Phylogenetic Relationships and Evolutionary History of Goats (Mammalia: Capra) From Türkiye and Iraq, Inferred From Complete Mitochondrial Genomes

Abstract

This study investigated genetic diversity, phylogenetic relationships, and evolutionary history of domestic goats from Türkiye and Iraq, along with wild goat and chamois species, using newly obtained mitogenomic sequences. Phylogenetic and phylogeographic analyses revealed a complex genetic structure among domestic goats, shaped by widespread distribution and gene flow. While haplotype A was predominant among domesticated breeds from both Türkiye and Iraq, haplotype G was also detected in the Turkish breeds. Notably, Turkish samples exhibited relatively higher nucleotide diversity (0.00133) compared to those from Iraq (0.00081), indicating greater genetic variability in the former population. Wild goat populations in Türkiye were clustered into two distinct lineages: (i) the Aegagrus lineage included the Artvin sample, some ancient genomes from the Taurus Mountains, and Iranian goats, and (ii) the Caucasian lineage contained Konya and Antalya samples, and some ancient genomes from the Taurus Mountains that were clustered closely with wild goats from the Caucasus. These findings suggest that geographic and ecological factors, such as the Anatolian Diagonal, influenced their diversification. Divergence time analyses indicated that the Caprinae began diversifying approximately 8.18 Mya, with initial splits in the Capra occurring around 3.22 Mya during the climatic fluctuations of the Late Pliocene/Early Pleistocene. The study also estimated the divergence of C. aegagrus and C. hircus at approximately 0.89 Mya in the Calabrian, with genetic diversification within domestic goats commencing 0.29 Mya in the Chibanian. The results provided robust evidence supporting Türkiye's role as a significant genetic center for goat domestication during the Neolithic period (~10,000 years ago). This hypothesis was further supported by the widespread presence of the common haplotype A in domestic goats, the high genetic diversity observed among domestic goats, and the region's proximity to the Fertile Crescent. The study underscored the importance of comprehensive genetic analyses in elucidating the evolutionary processes underlying goat domestication and highlighted the necessity for larger datasets and additional molecular markers to resolve the taxonomic complexities of wild goat populations in Türkiye, Iraq, and surrounding regions.

Keywords: Capra; Fertile Crescent; domestication; mitogenome; phylogeography; rupicapra.

FIGURE 1

Geographic locations of goat samples collected from Türkiye and Iraq.

FIGURE 2

Phylogenetic tree and divergence dating results based on Bayesian inference analyses using BEAST v1.8.0. A‐K on the nodes of the circular phylogenetic tree indicate the evolutionary divergence times among the Caprinae lineages presented in Table 6. The ML phylogenetic tree exhibited the same topology except the position of the Ovis clade (Supporting Information File 2). For specific node ages, posterior probability values, 95% highest posterior densities (HPDs) and also K‐2P distances for the main nodes, see Table 6.

FIGURE 3

The median‐joining haplotype network reconstructed based on complete mitochondrial genome sequences illustrates the relationships among the main haplogroups (haplogroups A, B, C, D, and G) in domestic goats (A) and species relationships among wild goats, and chamois (B and C, respectively). Shared haplotypes in haplogroup A and haplogroup D (Haplotypes 6 and 56) are shown in different colors. The circles are proportional to the sample size.