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Most speciation genomic studies thus aim to identify exceptionally divergent loci between populations, but divergence will be affected by many processes other than reproductive isolation (<jats:styled-content style=\"fixed-case\">RI<\/jats:styled-content>) and speciation. Through genomic studies of recombinant hybrids sampled in the wild, genetic variation associated with<jats:styled-content style=\"fixed-case\">RI<\/jats:styled-content>can be observed<jats:italic>in situ<\/jats:italic>, because selection against incompatible genotypes will leave detectable patterns of variation in the hybrid genomes. To better understand the mechanisms directly involved in<jats:styled-content style=\"fixed-case\">RI<\/jats:styled-content>, we investigated three natural \u2018replicate\u2019 hybrid zones between two divergent<jats:italic><jats:styled-content style=\"fixed-case\">P<\/jats:styled-content>opulus<\/jats:italic>species via locus\u2010specific patterns of ancestry across recombinant hybrid genomes. As expected, genomic patterns in hybrids and their parental species were consistent with the presence of underdominant selection at several genomic regions. Surprisingly, many loci displayed greatly increased between\u2010species heterozygosity in recombinant hybrids despite striking genetic differentiation between the parental genomes, the opposite of what would be expected with selection against intermediate genotypes. Only a limited, reproducible set of genotypic combinations was present in hybrid genomes across localities. In the absence of clearly delimited \u2018hybrid habitats\u2019, our results suggest that complex epistatic interactions within genomes play an important role in advanced stages of<jats:styled-content style=\"fixed-case\">RI<\/jats:styled-content>between these ecologically divergent forest trees. This calls for more genomic studies that test for unusual patterns of genomic ancestry in hybridizing species.<\/jats:p>","DOI":"10.1111\/j.1365-294x.2012.05744.x","type":"journal-article","created":{"date-parts":[[2012,9,18]],"date-time":"2012-09-18T12:09:08Z","timestamp":1347970148000},"page":"5042-5058","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":52,"title":["Recombinant hybrids retain heterozygosity at many loci: new insights into the genomics of reproductive isolation in<i><scp>P<\/scp>opulus<\/i>"],"prefix":"10.1111","volume":"21","author":[{"given":"Dorothea","family":"Lindtke","sequence":"first","affiliation":[{"name":"Unit of Ecology and Evolution Department of Biology University of Fribourg 1700 Fribourg Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C. 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