Phylogenetic relationships and genetic conservation status of a Creole sheep population

Conserving farmed animal genetic resources is essential for addressing global challenges such as climate change, emerging diseases, resource scarcity, and evolving market demands. Among mammalian species, sheep represent one of the groups with the highest proportion of breeds at risk. One such breed is the Uruguayan Creole sheep, which is well adapted to its natural environment and primarily found in Uruguay's temperate native grassland regions. Although this breed is believed to have originated from European breeds, the extent of its genetic divergence and distinctiveness remains unknown. Understanding its genetic relationships with other breeds, as well as assessing its within-breed genetic diversity, is crucial for identifying conservation priorities. In the present study, we used high-density single-nucleotide polymorphism panels to (i) determine the phylogenetic relationships between Uruguayan Creole sheep and potential ancestral breeds that may have contributed to its development; and (ii) assess the current genetic status of the breed. Two Uruguayan Creole populations were compared with 36 populations representing different breeds selected for their potential historical or genetic connections to the Creole. Different analytical methods, including Principal Component Analysis, phylogenetic reconstruction, admixture analysis and Wright's fixation index, were applied to investigate interbreed relationships. Historical and recent effective population sizes were estimated from the observed spectrum of linkage disequilibrium. The analyses show that the Uruguayan Creole sheep is genetically distinct from other breeds, including the Spanish breeds from which it is theoretically derived. This divergence is likely the result of genetic drift and natural selection. The two Creole populations also differed from each other and displayed distinct population structures, probably reflecting their differing selection histories. Critically, the Uruguayan Creole showed a very low effective population size (fewer than 50 individuals). Given these findings, the establishment of a genetic conservation programme is strongly recommended to prevent the extinction of this valuable breed. Such a programme should be informed by genetic relationships data and should implement strategies aimed at reducing rates of coancestry and inbreeding and enhancing effective population size. More broadly, these recommendations are applicable to the conservation of endangered livestock breeds across species.