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Öğe Assessment of intraspecific variability in the forest dormouse (dryomys nitedula) and woolly dormouse (dryomys laniger) from Türkiye and adjacent regions based on mitochondrial DNA(Multidisciplinary Digital Publishing Institute (MDPI), 2025) Çolak, Ercüment; Markov, Georgi; Selvi, Engin; Kankılıç, Teoman; Şeker, Perinçek Seçkinozan; Kocheva, Maria A.; Gospodinova, Milena K.; Çolak, Reyhan; Dimitrov, Hristo; Yiğit, NuriThis study aimed to reveal intraspecific variations in two Dryomys species distributed in Türkiye, based on mitochondrial DNA cytochrome b gene sequences, and to discuss the factors driving these variations in the context of phylogeography and genetic species concepts. As a result of Maximum Likelihood, Bayesian Inference, and Network analyses, which included haplogroups or lineages from Italy, Russia, the Caucasus, and Iran identified in previous studies, along with Turkish haplotypes, three major clades (MC1, MC2, and MC3) were identified within Dryomys nitedula. These clades began to diverge evolutionarily in the middle of the Late Miocene (8.82 million years ago) and exhibit significant genetic differences from one another. The Turkish haplotypes were divided into five distinct lineages (N1–N5), each within five subclades (SC1–SC5), which were nested within these MCs. These lineages, their geographical distributions, and the subspecies defined in previous studies that correspond to these lineages are as follows: N1 from the Thrace region (Dryomys nitedula wingei), N2 from the Black Sea region (potentially a new subspecies), N3 from western and central Anatolia (Dryomys nitedula phrygius), N4 from northeastern Anatolia (Dryomys nitedula tichomirowi), and N5 from eastern Anatolia (Dryomys nitedula pictus). The N2 lineage, distributed in areas close to the coastal side of the Eastern Black Sea region and with a range close to both N3 (D. n. phrygius) and N4 (D. n. tichomirowi), exhibited high genetic differentiation from these two lineages and was a candidate to be treated as a new subspecies of Dryomys nitedula in Türkiye. The N5 lineage, which includes haplotypes from the distribution areas of the populations initially classified as Dryomys pictus and later as Dryomys nitedula pictus in previous studies, was found to be more closely related to Dryomys nitedula kurdistanicus from the Zagros Mountains than to D. n. pictus from the central regions of Iran. Combining the results of this study with previous research, it is clear that the D. nitedula lineages in Türkiye, along with haplogroups or subspecies in neighboring regions diverged between the middle Late Miocene and Middle Pleistocene. This divergence is believed to have been driven by climatic cycles and geomorphological processes that shaped the topography of their distribution range. The high genetic diversity observed in the lineages of Anatolia suggests that the region may have served as a glacial refuge for D. nitedula. Similarly to the processes and factors shaping the evolution of D. nitedula, Dryomys laniger was found to have diverged into two lineages, western (L1) and eastern (L2 or Dryomys anatolicus), within its distribution range during the Late Pliocene (2.94 Mya). To make a more accurate taxonomic assessment of D. laniger, a larger number of samples is needed, and the distribution limits should be more clearly defined.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 G-banded Karyotypes of Some Species in Gliridae (Mammalia: Rodentia) from Turkey(Adiyaman University, 2021) Kankiliç, Teoman; Şeker, Perinçek Seçkinozan; Selvi, Engin; Özkan, Beytullah; Yiğit, Nuri; Çolak, ErcümentThe results of a cytogenetic study on some representatives of Gliridae from Turkey were introduced. The G-, C-, and AgNOR banded karyotypes of Muscardinus avellanarius abanticus from Abant (Bolu), and the G-banded karyotype of Myomimus roachi from Thrace were presented for the first time. Additionally, the G-banded karyotypes of Dryomys nitedula, and Myoxus glis were analysed. Because of not including a secondary constriction and the smallest chromosome being metacentric instead of acrocentric in the autosomal set, the karyotype of M. a. abanticus was different from that of M. a. trapezius. With the comparison of obtained G-banded patterns belonging to the other Glirid species, it was detected that obtained karyotypes displayed consistency at a great extent with the previously determined karyotypes.Öğe Geographical distribution pattern of mitochondrial DNA cytochrome b diversity in populations of arvicola amphibius (Linnaeus, 1758) (Mammalia: Rodentia) in Turkey as determined by PCR-RFLP(Institute of Zoology, 2018) Şeker, Perinçek Seçkinozan; Selvi, Engin; Kankılıç, Teoman; Çolak, ErcümentArvicola amphibius (Linnaeus, 1758) is a semiaquatic rodent living in and around wetland habitats covered by rich vegetation. It has a broad distribution in the Palearctic and three subspecies live in Turkey. In order to identify the geographical distribution of mitochondrial DNA cytochrome b diversity in A. amphibius populations in Turkey, the restriction fragment length polymorphism method was applied. The digestion patterns of four restriction enzymes (Alu I, Rsa I, Sau3A I and EcoR V) in 100 samples of A. amphibius from 20 localities in Turkey brought out four mtDNA lineages [Thrace (THR), central Anatolia (CA), southern Anatolia (SA) and eastern Anatolia (EA)], each having high genetic diversity. In contrast to the three lineages in THR, CA and SA, respectively, corresponding to the known subspecies A. a. cernjavskii, A. a. persicus and A. a. hintoni, separate populations constituting the fourth A. amphibius lineage in EA were determined. The results proved that the variable topography and geomorphological conglomeration process of Anatolia lead to an allopatric differentiation and had a large impact on the appearance and shaping of intraspecific genetic variations in water voles. Moreover, the existing high genetic variability in Turkish water vole populations propounds the importance of Anatolia as a potential refuge in the Pleistocene.Öğe Karyological and distributional contributions to Turkish rodent fauna (mammalia: rodentia) from islands in aegean and Marmara sea(Artvin Çoruh Üniversitesi, 2017) Şeker, Perinçek Seçkinozan; Selvi, Engin; Çolak, ErcümentA chromosomal study on five different rodent species (Mus domesticus, Mus macedonicus, Apodemus sylvaticus, Apodemus witherbyi and Rattus rattus) from Gökçeada and Bozcaada in Aegean Sea and Marmara Island in Marmara Sea was performed to fill the deficiency of karyological information about island populations of these species. Diploid chromosome sets (2n) and fundamental numbers of chromosomal arms (NF) were determined to be 2n = 40, 40, 48, 48 and 38, NF = 40, 40, 48, 48 and 60 for M. domesticus, M. macedonicus, A. sylvaticus, A. witherbyi and R. rattus respectively. Results showed that there was no difference between karyological values in island and continental populations of those rodents, although Aegean and Marmara seas have served as geographic barriers for a long time between islands and mainland. In addition to the karyotypes of M. domesticus, M. macedonicus, A. sylvaticus and R. rattus, their presence in Marmara Islands were firstly determined by current studyÖğe Nuclear and organelle genes based phylogeny of Dryomys (Gliridae, rodentia, mammalia) from Turkey(Hungarian Natural History Museum, 2019) Kankılıç, Teoman; Şeker, Perinçek Seçkinozan; Aydın, Burcu; Altunbaş, Derya; Selvi, Engin; Yiğit, Nuri; Çolak, ErcümentMolecular phylogeny, phylogeography and genetic structure of the genus Dryomys Thomas, 1906 from Turkey were identified by using partial sequences of beta-fibrinogen intron 7 and mitochondrially encoded 12S ribosomal RNA genes and also combined data of two genes. Within Dryomys nitedula species, both, nuclear and mitochondrial genes coherently separated the Thrace lineage from the other lineages in Anatolia. Contrary to this, complex and incomprehensible phylogenies were recovered for Anatolian populations of this species. The analysis of the combined data of these two genes resolved mentioned complexity and incongruity and made phylogeny compatible with the results of past studies for the relative position of the Anatolian lineages. Thus, the presence of four different lineages (one in Thrace and three in Anatolia) within D. nitedula in the localities exemplified across Turkey was confirmed. Genetic differentiation (K2P distances) between the lineages were moderate at the level of intraspecific diversity. In addition to this, genetic distance (K2P = 5.5%) determined between D. nitedula and D. laniger conformed the distance suggested for the separate species of mammals. Evolutionary divergence time estimations demonstrated that the probable divergence between D. laniger and D. nitedula and among its detected lineages started in the border of Late Miocene and Pliocene (5.3 Mya) and lasted to the beginning of the Calabrian Stage of Pleistocene (1.8 Mya) in line with the previous results obtained from fossil and molecular data.Öğe Phylogenetic and phylogeographic relationships of populations of Meriones tristrami Thomas, 1892 (Rodentia: Gerbillinae) in Turkey as inferred from Cytochrome-b and RFLP analysis(Bulgarska Akademiya na Naukite, 2020) Yiğit, Nuri; Çolak, Ercüment; Markov, Georgi; Yiğit, Fulya Saygılı; Çolak, Reyhan; Çetintürk, Derya; Şeker, Perinçek Seçkinozan; Selvi, EnginThe present study aimed to reveal the relationship between the genetic diversity of Tristram’s jird Meriones tristrami subpopulations by using cyt-b sequences, the amplified fragments of cyt-b produced by restriction endonuclease (RFLP; Msp I, Rsa I, Noc I and Hae III were used) and the distribution on the Anatolian Peninsula. Eighteen haplotypes were identified in the subpopulations of this species, with the highest nucleotide diversity in the Central Anatolia. The haplotype diversity was determined to be 0.970 among subpopulations. The fixation index (Fst) and the gene flow parameter (Nm) based on cyt-b sequences showed the effective gene flow between the western and south-eastern subpopulations. Both cyt-b sequences and RFLP analyses produced almost similar topology in the Bayesian and UPGMA trees, indicating a gene flow from subpopulations of the South-east to Central Anatolia and the Western Black Sea coast. The main factor for the genetic diversity is considered to be the intermittent distribution from west to east as a result of the great altitude of the Eastern Anatolian Plateau as well as the sea and lake system fragmenting the territory of Anatolia in the Pliocene – Pleistocene AgeÖğe Phylogenetic inference from 16S rRNA gene sequencing in chromosome races of the genus nannospalax species (rodentia: spalacidae)(Pleiades Publishing, 2024) Kankılıç, Teoman; Çelikbilek, Habibe Didem; Kankılıç, Tolga; Şeker, Perinçek Seçkinozan; Selvi, Engin; Civelek, İlkayIn this study, we aimed to develop a species-level phylogeny for the Nannospalax genus, identify cryptic species that are difficult to differentiate using standard methods, and further evaluate the relationships across chromosomal forms of several species. 16S rRNA gene sequences from 81 Turkish regions were evaluated and statistical analyzes were conducted. Results are as follows; (i) Nannospalax cilicicus was found to be monophyletic and sister in relation to Nannospalax xanthodon; (ii) We suggested for the first time that the Central-Anatolian populations should be classified under the species name Nannospalax cilicicus (stat. n.); (iii) the unidentified 2n = 52 cytotypes from Bolu and Nannospalax leucodon cytotypes were reciprocally monophyletic, these data support the notion that the 2n = 52 cytotypes from Bolu belong to an unidentified taxon; (iv) study also offered evidence for the monophyly of N. tuncelicus for the first time; (v) Nannospalax xanthodon (2n = 36, 38, and 40) and Nannospalax nehringi composed several species-specific clades, which form polytomy structure, so relationships between these species are still unclear.Öğe Variation in the Conventional and Banded Karyotypes among Populations of Arvicola amphibius (L., 1758) (Mammalia: Rodentia) from Turkey(Institute of Zoology, 2018) Şeker, Perinçek Seçkinozan; Arslan, Atilla; Selvi, Engin; Kankılıç, Teoman; Zima, JanChromosomal characteristics of water voles (Arvicola amphibius) were studied in ten populations including 33 samples from Anatolia, Turkey. The C-banding pattern and NORs distribution were analysed in four samples from Eastern Anatolia. The conventionally stained karyotypes showed the standard complement of the species (2n = 36, NFa = 60-62, NF = 64-66). Variation in the number of autosomal arms originated from the alternative presence of a subtelocentric or an acrocentric autosomal pair. C-banding provided further support for differentiation of the amount and distribution of C-heterochromatin between populations from Central Europe and Asia Minor. Chromosomal variation among Turkish populations was manifested by the number of autosomal arms, positive C-bands and NOR-carrying autosomes.
