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Different types of approaches have been developed that can detect genomic regions influenced by selection. Here, we address the question whether two highly different methods\u2014<jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub> outlier analysis and admixture analysis\u2014detect largely the same set of non\u2010neutral genomic elements or, instead, complementary sets. We study genetic architecture in a natural secondary contact zone where extensive admixture occurs. The marine bivalves <jats:italic>Macoma balthica rubra<\/jats:italic> and <jats:italic>M. b. balthica<\/jats:italic> descend from two independent trans\u2010Arctic invasions of the north Atlantic and hybridize extensively where they meet, for example in the Kattegat\u2013Danish Straits\u2013Baltic Sea region. The Kattegat\u2013Danish Straits region forms a steep salinity cline and is the only entrance to the recently (ca. 8000\u2003years ago) established brackish water basin the Baltic Sea. Salinity along the contact zone drops from 30\u2030 (Skagerrak, <jats:italic>M.b.rubra<\/jats:italic>) to 3\u2030 (Baltic, <jats:italic>M.b.balthica<\/jats:italic>). Both outlier analysis and genomic clines analysis suggest that large parts of the genome are influenced by non\u2010neutral effects. Contrasting samples from well outside the hybrid zone, outlier analysis detects 16 of 84 amplified fragment length polymorphism markers as significant <jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub> outliers. Genomic clines analysis detects 31 of 84 markers as non\u2010neutral inside the hybrid zone. Remarkably, only three markers are detected by both methods. We conclude that the two methods together identify a suite of markers that are under the influence of non\u2010neutral effects.<\/jats:p>","DOI":"10.1111\/j.1365-294x.2012.05586.x","type":"journal-article","created":{"date-parts":[[2012,5,3]],"date-time":"2012-05-03T12:18:18Z","timestamp":1336047498000},"page":"3048-3061","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":46,"title":["Genetic architecture in a marine hybrid zone: comparing outlier detection and genomic clines analysis in the bivalve <i>Macoma balthica<\/i>"],"prefix":"10.1111","volume":"21","author":[{"given":"P. C.","family":"LUTTIKHUIZEN","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J.","family":"DRENT","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"K. T. C. 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