Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate

Abstract

Understanding how evolutionary pressures related to climate change have shaped the current genetic background of domestic animals is a fundamental pursuit of biology. Here, we generated whole-genome sequencing data from native goat populations in Iraq and Pakistan. Combined with previously published data on modern, ancient (Late Neolithic to Medieval periods), and wild Capra species worldwide, we explored the genetic population structure, ancestry components, and signatures of natural positive selection in native goat populations in Southwest Asia (SWA). Results revealed that the genetic structure of SWA goats was deeply influenced by gene flow from the eastern Mediterranean during the Chalcolithic period, which may reflect adaptation to gradual warming and aridity in the region. Furthermore, comparative genomic analysis revealed adaptive introgression of the KITLG locus from the Nubian ibex ( C. nubiana ) into African and SWA goats. The frequency of the selected allele at this locus was significantly higher among goat populations located near northeastern Africa. These results provide new insights into the genetic composition and history of goat populations in the SWA region.

Genomic analysis uncovers novel candidate genes related to adaptation to tropical climates and milk production traits in native goats

“…PC1 divided European and African goat groups from each other and also from Asian goat individuals. In agreement with the previous studies, those samples from East African regions showed a relatively close relationship with those from West Asian groups [ 2 , 3 ]. In contrast, PC2 indicated the variation between goat samples from northern Europe and those from African regions.…”

“…These results agree with those of the earlier research, which suggested that the genomic architecture of the goat populations from Southwest Asia has been affected by broad historical processes such as gene flow from ancient periods [ 2 ]. In line with previous studies on different species [ 3 , 16 , 26 , 42 ], we discovered that all groups experienced the same pattern of reduction in LD decay as the genomic distance (Kb) increased, while a relatively rapid change in LD over increasing physical distance was detected in the African population (Fig. 2 C).…”

A missense mutation in RRM1 contributes to animal tameness

“…We next try to identify the functional SNPs in STIM1-RRM1 dom from ancient genomes and comparative genomics (table S3). We collected 70 published ancient goat genomes (12,(20)(21)(22) mainly from the Fertile Crescent, the center of goat domestication (fig. S3A).…”

Hidden in the sand: phylogenomics unravel an unexpected evolutionary history on the desert-adapted vipers of the genusCerastes

“…2C). This discovery opens up avenues for future research to investigate the introgressed DNA regions and how this introgression could have affected the populations of C. c. cerastes compared to C. c. hoofieni , as introgression has been suggested as a source of adaptive variation (Hedrick, 2013) and has been proven fundamental for the arid adaption of some species of mammals (Liu et al, 2021; Nanaei et al 2023; Rocha et al 2023). Undoubtedly, additional individuals of C. vipera from northeastern Africa should be sampled to verify whether this introgression is maintained along the whole species’ range.…”

“…Remarkably, the advent of molecular genomics has allowed for the identification and characterization of introgression (i.e., the process by which genetic material from one species is incorporated into the genome of another species through interbreeding; Harrison & Larson, 2014) with increasing accuracy (Cahill et al, 2015; Leonard et al, 2013; Ottenburghs et al, 2017), confirming its significant impact on the evolution, adaptation and diversity of many species, including adaptive radiations (Seehausen, 2004). Adaptive introgression (the transfer of alleles from one species to another favored by natural selection) has even been proposed as another potential source of adaptation, aside from new mutations or standing variation (Hedrick, 2013), and has been reported to be involved in pesticide resistance, color polymorphism or adaptation to arid environments, among others (Anderson et al, 2009; Liu et al, 2021; Nanaei et al 2023; Rocha et al 2023; Song et al 2011).…”