Data from: Demography and rapid local adaptation shape Creole cattle genome diversity in the tropics

The introduction of Iberian cattle in the Americas after Columbus’ arrival
imposed high selection pressures on a limited number of animals over a
brief period of time. Knowledge of the genomic regions selected during
this process may help in enhancing climatic resilience and sustainable
animal production. We first determined taurine and indicine contributions
to the genomic structure of modern Creole cattle. Second, we inferred
their demographic history using approximate Bayesian computation (ABC),
linkage disequilibrium (LD), and Ne Slope (NeS) analysis. Third, we
performed whole genome scans for selection signatures based on
cross-population extended haplotype homozygosity (XP-EHH) and population
differentiation (FST) to disentangle the genetic mechanisms involved in
adaptation and phenotypic change by a rapid and major environmental
transition. To tackle these questions, we combined SNP array data (~54,000
SNPs) in Creole breeds with their modern putative Iberian ancestors.
Reconstruction of the population history of Creoles from the end of the
15th century indicated a major demographic expansion until the
introduction of zebu and commercial breeds into the Americas ~180 years
ago, coinciding with a drastic Ne contraction. NeS analysis provided
insights into short-term complexity in population change and depicted a
decrease/expansion episode at the end of the ABC-inferred expansion, as
well as several additional fluctuations in Ne with the attainment of the
current small Ne only towards the end of the 20th century. Selection
signatures for tropical adaptation pinpointed the thermoregulatory slick
hair coat region, identifying a new candidate gene (GDNF), as well as
novel candidate regions involved in immune function, behavioural
processes, iron metabolism and adaptation to new feeding conditions. The
outcomes from this study will help in future-proofing farm animal genetic
resources (FAnGR) by providing molecular tools that allow selection for
improved cattle performance, resilience and welfare under climate change.