Abstract
Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species.
Highlights
Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change
Reduced diversity is an expected consequence of domestication, in sheep the magnitude of change appears smaller than for some other domesticates[8,25]. This suggests sheep domestication captured a wide sampling of diversity from Asiatic mouflon, consistent with the finding that many modern breeds retain higheffective population size[4] and a diverse representation of mtDNA haplogroups[26]
We evaluated the relationship between individual genomes using Principal Component Analysis (PCA), identifying two distinct clusters of Mouflon from geographically separate areas of their range (Supplementary Fig. 1)
Summary
Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. To extend our understanding beyond key genes, multiple studies have sought to identify categories of sites or genomic features over-represented in sweep regions These have included evolutionarily conserved elements and proximity to transcription start sites[6,8,10]; the approach has been severely hampered by the paucity of detailed functional annotation available for livestock animal species. We find strong and significant overlap for multiple components of the proximal gene regulatory machinery, including promoters and chromatin states indicative of active transcription These results provide both a high-resolution genomic view of positive selection and a first draft functional annotation of the sheep genome. Considered together, our results suggest modification to gene regulatory networks has been an important evolutionary driver of the phenotypic changes that distinguish domestic sheep from their wild ancestors
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