Türkiye’deki Fırat Nehri Drenajından Oxynoemachelius (Teleostei: Nemacheilidae) Türlerinin COI-barkod Bölgesine Dayalı Genetik Tanımlaması ve Filogenetik İlişkileri

Bu çalışmada, DNA barkodlama tekniği ile Türkiye’nin Fırat nehir havzasındaki Oxynoemacheilus türlerini güvenilir bir şekilde tanımlama yeteneği araştırılmıştır. Oxynoemacheilus genusunu temsilen 6 türe ait 167 bireyi barkodlamak için mitokondri sitokrom c oksidaz altünite I' in (COI) barkod bölgesi (627 bp) kullanıldı. Kimura 2 parametresine dayalı olarak (K2P), maksimum tür içi ve minimum türlerarası genetik mesafeleri sırasıyla % 0.59 ve % 1.62‘dır. En yakın komşu türler arası mesafeler, ortalama tür içi mesafeden 7 kat daha yüksektir ve belirgin bir DNA barkod aralığı fark edilmiştir. Filogeni tabanlı DNA barkodlama başarısı testine göre komşu-birleştirme fenogramları K2P modeli kullanılarak 1000 seç-bağla replikasyonu ile üretildi ve örneklerin tümünün türlerin taksonomik durumları ile uyumlu olarak kümelendiği belirlenmiştir. MP ve ML filogenileri, Doğu ve Batı Anadolu gruplarına karşılık gelen iki klad içeren bir ortak ağaç topolojisi gösterdi. Bu çalışmanın sonuçları, COI geninin yaklaşık % 81 başarı oranıyla Oxynoemacheilus türlerinin belirlenmesi ve sınırlandırılması için uygun bir DNA barkod belirleyicisi olabileceğini göstermektedir.

Anahtar Kelimeler:

COI, COI, Endemizm, taş ısıran balığı, taş ısıran balığı, taş ısıran balığı, Türkiye

Genetic identification and phylogenetic relations of Oxynoemachelius species (Teleostei: Nemacheilidae) from drainage of Euphrates in Turkey based on COI-barcode region

The present study investigated the ability of DNA barcoding to reliably identify Oxynoemacheilus species in Euphrates River basin of Turkey, known as biodiversity hotspots. The barcode region (627 bp) of the mitochondrial cytochrome c oxidase I (COI) were used to barcode 167 individuals belonging to six Oxynoemacheilus species. Based on Kimura two-parameter (K2P), the intraspecific diversity and minimuminterspecific genetic distance were 0.59% and 1.62% respectively. Nearest neighbor distance was 7-fold higher than maximum intra-specific distance on average and a distinct DNA barcoding gap was observed.According to the phylogeny-based succes test neighbour-joining phenograms were generated with 1000 bootstrap replications using the K2P model and all the specimens clustered in concurrence with the taxonomic status of the species. The MP and ML phylogenies indicated a consensus tree topology containing two cladescorresponding to the geographical origins: Western and Eastern Anatolia groups. The results of present study indicated that the COI gene could be a suitable DNA barcode marker for the Oxynoemacheilus species identification and delimitation with approximately 81% success rate.

Keywords:

DNA BArcoding, Turkey, Spined loach, DNA barkodlama, DNA barkodlama, COI COI, COI, COI, taş ısıran balığı, taş ısıran balığı, taş ısıran balığı, taş ısıran balığı,

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April, J., Mayden, R.L., Hanner, R.H. and Bernatchez, L. (2011). Genetic calibration of species diversity among North America’s freshwater fishes. Proceedings of the National Academy of Sciences of the United States of America, 108, 10602–10607.
Aquilino, S.V.L., Tango, J.M., Fontanilla, I.K.C., Pagulayan, R.C., Basiao, Z.U., Perry, S.O. and Quilang, J.P. (2011). DNA barcoding of the ichthyofauna of Taal Lake, Philippines. Molecular Ecology Resource, 11, 612–619.
Ardura, A., Linde, A. R., Moreira, J.C. and Garcia-Vazquez E. (2010). DNA barcoding for conservation and management of Amazonian commercial fish. Biological Conservation, 143, 1438-1443.
Avise, J.C., Neigel, J.E., and Arnold. J. (1984). Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Journal of Molecular Evolution, 20, 99–105.
Bektaş. Y., Turan, D., Aksu, İ., Çiftçi, Y., Eroglu, O., Kalayci, G. and Beldüz, A.O. (2017). Molecular phylogeny of the genus Capoeta (Teleostei. Cyprinidae) in Anatolia, Turkey. Biochemical Systematics and Ecology, 70, 80-94
Bingpeng, X, Heshan, L, Zhilan, Z, Chunguang, W, Yanguo, W. and Jianjun, W. (2018). DNA barcoding for identification of fish species in the Taiwan Strait. Plos One, 13, 0198109.
Brown, S.D., Collins, R.A., Boyer, S., Lefort, M-C., Malumbres-Olarte, J., Vink, C.J. and Cruickshank, R.H. (2012). Spider: an R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Molecular Ecology Resources, 12, 562–565. doi: 10.1111/j.1755-0998.2011.03108.x
Dayrat, B. (2005). Towards integrative taxonomy. Biological Journal of the Linnean Society, 85, 407–415.
Erk’akan, F., Nalbant and T.T. and Özeren, S.C. (2007). Seven new species of Barbatula, three new species of Schistura and a new species of Seminemacheilus (Ostariophsi: Balitoridae: Nemachilinae) from Turkey. Journal of Fisheries International, 2, 69-85. https://doi=jfish.2007.69.85
Erk’akan, F., Özeren and S.C. and Nalbant, T.T. (2008). Two new species of stone loaches from Turkey (Teleostei: Nemacheilidae), Journal of Fisheries International, 3, 115-119. https://doi=jfish.2008.115.119
Freyhof, J., Erk’akan, F., Özeren, C., and Perdices, A. (2011). An overview of the western Palaearctic loach genus Oxynoemacheilus (Teleostei: Nemacheilidae). Ichthyological Exploration of Freshwaters, 22(4), 301-312.
Freyhof, J. and Geiger, M. (2017). Oxynoemacheilus zarzianus, a new loach from the Lesser Zab River drainage in Iraqi Kurdistan (Teleostei: Nemacheilidae). Zootaxa, 4273, 258–270.
Freyhof, J. and Özuluğ, M. (2017). Oxynoemacheilus hazarensis, a new species from Lake Hazar in Turkey, with remarks on O. euphraticus (Teleostei: Nemacheilidae). Zootaxa, 4247(4), 378-390.
Freyhof, J., Kaya, C., Turan, D., Geiger, M. (2019). Review of the Oxynoemacheilus tigris group with the description of two new species from the Euphrates drainage (Teleostei: Nemacheilidae). Zootaxa, 4612 (1).
Geiger, M.F., Herder, F., Monaghan, M.T., Almada, V., Barbieri, R., Bariche, M., Berrebi, P. and et al. (2014). Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes. Molecular Ecology Resources, 14, 1210–1221.
Grant, W.A.S. and Bowen, B.W. (1998). Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. Journal of Heredity, 89, 415–426.
Hall, T.A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95- 98.
Hebert, P.D.N., Cywinska, A., Ball, S.L. and deWaard, J.R. (2003a). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B, 270, 313–321.
Hebert, P.D.N., Ratnasingham, S. and deWaard, J.R. (2003b). Barcoding animal life: cytochrome c oxidase 1 divergences among closely related species. Proceedings of the Royal Society London, 270, 596–599.
Hebert, P.D.N., Penton, E. H., Burns, J. M., Janzen, D. H. and Hallwachs, W. (2004). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astrapes fulgerator. Proceedings of the National Academy of Sciences of the United States of America, 101, 14812–14817.
Hebert, P.D.N. and Gregory, T.R. (2005). The Promise of DNA Barcoding for Taxonomy. Systematic Biology. 54, 852-859.
Hubert, N., Hanner, R. and Holm, E. (2008). Identifying Canadian freshwaterfishes through DNA barcodes. PloS One, 3, 2490.
Jouladeh-Roudbar, A., Eagderi, S. and Hosseinpour, T. (2016). Oxynoemacheilus freyhofi, a new nemacheilid species (Teleostei, Nemacheilidae) from the Tigris basin, Iran. Fish Taxa, 1, 94-107.
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111–120.
Knebelsberger, T., Dunz, A.R., Neumann, D. and Geiger, M.F. (2014). Molecular diversity of Germany’s freshwater fishes and lampreys assessed by DNA barcoding. Molecular Ecology Resources, 15, 562-572.
Kress, W.J., Wurdack, K.J., Zimmer, E.A., Weigt L.A. and Janzen, D.H. (2005). Use of DNA barcodes to identify flo wering plants. Proceedings of the National Academy of Sciences, 102, 8369–8374.
Kumar, S., Stecher, G. Li. M., Knyaz, C. and Tamura, K., 2018. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology, 35, 1547–1549.
Levin, B.A., Freyhof, J., Lajbner, Z., Perea, S., Abdoli, A., Gaffaroğlu, M., Özuluğ, M., Rubenyan, H.R., Salnikov, V.B. and Doadrio, I. (2012). Phylogenetic relationships of the algae scraping cyprinid genus Capoeta (Teleostei: Cyprinidae). Molecular Phylogenetics and Evolution, 62, 542–549.
Librado, P. and Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
Liu, Z. J. and Cordes, J. F. (2004). DNA marker technologies and their applications in aquaculture genetics. Aquaculture, 238, 1–37. Lleonart, J., Taconet, M. and Lamboeuf, M. (2006). Integrating information on marine species identification for fishery purposes. Marine Ecology Progress Series, 316, 231–238.
Ma, H., Ma, C. and Ma, L. (2011). Population genetic diversity of mud crab (Scylla paramamosain) in Hainan Islan d of China based on mitochondrial DNA. Biochemical Systematics and Ecology, 39, 434-440.
McCusker, M.R., Denti, D., Van Guelpen, L., Kenchington, E., and Bentzen P. (2013). Barcoding Atlantic Canada's commonly encountered marine fishes. Molecular Ecology Resources, 13, 177–188.
Meier, R., Kwong, S., Vaidya, G. and Ng, P. K. L. (2006). DNA barcodingand taxonomy in Diptera: A tale of high intraspecific variability andlow identification success. Systematic Biology, 55, 715–728.
Meier, R., Zhang, G.Y. and Ali, F. (2008). The use of mean instead of smallest interspecific distances exaggerates the size of the ‘Barcoding Gap’ and leads to misidentification, Systematic Biology, 57, 809–813.
Nelson, J.S., Grande, T.C. and Wilson, M.V.H. (2016). Fishes of the World. Fifth Edition. John Wiley and Sons, Inc., Hoboken, New Jersey,1-707.
Posada, D. (2008). jModelTest: phylogenetic model averaging. Molecular Biology, 25, 1253–1256.
Prokofiev, A.M. (2009). Problems of the classification and phylogeny of Nemacheiline loaches of the group lacking the preethmoid I (Cypriniformes: Balitoridae: Nemacheilinae). Journal of Ichthyology, 49, 874- 898.
Prokofiev, A.M. (2010). Morphological classification of loaches (Nemacheilinae). Journal of Ichthyology, 50, 827-913.
Rogers, A.R. and Harpending, H. (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552-569.
Sayyadzadeh, G., Eagderi, S. and Esmaeıli, H.R. (2016). A new loach of the genus Oxynoemacheilus from the Tigris River drainage and its phylogenetic relationships among the nemacheilid fishes (Teleostei: Nemacheilidae) in the Middle East based on mtDNA COI sequences. Iranian journal of ichthyology, 3, 236–250. DOI: 10.7508/iji.2016.
Sayyadzadeh, G., Esmaeili, H.R., Eagderi, S., Jouladeh-Roudbar, A., Masoudi, M., Vatandoust, S. (2017). Re-description of Oxynoemacheilus longipinnis from the Persian Gulf basin (Teleostei: Nemacheilidae). Zoology in the Middle East, 63(3), 228-238.
Seyrek, A., Demir, T., Pringle, M.S., Yurtmen, S., Westaway, R., Beck, A. and Rowbotham, G. (2007). Kinematics of the Amanos Fault, southern Turkey, from Ar/Ar dating of offset Pleistocene basalt flows: Transpression between the African and Arabian plates. Geological Society, 290, 255–284.
Shen, Y.J., Guan, L.H., Wang, D.Q. and Gan, X.N. (2016). DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River. Ecology and Evolution, 6, 2702-13.
Strauss, R.E. and Bond, C.E. (1990). Taxonomic methods: morphology. In: Schreck CB, Moyle PB (eds) Methods for fish biology. American Fisheries Society, 109–140.
Sungur, S. (2020). Oxynoemacheilus kosswigi a Junior Synonym of O. seyhanensis (Teleostei: Nemacheilidae). Iranian Journal of Science and Technology, Transactions A: Science, 44, 563–573
Triantafyllidis, A., Bobori, D., Koliamitra, C., Gbandi, E., Mpanti, M., Petriki, O. and Karaiskou, N. (2011). DNA barcoding analysis of fish species diversity in four north Greek lakes. Mitochondrial DNA, 22, 37–42.
Tsukihara, T., Aoyama, H., Yamashita, E., Tomizaki, T., Yamaguchi, H., Shinzawa-Itoh, K., Nakashima, R., Yaono, R. and Yoshikawa S., 1996. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Science, 272, 1136-1144.
Turan, D., Kaya, C., Kalayci, G., Bayçelebi, E. and Aksu, İ. (2019). Oxynoemacheilus cemali, a new species of stone loach (Teleostei: Nemacheilidae) from the Çoruh River drainage, Turkey. Journal of Fish Biology, 94, 458-468.
Turnbull, H., Lax, N., Diodato, D., Ansorge, O. and Turnbull, D. (2010). The mitochondrial brain: From mitochondrial genome to neurodegeneration. Biochimica et Biophysica Acta, 1802, 111- 21.
Ward, R.D., Zemlak, T.S., Innes, B.H,, Last, P.R. and Hebert, P.D.N. (2005). DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society of London, Series B, 360, 1847–1857.
Ward, R.D., Hanner, R. and Hebert, P.D.N. (2009). The campaign to DNA barcode all fishes, Journal of Fish Biology, 74, 329–356.
Ward, R. (2012). A case study for DNA barcodes. Pp. 423– 439 in W. J. Kress, D. L. Erickson, eds. DNA barcodes: methods and protocols, methods in molecular biology. Springer Science Business Media, LLC, New York, FISH‐BOL. 858.
Westaway, R. (2004). Kinematic consistency between the Dead Sea Fault Zone and the Neogene and Quaternary left-lateral faulting in SE Turkey, Tectonophysics, 391, 203–237.
Zareian, H., Esmaeili, H.R., Heidari, A., Khoshkholgh, M.R. and Mousavi-Saber, H. (2016). Contribution to the molecular systematics of the genus Capoeta from the south Caspian Sea basin using mitochondrial cytochrome b sequences (Teleostei: Cyprinidae). Molecular Biology Research Communications, 5, 65-75.