• Energy Research

Abstract How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667–248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.

When faced with rapidly changing environments, wildlife species are left to adapt, disperse or disappear. Consequently, there is value in investigating the connectivity of populations of species inhabiting different environments in order to evaluate dispersal as a potential strategy for persistence in the face of climate change. Here, we begin to investigate the processes that shape genetic variation within American pika populations from the northern periphery of their range, the central Coast Mountains of British Columbia, Canada. At these latitudes, pikas inhabit sharp elevation gradients ranging from sea level to 1500 m, providing an excellent system for studying the effects of local environmental conditions on pika population genetic structure and gene flow. We found low levels of neutral genetic variation compared to previous studies from more southerly latitudes, consistent with the relatively recent post-glacial colonization of the study location. Moreover, significant levels of inbreeding and marked genetic structure were detected within and among sites. Although low levels of recent gene flow were revealed among elevations within a transect, potentially admixed individuals and first generation migrants were identified using discriminant analysis of principal components between populations separated by less than five kilometers at the same elevations. There was no evidence for historical population decline, yet there was signal for recent demographic contractions, possibly resulting from environmental stochasticity. Correlative analyses revealed an association between patterns of genetic variation and annual heat-to-moisture ratio, mean annual precipitation, precipitation as snow and mean maximum summer temperature. Changes in climatic regimes forecasted for the region may thus potentially increase the rate of population extirpation by further reducing dispersal between sites. Consequently, American pika may have to rely on local adaptations or phenotypic plasticity in order to survive predicted climate changes, although additional studies are required to investigate the evolutionary potential of this climate change sensitive species.