography explain secondary contact between lineages. This scenario provides an explanation for the origin of population genetic breaks despite a lack of obvious present-day geographical barriers and highlights the need for including palaeo-oceanography in unravelling extant population patterns.<\/jats:p>","DOI":"10.1098\/rsbl.2014.0330","type":"journal-article","created":{"date-parts":[[2014,6,25]],"date-time":"2014-06-25T09:35:06Z","timestamp":1403688906000},"page":"20140330","update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":41,"title":["Variation in palaeo-shorelines explains contemporary population genetic patterns of rocky shore species"],"prefix":"10.1098","volume":"10","author":[{"given":"Jessica A.","family":"Toms","sequence":"first","affiliation":[{"name":"Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag XI, Matieland 7602, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John S.","family":"Compton","sequence":"additional","affiliation":[{"name":"Department of Geological Sciences, University of Cape Town, Rondebosch 7701, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Malcolm","family":"Smale","sequence":"additional","affiliation":[{"name":"Department of Zoology, Nelson Mandela Metropolitan University, PO Box 77000, Port Elizabeth, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sophie","family":"von der Heyden","sequence":"additional","affiliation":[{"name":"Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag XI, Matieland 7602, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"175","published-online":{"date-parts":[[2014,6]]},"reference":[{"key":"e_1_3_1_2_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2699.2008.02032.x"},{"key":"e_1_3_1_3_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1420-9101.2011.02382.x"},{"key":"e_1_3_1_4_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00338-007-0261-7"},{"key":"e_1_3_1_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2013.01.018"},{"key":"e_1_3_1_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/35016000"},{"key":"e_1_3_1_7_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1472-4642.2008.00481.x"},{"key":"e_1_3_1_8_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2148-11-189"},{"key":"e_1_3_1_9_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.0014-3820.2001.tb00760.x"},{"key":"e_1_3_1_10_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0012008"},{"key":"e_1_3_1_11_2","first-page":"43","article-title":"A review of marine phylogeography in southern Africa","volume":"107","author":"Teske PR","year":"2011","journal-title":"South Afr. 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