The comparative landscape of duplications in Heliconius melpomene and Heliconius cydno

Gene duplications can facilitate adaptation and may lead to interpopulation divergence, causing reproductive isolation. We used whole-genome resequencing data from 34 butterflies to detect duplications in two Heliconius species, Heliconius cydno and Heliconius melpomene. Taking advantage of three distinctive signals of duplication in short-read sequencing data, we identified 744 duplicated loci in H. cydno and H. melpomene 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 H. melpomene, consistent with the action of background selection against duplicates in functional regions of the genome. Duplicate loci that are highly differentiated between H. melpomene and H. cydno 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.

AP is funded by a NERC studentship (PFZE/063). CDJ, SLB, JWD and SHM are funded by ERC grant SpeciationGenetics (Grant Number 339873). Pacific Biosciences sequencing was carried out by Karen Oliver in collaboration with Richard Durbin at the Sanger Institute, supported by European Research Council (ERC) Grant Number 339873, Wellcome Trust Grant Number 098051. We thank Jenny Barna and Stuart Rankin for computing support. Analyses were carried out using the Darwin Supercomputer of the University of Cambridge High Performance Computing Service (http://www.hpc.cam.ac.uk/), provided by Dell Inc. using Strategic Research Infrastructure Funding from the Higher Education Funding Council for England, and funding from the Science and Technology Facilities Council. We thank the editor and three anonymous reviewers for their comments that helped us to improve this manuscript.