Unravelling local adaptation in the genome of livestock

Livestock have been a cornerstone to human sustenance, wealth, culture, and production for over 10,000 years. Each contemporary livestock species is comprised of a vast assemblage of locally adapted breeds containing unique genetic variation. While most of this variation remains uncharacterised, understanding the genetic diversity is highly valuable in conserving and improving extant livestock breeds. Chapters two to four utilise SNP array data comprised of tens of thousands of loci distributed relatively uniformly across the genome. Firstly, the demographic history of taurine (Bos taurus) and indicine (Bos indicus) cattle was modelled with approximate Bayesian computation (ABC) to determine if domestication occurred across two or three independent events, with model rejection sampling indicating only two domestications took place. Additionally, characterising population structure, admixture, and gene flow to identify migratory events and potential sources adaptive introgression. Secondly, the 15th century colonisation of the Americas by taurine Creole cattle from their putative Iberian ancestors was modelled using ABC. Identifying a founding effective population size (Ne) of 84, followed by a large demographic expansion and subsequent contraction, with higher resolution of recent demographic fluctuations visualised with Ne Slope (NeS) analysis. Furthermore, signals of selective sweeps were scanned for, identifying loci important for tropical adaptation including suggesting a new candidate gene (GDNF) for the slick hair coat phenotype. Thirdly, population structure and selective signals were identified in Ryeland sheep (Ovis aries), which is a resilient and ancient British breed. Haplotype-based detection of selective sweeps and landscape genomics which incorporated environmental, land use, and topographical data identified prominent pathways involved in prion disease pathways and cancer regulation (specifically hepatocellular carcinoma); environmental associations indicate selection may be driven by liver fluke abundance. The final data chapter utilises whole-genome resequencing (WGRS) data to identify SNPs in the feral Chillingham cattle (Bos taurus) herd which has been isolated from gene flow for at least 300 years with minimal management. WGRS bypasses most ascertainment biases inherent to SNP arrays, allowing a more comprehensive characterisation of variation - identifying consistently long runs of homozygosity interspersed with islands of excess heterozygosity. Heterozygous peak windows were putatively maintained by balancing selection and were enriched with quantitative trait loci associated with fertility and milk. Unexpectedly, the major histocompatibility regions were almost absent of SNP variation in Chillingham.