Feralisation targets different genomic loci to domestication in the chicken.

Feralisation occurs when a domestic population recolonizes the wild, escaping its previous restricted environment, and has been considered as the reverse of domestication. We have previously shown that Kauai Island's feral chickens are a highly variable and admixed population. Here we map selective sweeps in feral Kauai chickens using whole-genome sequencing. The detected sweeps were mostly unique to feralisation and distinct to those selected for during domestication. To ascribe potential phenotypic functions to these genes we utilize a laboratory-controlled equivalent to the Kauai population-an advanced intercross between Red Junglefowl and domestic layer birds that has been used previously for both QTL and expression QTL studies. Certain sweep genes exhibit significant correlations with comb mass, maternal brooding behaviour and fecundity. Our analyses indicate that adaptations to feral and domestic environments involve different genomic regions and feral chickens show some evidence of adaptation at genes associated with sexual selection and reproduction.The prevous status of this article was Manuscript and the title was The genomic signals of feralisation: Not just domestication in reverse?Funding agencies: We thank Tony Lydgate and the Steelgrass Institute for invaluable assistance and accommodation on Kauai. The research was carried out within the framework of the Linkoping University Neuro-network. WGS was performed by the Uppsala Genome Center as part of NGI Sweden. Computations were performed at UPPMAX as part of SNIC Sweden. The project was supported by grants from the Swedish Research Council (VR), the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS), the Carl Trygers Stiftelse and by the National Science Foundation under Cooperative Agreement No. DBI-0939454. S.L. is supported by BBSRC (grant number BB/L009382/1). L.V.D. is supported by CoMPLEX via EPSRC (grant number EP/F500351/1). G.H. is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 098386/Z/12/Z) and supported by the National Institute for Health Research University College London Hospitals Biomedical Research Centre. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.