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

TL;DR

This study uses mitochondrial genomes to explore the evolutionary history and genetic diversity of goats in Türkiye and Iraq, revealing two wild goat lineages and supporting Türkiye as a key domestication center.

Contribution

The study provides new insights into the phylogenetic structure and diversification of goats using complete mitogenomes from Türkiye and Iraq.

Findings

Domestic goats from Türkiye showed higher genetic diversity than those from Iraq.

Two distinct wild goat lineages were identified in Türkiye, influenced by geographic barriers like the Anatolian Diagonal.

Türkiye is highlighted as a significant center for goat domestication during the Neolithic period.

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.

This study explores the genetic diversity, phylogenetic relationships, and evolutionary history of domestic (
Capra hircus
) and wild goats (
Capra aegagrus
), as well as chamois (
Rupicapra rupicapra
) from Türkiye and Iraq, using complete mitochondrial genomes. The findings reveal two distinct wild goat lineages in Türkiye, shaped by geographic factors such as the Anatolian Diagonal, and highlight Türkiye's role as a key genetic center for goat domestication during the Neolithic period. Divergence time estimates suggest that
C. aegagrus
and
C. hircus
split around 0.89 million years ago, reinforcing the evolutionary significance of the region.

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