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Canoglu H, Aksu I, Turan D, Bektas Y. DNA barcoding of the genus Alburnoides Jeitteles, 1861 (Actinopterygii, Cyprinidae) from Anatolia, Turkey. ZOOSYST EVOL 2023. [DOI: 10.3897/zse.99.94333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
The present study investigated the ability of DNA barcoding to reliably identify the endemic freshwater species in Turkey, known as biodiversity hotspots. The barcode region (652 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) was used to barcode 153 individuals from 13 morphologically identified species of the genus Alburnoides. Based on the Kimura two-parameter (K2P) evolution model, the average interspecific distance (0.0595) was 31-fold higher than the average intraspecific distance (0.0019). There was a clear-cut barcode gap (0.0158–0.0187) between maximum intraspecific distance (A. tzanevi and A. velioglui) and minimum nearest-neighbour distance (A. freyhofi and A. kurui) for Anatolian Alburnoides species and a common genetic threshold of 0.0158 sequence divergence was defined for species delimitation. The multiple species delimitation methods (ABGD, ASAP, GMYC and bPTP) revealed a total of 11 molecular operational taxonomic units (MOTUs) for 13 morphospecies. Neighbour-joining (NJ), Maximum Likelihood (ML) and Bayesian Inference (BI) tree analysis indicated that all haplotypes were clustered into two major clades, which corresponded to eleven Alburnoides species clusters, with strong bootstrap support. Furthermore, all the specimens clustered in concurrence with the morpho-taxonomic status of the species, except for two species (A. coskuncelebii and A. emineae) that were morphologically differentiated, but showed overlap in variation for COI-based DNA barcode data with other species. Overall, present results identified that COI-based DNA barcoding is effective for species identification and cataloguing of genus Alburnoides in Turkey.
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Bektas Y, Aksu İ, Kaya C, Bayçelebi E, Turan D. DNA barcoding and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae) in Anatolia. J Fish Biol 2022; 101:505-514. [PMID: 35607971 DOI: 10.1111/jfb.15114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The DNA barcoding approach was used for the determination of evolutionary relationships and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae). The COI barcode region (615 bp amplicon) was used to barcode 444 individuals from 64 morphologically identified species in the genus Oxynoemacheilus and 189 haplotypes were identified. The average of the interspecific p distance (9.59%) was about 21-fold higher than the average intraspecific distance (0.44%). A general genetic threshold of 1.46% sequence divergence was defined for species delimitation. The multiple species delimitation methods (BCM, GMYC, bPTP and TCS) revealed a total of 62 molecular operational taxonomic units for 64 morphospecies with a new loach species from the BuyukMelen River. Neighbour-joining, maximum likelihood and Bayesian inference analyses indicated that all haplotypes were clustered into 62 clades, which corresponded to Oxynoemacheilus species, with strong bootstrap support (≥95%). Furthermore, all samples grouped in concurrence with the taxonomic status of the species except for species groups (O. germencicus-O. cinicus-O. mesudae and O. leontinae-O. namiri) that were showed intraspecific overlap in genetic diversity for COI-based barcodes. In conclusion, our analyses indicate that COI-based barcodes provide reliable species discrimination. Therefore, we currently recommend COI barcodes as the suitable barcode for genus Oxynoemacheilus.
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Affiliation(s)
- Yusuf Bektas
- Deparment of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - İsmail Aksu
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Cüneyt Kaya
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Esra Bayçelebi
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Davut Turan
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
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Bektas Y, Aksu I, Kaya C, Bayçelebi E, Küçük F, Turan D. Molecular systematics and phylogeography of the genus Alburnus Rafinesque, 1820 (Teleostei, Leuciscidae) in Turkey. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:273-284. [PMID: 32654564 DOI: 10.1080/24701394.2020.1791840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In this study, the phylogeny of Alburnus genus distributed in Turkish freshwaters was performed by analyzing mitochondrial cyt b gene (1141 bp) and COI gene (1551 bp) sequences from 1172 samples representing 112 populations of 24 species through their geographical distribution. According to our findings, 20 valid species are distributed in Turkey of which 18 have already been known. While six Alburnus species (A. battalgilae, A. istanbulensis, A. carinatus, A. schischkovi, A. nasreddini ve A. adanensis) have been synonomized, two new species (Alburnus sp.1 and Alburnus sp.2) from Dicle River and Çapraz Stream/Susurluk River have been identified. Extinct species such as A. akili and A. nicaeensis have not been observed in situ. Phylogenetic tree topologies and haplotype network of the 119 cyt b and 80 COI haplotypes detected in Alburnus species have indicated a consensus tree topology containing twenty lineages, each of corresponding to one species, and three Alburnus haplogroups corresponding to the geographical origins: Eastern Anatolia (I), Mediterranean (2) and Western & Northern Anatolia (3). The results indicate that the divergence between those haplogroups may have occurred during the Middle Miocene-Middle Pleistocene periods (from 14.9 to 5.29 million years).
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Affiliation(s)
- Yusuf Bektas
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Ismail Aksu
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
| | - Cüneyt Kaya
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
| | - Esra Bayçelebi
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
| | - Fahrettin Küçük
- Department of Basic Sciences, Eğirdir Fisheries Faculty, Isparta University of Applied Sciences, Isparta, Turkey
| | - Davut Turan
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
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Bektas Y, Aksu I, Kaya C, Baycelebi E, Atasaral S, Ekmekci FG, Turan D. Phylogeny and phylogeography of the genusAlburnoides(Teleostei, Cyprinidae) in Turkey based on mitochondrial DNA sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:794-805. [DOI: 10.1080/24701394.2019.1664493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Yusuf Bektas
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Ismail Aksu
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
| | - Cuneyt Kaya
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
| | - Esra Baycelebi
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
| | - Sebnem Atasaral
- Department of Fisheries Technology Engineering, Faculty of Marine Sciences, Karadeniz Technical University, Trabzon, Turkey
| | | | - Davut Turan
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
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Bartáková V, Bryja J, Šanda R, Bektas Y, Stefanov T, Choleva L, Smith C, Reichard M. High cryptic diversity of bitterling fish in the southern West Palearctic. Mol Phylogenet Evol 2018; 133:1-11. [PMID: 30586649 DOI: 10.1016/j.ympev.2018.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/24/2018] [Accepted: 12/20/2018] [Indexed: 11/17/2022]
Abstract
South-east Europe, along with the adjacent region of south-west Asia, is an important biodiversity hotspot with high local endemism largely contributed by contemporary continental lineages that retreated to southern refugia during colder Quaternary periods. We investigated the genetic diversity of the European bitterling fish (Rhodeus amarus) species complex (Cyprinidae) across its range in the western Palearctic, but with a particular emphasis in the region of Balkan, Pontic and Caspian refugia. We genotyped 12 polymorphic microsatellite loci and a partial sequence of mitochondrial gene cytochrome b (CYTB) for a set of 1,038 individuals from 60 populations. We used mtDNA sequences to infer phylogenetic relationships and historical demography, and microsatellite markers to describe fine-scale genetic variability and structure. Our mtDNA analysis revealed six well-supported lineages, with limited local co-occurrence. Two lineages are distributed throughout central and western Europe (lineages "A" and "B"), with two zones of secondary contact. Another two lineages were restricted to the Ponto-Aegean region of Greece (lineages "C" and "D") and the final two lineages were restricted south of the Caucasus mountains (lineage "E" from the Black Sea watershed and lineage "F" from the Caspian watershed). A signal of recent expansion was revealed in the two widespread lineages and the Ponto-Aegean lineage "C". The geographic distribution of clusters detected by nuclear microsatellites corresponded well with mitochondrial lineages and demonstrated finely sub-structured populations. A profound population structure suggested a significant role of genetic drift in differentiation among lineages. Lineage divergence in the Ponto-Aegean and Caspian regions are substantial, supporting the validity of two described endemic species (Rhodeus meridionalis as lineage "D" and Rhodeus colchicus as lineage "E") and invite taxonomic evaluation of the other two southern lineages (Thracean "C" and Caspian "F").
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Affiliation(s)
- Veronika Bartáková
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Josef Bryja
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Radek Šanda
- National Museum, Department of Zoology, Václavské nám. 68, 115 79 Prague 1, Czech Republic
| | - Yusuf Bektas
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, 53100 Rize, Turkey
| | - Tihomir Stefanov
- National Museum of Natural History, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blv., 1000 Sofia, Bulgaria
| | - Lukáš Choleva
- The Czech Academy of Sciences, Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, Rumburská 89, 277 21 Liběchov, Czech Republic; Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava 710 00, Czech Republic
| | - Carl Smith
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65 Brno, Czech Republic; Department of Ecology & Vertebrate Zoology, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; School of Biology and Bell-Pettigrew Museum of Natural History, University of St Andrews, St Andrews KY16 8LB, UK
| | - Martin Reichard
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65 Brno, Czech Republic.
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Bektas Y, Turan D, Aksu I, Ciftci Y, Eroglu O, Kalayci G, Belduz AO. Molecular phylogeny of the genus Capoeta (Teleostei: Cyprinidae) in Anatolia, Turkey. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Akhan S, Bektas Y, Berber S, Kalayci G. Population structure and genetic analysis of narrow-clawed crayfish (Astacus leptodactylus) populations in Turkey. Genetica 2014; 142:381-95. [PMID: 25139434 DOI: 10.1007/s10709-014-9782-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 08/08/2014] [Indexed: 11/26/2022]
Abstract
The genetic differentiation among Turkish populations of the narrow-clawed crayfish was investigated using a partial sequence of cytochrome oxidase subunit I gene (585 bp) of 183 specimens from 17 different crayfish populations. Median joining network and all phylogenetic analyses disclosed a strong haplotype structure with three prominent clades diverged by a range between 20 and 50 mutations and substantial inter-group pairwise sequence divergence (5.19-6.95 %), suggesting the presence of three distinct clades within the Anatolian populations of Astacus leptodactylus. The divergence times among the three clades of Turkish A. leptodactylus are estimated to be 4.96-3.70 Mya using a molecular clock of 1.4 % sequence divergence per million years, pointing to a lower Pliocene separation. The high level of genetic variability (H d = 95.8 %, π = 4.17 %) and numerous private haplotypes suggest the presence of refugial populations in Anatolia unaffected by Pleistocene habitat restrictions. The pattern of genetic variation among Turkish A. leptodactylus populations, therefore, suggests that the unrevealed intraspecific genetic structure is independent of geographic tendency and congruent with the previously reported geographic distribution and number of subspecies (A. l. leptodactylus and A. l. salinus) of A. leptodactylus.
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Affiliation(s)
- Suleyman Akhan
- Department of Aquaculture, Faculty of Fisheries, Akdeniz University, 07058, Antalya, Turkey
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Akil A, Api O, Bektas Y, Yilmaz AO, Yalti S, Unal O. Paracetamol vs dexketoprofen for perineal pain relief after episiotomy or perineal tear. J OBSTET GYNAECOL 2014; 34:25-8. [PMID: 24359044 DOI: 10.3109/01443615.2013.828026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A randomised controlled trial was conducted to investigate efficacy of paracetamol and dexketoprofen trometamol for perineal pain relief after perineal repair. Subjects were randomly assigned to receive two doses of either 50 mg of intravenous dexketoprofen trometamol via slow i.v. infusion (Group I, n = 49) or 1,000 mg of paracetamol via intravenous infusion (Group II, n = 46). The main outcome measure was a VAS (visual analogue scale) for pain recorded at 1 h (VAS 1). A total of 82 patients were included in the final analysis (Group I, n = 41; Group II, n = 41). There was no difference among groups in terms of pain scores at the beginning (VAS 0). The pain was decreased in 70% of the patients in Group I and in 62% of the patients in Group II (p = 0.502). Both paracetamol and dexketoprofen are effective in perineal pain relief after episiotomy or perineal tear repair.
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Affiliation(s)
- A Akil
- Bodrum Acıbadem Hospital , Bodrum , Mugla
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Mirici A, Bektas Y, Ozbakis G, Erman Z. Effect of Inhaled Corticosteroids on Respiratory Function Tests and Airway Inflammation in Stable Chronic Obstructive Pulmonary Disease. Clin Drug Investig 2001. [DOI: 10.2165/00044011-200121120-00006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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