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We used whole-genome resequencing data from 34 butterflies to detect duplications in two <jats:italic>Heliconius<\/jats:italic> species, <jats:italic>Heliconius cydno<\/jats:italic> and <jats:italic>Heliconius melpomene<\/jats:italic>. Taking advantage of three distinctive signals of duplication in short-read sequencing data, we identified 744 duplicated loci in <jats:italic>H. cydno<\/jats:italic> and <jats:italic>H. melpomene<\/jats:italic> and evaluated the accuracy of our approach using single-molecule sequencing. We have found that duplications overlap genes significantly less than expected at random in <jats:italic>H. melpomene<\/jats:italic>, consistent with the action of background selection against duplicates in functional regions of the genome. Duplicate loci that are highly differentiated between <jats:italic>H. melpomene<\/jats:italic> and <jats:italic>H. cydno<\/jats:italic> map to four different chromosomes. Four duplications were identified with a strong signal of divergent selection, including an odorant binding protein and another in close proximity with a known wing colour pattern locus that differs between the two species.<\/jats:p>","DOI":"10.1038\/hdy.2016.107","type":"journal-article","created":{"date-parts":[[2016,12,7]],"date-time":"2016-12-07T15:32:04Z","timestamp":1481124724000},"page":"78-87","update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["The comparative landscape of duplications in Heliconius melpomene and Heliconius cydno"],"prefix":"10.1038","volume":"118","author":[{"given":"A","family":"Pinharanda","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S H","family":"Martin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S L","family":"Barker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J W","family":"Davey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C D","family":"Jiggins","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,12,7]]},"reference":[{"key":"BFhdy2016107_CR1","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1101\/gr.114876.110","volume":"21","author":"A Abyzov","year":"2011","unstructured":"Abyzov A, Urban AE, Snyder M, Gerstein M . 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