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Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that <jats:italic>NPR1<\/jats:italic> and <jats:italic>RPP5<\/jats:italic> loci cause a genetic incompatibility between the incipient species <jats:italic>Capsella grandiflora<\/jats:italic> and <jats:italic>C. rubella<\/jats:italic>, and the more distantly related <jats:italic>C. rubella<\/jats:italic> and <jats:italic>C. orientalis<\/jats:italic>. The incompatible <jats:italic>RPP5<\/jats:italic> allele results from a mutation in <jats:italic>C. rubella<\/jats:italic>, while the incompatible <jats:italic>NPR1<\/jats:italic> allele is frequent in the ancestral <jats:italic>C. grandiflora<\/jats:italic>. Compatible and incompatible <jats:italic>NPR1<\/jats:italic> haplotypes are maintained by balancing selection in <jats:italic>C. grandiflora<\/jats:italic>, and were divergently sorted into the derived <jats:italic>C. rubella<\/jats:italic> and <jats:italic>C. orientalis<\/jats:italic>. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles.<\/jats:p>","DOI":"10.1038\/ncomms8960","type":"journal-article","created":{"date-parts":[[2015,8,13]],"date-time":"2015-08-13T09:24:56Z","timestamp":1439457896000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":88,"title":["Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella"],"prefix":"10.1038","volume":"6","author":[{"given":"Adrien","family":"Sicard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Kappel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily B.","family":"Josephs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Young Wha","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cindy","family":"Marona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John R.","family":"Stinchcombe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen I.","family":"Wright","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Lenhard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2015,8,13]]},"reference":[{"key":"BFncomms8960_CR1","unstructured":"Coyne, J. 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