Search

Background: Since domestication, both evolutionary forces and human selection have played crucial roles in producing adaptive and economic traits, resulting in animal breeds that have been selected for specific climates and different breeding goals. Pakistani goat breeds have acquired genomic adaptations to their native climate conditions, such as tropical and hot climates. In this study, using next-generation sequencing data, we aimed to assess the signatures of positive selection in three native Pakistani goats, known as milk production breeds, that have been well adapted to their local climate. Results: To explore the genomic relationship between studied goat populations and their population structure, whole genome sequence data from native goat populations in Pakistan (n = 26) was merged with available worldwide goat genomic data (n = 184), resulting in a total dataset of 210 individuals. The results showed a high genetic correlation between Pakistani goats and samples from North-East Asia. Across all populations analyzed, a higher linkage disequilibrium (LD) level (– 0.59) was found in the Pakistani goat group at a genomic distance of 1 Kb. Our findings from admixture analysis (K = 5 and K = 6) showed no evidence of shared genomic ancestry between Pakistani goats and other goat populations from Asia. The results from genomic selection analysis revealed several candidate genes related to adaptation to tropical/hot climates (such as; KITLG, HSPB9, HSP70, HSPA12B, and HSPA12B) and milk production related-traits (such as IGFBP3, LPL, LEPR, TSHR, and ACACA) in Pakistani native goat breeds. Conclusions: The results from this study shed light on the structural variation in the DNA of the three native Pakistani goat breeds. Several candidate genes were discovered for adaptation to tropical/hot climates, immune responses, and milk production traits. The identified genes could be exploited in goat breeding programs to select efficient breeds for tropical/hot climate regions. [ABSTRACT FROM AUTHOR]

Different scales and frequencies of glaciations developed in Europe and Asia during the Pleistocene. Because species' responses to climate change are influenced by interactive factors including ecology and local topography, the pattern and tempo of species diversification may vary significantly across regions. The great tit Parus major is a widespread Eurasian passerine with a range that encircles the central Asian desert and high-altitude areas of the Tibetan Plateau. A number of genetic studies have assessed the effect of paleo-climate changes on the distribution of the European population. However, none have comprehensively addressed how paleo-climate change affected the distribution of the great tit in China, an apparent hotspot of P. major subspecific diversity. Here, we describe likely paleo-climatic effects on P. major populations in China based on a combination of phylogeography and ecological niche models (ENMs). We sequenced three mitochondrial DNA markers from 28 populations (213 individuals), and downloaded 112 sequences from outside its Chinese range. As the first step in clarifying the intra-specific relationships among haplotypes, we attempted to clarify the divergence and demography of populations in China. Phylogeographic analysis revealed that P. major is comprised of five highly divergent clades with geographic breaks corresponding to steep mountains and dry deserts. A previously undescribed monophyletic clade with high genetic diversity, stable niches and a long and independent evolutionary history was detected in the mountainous areas of southwest China. The estimated times at which these clades diverged was traced back to the Early-Middle Pleistocene (2.19-0.61 mya). Contrary to the post-LGM (the Last Glacial Maximum) expansion of European populations, demographic history indicates that Asian populations expanded before the LGM after which they remained relatively stable or grew slowly through the LGM. ENMs support this conclusion and predict a similar distribution in the present and the LGM. Our genetic and ecological results demonstrate that Pleistocene climate changes shaped the divergence and demography of P. major in China. [ABSTRACT FROM AUTHOR]