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    Comparative mitogenome sequences and phylogenetic relationships of two mongooses (Herpestes ichneumon and Urva auropunctata) from Turkiye and Iraq
    (SPRINGER HEIDELBERG, 2025) Yıldız, Barış; Selçuk, Ahmet Yesari; Naji, Ahmed Qasim; Şeker, Perinçek Seçkinozan; Baran, Mehmet; Teber, Saffet; Al-Abbasi, Husham Abdulrahman Mahdi; Tez, Coskun; İbiş, Osman
    Mongoose species (Herpestidae) exhibit a wide geographic distribution across Africa, Asia, and several island regions, yet mitogenomic data remain scarce for many taxa and regions. In this study, the complete mitochondrial genomes of the Egyptian mongoose (Herpestes ichneumon) from Turkiye and the small Indian mongoose (Urva auropunctata) from Iraq are analyzed for the first time to explore their genetic structure and phylogenetic relationships within the Herpestidae. The mitogenomes are similar in overall organization and size (16,660 bp in H. ichneumon and 16,761 bp in U. auropunctata), with variations primarily found in the D-loop (control region), which influences genome length through repeated motifs. The Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic analyses using complete mitochondrial genome and cytochrome b (CYTB) sequences reinforce the previous findings on Herpestidae phylogeny. Results support the division of Herpestidae into two subfamilies (Herpestinae and Mungotinae), confirm the monophyly of Urva, and highlight the paraphyly of Herpestes. Based on the complete mitogenome sequences, the Iraqi U. auropunctata specimens are clustered with Japanese and Fijian specimens, indicating low level of intraspecific variation. Herpestes ichneumon is clustered with the Galerella sanguine based on the mitogenome sequences. Additionally, H. ichneumon haplotypes are grouped into three haplogroups (Iberian, Levantine, and South African) based on the CYTB sequences, reflecting regional genetic differentiation. Molecular dating estimated Herpestidae diverges from Eupleridae similar to 30.76 million years ago (Mya), with subfamily divergence occurring in the Early Miocene (similar to 19.87 Mya). Within Urva, species begin diverging around 12.5 Mya, with U. javanica and U. auropunctata separating similar to 4.67 Mya. Recent divergence is also noted between H. ichneumon specimens from Turkiye and Lebanon (similar to 150 Kya) and among U. auropunctata populations from Iraq, Japan, and Fiji (similar to 600 Kya), supporting ongoing intraspecific diversification within both species. This study provides valuable insights into the phylogeny and evolutionary history of two mongoose species by comparing the structural and organizational features of their mitogenomes from biogeographically related regions, along with phylogenetic and evolutionary dating analyses based on complete mitogenome and CYTB sequences.
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    Phylogenetic relationships and evolutionary history of goats (Mammalia: Capra) from Türkiye and Iraq, Inferred from complete mitochondrial genomes
    (John Wiley and Sons Ltd, 2025) Teber, Saffet; Al-Abbasi, Husham Abdulrahman Mahdi; Şeker, Perinçek Seçkinozan; Koepfli, Klaus-Peter; Selçuk, Ahmet Yesari; Baran, Mehmet; Tez, Coşkun; İbiş, Osman
    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.