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Öğe 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, OsmanMongoose 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.Öğe Complete mitochondrial genomes of Chionomys roberti and Chionomys nivalis (Mammalia: Rodentia) from Turkey: Insight into their phylogenetic position within Arvicolinae(Springer Heidelberg, 2022) Şeker, Perinçek Seçkin Ozan; Selçuk, Ahmet Yesari; Selvi, Engin; Baran, Mehmet; Teber, Saffet; Keleş, Gökçe Ali; Kefelioğlu, Haluk; Tez, Coşkun; İbiş, OsmanThe complete mitochondrial DNA (mitogenome) sequences of Chionomys nivalis and C. roberti were first presented as reference mitogenomes by the current study using Long-Range PCR and Next-Generation Sequencing. The structure and organization of the circular mitogenomes were similar for each species. Each mitogenome included 22 tRNA genes, two rRNA genes, 13 protein-coding genes (PCGs), a control region (D-loop), and an origin of the light-strand region (OL), with the mitogenome lengths of 16.293 for C. nivalis and 16.300 for C. roberti. Phylogenetic analyses based on whole mitogenomes sequences allowed us to see better the relative position of the Chionomys within Arvicolinae. According to this, Chionomys was in a close phylogenetic relationship with Microtus rather than Arvicola. Contrary to the results of past studies, the relative positions of the species within Chionomys varied in the cytochrome b sequence-based phylogenetic analyses. Additionally, the presence of 10 genetic lineages determined by previous works within C. nivalis was approved. Among them, the Central Taurus lineage genetically was the lineage most distant from others. On the other hand, Turkish C. roberti specimens were clustered with the Transcaucasian specimens (Datvisi- Georgia and Alania-North Ossetia-Russia) splitting from other GenBank specimens of Russia and Georgia. Divergence-time analyses demonstrated that the first appearance of Arvicolinae dates back to the Early Pliocene (4.96 mya, 95% HPD: 4.09-5.82, BPP: 1), compatible with the past findings. Also, it was detected that the split of Arvicola / Chionomys + Microtus took place at the beginning of the Quaternary period (2.35 mya, 95% HPD: 1.97-2.75, BPP: 0.98). This corresponded to the Early Pleistocene divergence (approximately 2.4 mya) of these three genera suggested by the fossil record. In addition to this, molecular dating analyses demonstrated that the divergence between C. nivalis and C. roberti occurred in the Middle Pleistocene (1.06 mya, 95% HPD: 0.87-1.25, BPP: 1). Further studies using other molecular markers are needed to make definite judgments on the taxonomy and evolution of Chionomys.Öğe Complete mitogenomes of Turkish tree squirrels, sciurus anomalus and S. Vulgaris, (sciuridae: rodentia: mammalia) and their phylogenetic status within the tribe sciurini(Elsevier B.V., 2022) İbiş, Osman; Selçuk, Ahmet Yesari; Teber, Saffet; Baran, Mehmet; Kaya, Aleattin; Özcan, Servet; Kefelioğlu, Haluk; Tez, CoşkunThe genus Sciurus, a member of the family Sciuridae, is widely distributed in the Holarctic region. To better understand mitogenomic characteristics and to reveal internal phylogenetic relationships of the genus, 20 complete mitogenomes of Turkish tree squirrels were successfully sequenced for the first time, including 19 for S. anomalus (from 16,505 bp to 16,510 bp) and one for S. vulgaris (16,511 bp). The mitogenomes of two species were AT-biased. All tRNAs for two species displayed a typical clover-leaf structure, except for tRNASer(AGY). The tRNA Serine1 (S1)-GCT structure lacked the dihydrouridine (DHU) loop and stem. Based on mitogenomic dataset for phylogeny of Sciurinae, phylogenetic analyses (Bayesian Inference and Maximum Likelihood) did not support monophyly of Sciurus and proposed that S. anomalus, the most basal taxa in the Sciurini tribe, had at least five mitogenome lineages, which were also supported by network analysis. The dissimilarities among the five lineages of S. anomalus ranged from 0.0042 (0.42%) to 0.0062 (0.62%) using K2P sequence pairwise distances. In addition to this mitogenomic analysis result, phylogenetic analyses using the CYTB + D-loop dataset proposed the existence of at least nine lineages for S. anomalus, which was different than those of the previous studies. The current study proposed that the use of mitogenomic data for reconstructing the phylogeny of Turkey's Sciurus holds an important value for revealing evolutionary relationships.Öğe Mitogenomic analysis of glirids (gliridae) and squirrels (sciuridae) from Türkiye: Evolutionary and taxonomic implications within the suborder sciuromorpha(John Wiley and Sons Ltd, 2025) İbiş, Osman; Selçuk, Ahmet Yesari; Teber, Saffet; Baran, Mehmet; Baran, Mehmet; Koepfli, Klaus-Peter; Kefelioğlu, Haluk; Tez, CoşkunGliridae and Sciuridae, the most impressive mammalian radiations within the suborder Sciuromorpha, encompass a total of 327 extant species. This study aimed to: (i) characterize the mitogenomes of three sciurid (Spermophilus citellus, Spermophilus taurensis, and Spermophilus xanthoprymnus) and three glirid (Glis glis, Dryomys nitedula, and Dryomys laniger) species from Türkiye; (ii) elucidate the phylogeographic relationships within D. laniger and D. nitedula using both mitogenomes and mitochondrial cytochrome b (CYTB) sequences; and (iii) reconstruct the phylogenetic relationships among extant members of the suborder Sciuromorpha. Sixteen new mitogenomes were sequenced from Turkish samples, containing 37 genes (2 ribosomal RNAs, 13 protein-coding genes, 22 transfer RNAs), exhibiting similarity to those of other Gliridae and Sciuridae species. Based on mitogenomic data, Bayesian Inference and Maximum Likelihood phylogenetic analyses revealed two major phylogroups corresponding to the two families, Gliridae and Sciuridae, which were both monophyletic. Analyses of mitogenomic and CYTB sequences revealed at least two major lineages (i: Anatolia and ii: Lesser Caucasus and Alborz) of D. nitedula in the Anatolian region of Türkiye. The mitochondrial CYTB data indicated that D. laniger exhibited at least two major lineages (Eastern and Western), whereas D. nitedula comprised multiple lineages and sublineages. The mean genetic distance between the two mitogenomic lineages of D. nitedula was 7.69%. Based on the CYTB data, the mean genetic distance between the Eastern and Western lineages of D. laniger was 7%, whereas the mean genetic distances among the lineages of D. nitedula ranged from 6% to 13%. Major lineages of both D. laniger and D. nitedula might be considered distinct species throughout the species' range. This study demonstrates that complete mitogenomes for reconstructing the Gliridae phylogeny provides important information for revealing phylogenetic and phylogeographic relationships.Öğe 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, OsmanThis 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.
