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.