1. Introduction
The Fertile Crescent in Southwest Asia (SWA) and adjacent area were the origin of domestication of most livestock and plant species (Zeder 2008). However, during the past thousands of years, this important geographical place has been subjected to different prolonged drought episodes. For instance, paleoenvironmental reconstructions have indicated a gradual shift to drier and warmer conditions in eastern parts of this region at the end of the mid-Holocene (Clarke et al. 2016, Sun et al. 2021), which coincided with the early development of agriculture. It has been reported that the worst drought-affected regions of the Fertile Crescent are located in Iraq and Iran countries that are also part of Afro-Asian belt of deserts, a hot-arid region in the globe (Kaniewski et al. 2012, Ashraf et al. 2021). Indigenous domesticated animals of this region are consequently well adapted to their local conditions such as hot-desert environments (Al-Thuwaini et al. 2019, Mohamadipoor et al. 2021, Asadollahpour Nanaei et al. 2022).
Previous studies have demonstrated that gene flow between populations may allow the spread of adaptive alleles (Arnold and Kunte 2017, Razgour et al. 2018). Studies of human and other species have shown that heterogeneity in ancestry and introgression offered insight into evolutionary processes (Kingston et al. 2017). Nevertheless, ancient introgression in farm animals has been rarely explored at the genome-wide scale, but would provide new insights into their evolutionary history and adaptation to a changing environment.
Goat (Capra hircus) is one of the earliest domestic animals (Daly et al. 2018, Alberto et al. 2018). Archaeozoological dating indicates that goat was domesticated as far back as the 10th millennium before present (BP) in the area spanning southeastern Anatolia, western of Iran and northern Iraq (Zagros Mountains). After domestication of their wild ancestors, the bezoar, goats followed the spread of agriculture, reaching the Mediterranean 8,000 years BP and north Africa in 7,000 BP (Zeder 2017, Taylor et al. 2021).
Recent genetic efforts have provided a snapshot of domestic goat genetic diversity and its pattern of geographic distribution of both mitochondrial and nuclear DNA variants. Although mtDNA sequences suggested a weak geographic differentiation of present-day goat populations (Luikart et al. 2001), this was refuted by genome-wide SNP studies (Bertolini et al. 2018, Colli et al. 2018). A recent paleogenomic study of ancient genomes from SWA indicated that three distinct Neolithic goat groups belong to different parts of the Fertile Crescent contributed differentially to the present-day populations in Europe, Africa and Asia (Daly et al. 2018). A minority of the early domesticates from the Zagros mountains had a relatively strong genetic affinity to the bezoar (Daly et al. 2021). This evidence suggest that domestication and post-domestication split do not preclude subsequent contacts between wild and domestic goats or between goat groups from different geographical regions.
In this study, we performed a large-scale genomic analysis of goat populations, including 50 ancient, 211 domestic and 72 wild Capra genomes to reconstruct historical migration and introgression processes that formed the current genetic architecture of domestic goats in SWA, and to identify the genetic basis underlying variation in the adaptation to desert climate in this region.