Genetic structure and demographic history of endangered Alburnus tarichi (Güldenstädt, 1814) populations from Lake Van basin in Turkey inferred from mtDNA analyses

References

• Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr. 19(6):716–723.
   Web of Science ®Google Scholar
• Akib NAM, Tam BM, Phumee P, Abidin MZ, Tamadoni S, Mather PB, Nor SAM. 2015. High connectivity in Rastrelliger kanagurta: influence of historical signatures and migratory behaviour inferred from mtDNA cytochrome b. PLoS One. 10(3):e0119749.
   PubMed Web of Science ®Google Scholar
• Allio R, Donega S, Galtier N, Nabholz B. 2017. Large variation in the ratio of mitochondrial to nuclear mutation rate across animals: implications for genetic diversity and the use of mitochondrial DNA as a molecular marker. Mol Biol Evol. 34(11):2762–2772.
   PubMed Web of Science ®Google Scholar
• Alves MJ, Coelho H, Collares-Pereira MJ, Coelho MM. 2001. Mitochondrial DNA variation in the highly endangered cyprinid fish Anaecypris hispanica: importance for conservation. Heredity (Edinb). 87(Pt 4):463–473.
   PubMedGoogle Scholar
• Araguas RM, Vidal O, Pla C, Sanz N. 2012. High genetic diversity of the endangered Iberian three‐spined stickleback (Gasterosteus aculeatus) at the Mediterranean edge of its range. Freshw Biol. 57(1):143–154.
   Web of Science ®Google Scholar
• Avise JC. 2000. Phylogeography: the history and formation of species. Cambridge: Harvard University Press, p. 464.
   Google Scholar
• Avise JC, Neigel JE, Arnold J. 1984. Demographic influences on mitochondrial DNA lineage survivorship in animal populations. J Mol Evol. 20(2):99–105.
   PubMed Web of Science ®Google Scholar
• Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16(1):37–48.
   PubMed Web of Science ®Google Scholar
• Behera BK, Baisvar VS, Kunal SP, Meena DK, Panda D, Pakrashi S, Paria P, Das P, Bhakta D, Debnath D. 2018. Population structure and genetic diversity of Indian Major Carp, Labeo rohita (Hamilton, 1822) from three phylo-geographically isolated riverine ecosystems of India as revealed by mtDNA cytochrome b region sequences. Mitochondrial DNA A DNA Mapp Seq Anal. 29(2):199–205.
   PubMedGoogle Scholar
• Bektaş Y, Turan D, Aksu I, Ciftci Y, Eroglu O, Kalayci G, Belduz AO. 2017. Molecular phylogeny of the genus Capoeta (Teleostei: Cyprinidae) in Anatolia, Turkey. Biochem Syst Ecol. 70:80–94.
   Web of Science ®Google Scholar
• Bektaş Y, Aksu I, Kaya C, Baycelebi E, Küçük F, Turan D. 2020. Molecular systematics and phylogeography of the genus Alburnus Rafinesque, 1820 (Teleostei, Leuciscidae) in Turkey. Mitochondrial DNA A DNA Mapp Seq Anal. 31(7):273–284.
   PubMedGoogle Scholar
• Bianco PG. 1990. Potential role of the palaeohistory of the Mediterranean and Paratethis basins on the early dispersal of Euro-Mediterranean freshwater fishes. Ichthyol Explor Freshw. 1:167–184.
   Google Scholar
• Bostancı D, Polat N. 2011. Age and growth of Alburnus tarichi (Güldenstädt, 1814): an endemic fish species of Lake Van (Turkey). J Appl Ichthyol. 27(6):1346–1349.
   Web of Science ®Google Scholar
• Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N. 2019. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 15(4):e1006650.
   PubMed Web of Science ®Google Scholar
• Britannica: The Editors of Encyclopaedia. 2013. "Van". Encyclopedia Britannica, 9 Aug. [accessed 2021 May 12]. https://www.britannica.com/place/Van.
   Google Scholar
• Brito MR, Chávez EL, Quiroz AJ, Yukich JE. 1997. Connectivity of the mutual k-nearest-neighbor graph in clustering and outlier detection. Stat Probab Lett. 35(1):33–42.
   Web of Science ®Google Scholar
• Casey J, Jardim E, Martinsohn JT. 2016. The role of genetics in fisheries management under the EU common fisheries policy. J Fish Biol. 89(6):2755–2767.
   PubMed Web of Science ®Google Scholar
• Çetinkaya O. 1996. A freshwater mussel species Unio stevenianus Krynicki 1837 (Mollusca: Bivalvia: Unionidae) from the river Karasu flowing into Lake Van, Turkey. Turk J Zool. 20(2):169–173.
   Google Scholar
• Çetinkaya O, Sarı M, Arabacı M. 1995. Van Gölü (Türkiye) inci kefali (Chalcalburnus tarichi, Pallas 1811) avcılığında kullanılan fanyalı uzatma ağlarının av verimleri ve seçiciliği üzerine bir ön çalışma. Ege Univ J Fish Aquat Sci. 12(1-2):1–13.
   Google Scholar
• Çetinkaya O, Sarı M, Şen F, Arabacı M, Uyar HA. 1994. Van Gölüne dökülen karasu çayının limnolojik özellikleri. Yuzuncu Yil Univ J Agric Sci. 4(1):151–168.
   Google Scholar
• Chang YS, Huang FL, Lo TB. 1994. The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J Mol Evol. 38(2):138–155.
   PubMed Web of Science ®Google Scholar
• Çiftci Y, Eroğlu O, Firidin Ş, Savaş H, Bektaş Y. 2021. Genetic diversity and population structure of Tarek (Alburnus tarichi), an endemic species to the Lake Van basin, Turkey. Aquat Living Resour. 34:3.
   Web of Science ®Google Scholar
• Çukur D, Krastel S, Demirel-Schlüter F, Demirbağ E, Imren C, Niessen F, Toker M, PaleoVan-Working Group. 2013. Sedimentary evolution of Lake Van (Eastern Turkey) reconstructed from high-resolution seismic investigations. Int J Earth Sci (Geol Rundsch). 102(2):571–585.
   Web of Science ®Google Scholar
• Cunningham CW. 1997. Can three incongruence tests predict when data should be combined? Mol Biol Evol. 14(7):733–740.
   PubMed Web of Science ®Google Scholar
• Daştan SD, Bardakçı F, Değerli N. 2012. Genetic diversity of Cyprinion macrostomus Heckel, 1843 (Teleostei: Cyprinidae) in Anatolia. Turk J Fish Aquat Sci. 12:651–659.
   Web of Science ®Google Scholar
• Delrieu-Trottin E, Maynard J, Planes S. 2014. Endemic and widespread coral reef fishes have similar mitochondrial genetic diversity. Proc R Soc B. 281(1797):20141068.
   PubMed Web of Science ®Google Scholar
• Dowling TE, Tibbets CA, Minckley WL, Smith GR. 2002. Evolutionary relationships of the plagopterins (Teleostei: Cyprinidae) from cytochrome b sequences. Copeia. 2002(3):665–678.2.0.CO;2]
   Google Scholar
• Drummond AJ, Ho SY, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4(5):e88.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Rambaut A, Shapiro BETH, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 22(5):1185–1192.
   PubMed Web of Science ®Google Scholar
• Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Mol Ecol. 11(12):2571–2581.
   PubMed Web of Science ®Google Scholar
• Durand JD, Bianco PG, Laroche J, Gilles A. 2003. Insight into the origin of endemic Mediterranean ichthyofauna: phylogeography of Chondrostoma genus (Teleostei, Cyprinidae). J Hered. 94(4):315–328.
   PubMed Web of Science ®Google Scholar
• Durand JD, Tsigenopoulos CS, Ünlü E, Berrebi P. 2002. Phylogeny and biogeography of the family Cyprinidae in the Middle East inferred from cytochrome b DNA evolutionary significance of this region. Mol Phylogenet Evol. 22(1):91–100.
   PubMed Web of Science ®Google Scholar
• Durand JD, Unlü E, Doadrio I, Pipoyan S, Templeton AR. 2000. Origin, radiation, dispersion and allopatric hybridization in the chub Leuciscus cephalus. Proc Biol Sci. 267(1453):1687–1697.
   PubMed Web of Science ®Google Scholar
• Elp M, Çetinkaya O. 2000. A research on reproductive biology of pearl mullet (Chalcalburnus tarichi Pallas, 1811). Fourth East Anatolian Fisheries Symposium, Erzurum (Turkey), 28–30 June. Ataturk University Faculty of Agriculture, pp. 51–66.
   Google Scholar
• Elp M, Özuluğ M, Şen F, Freyhof J. 2013. Validation of Alburnus timarensis from the Lake Van basin, eastern Anatolia (Teleostei: Cyprinidae). Zool Middle East. 59(3):235–244.
   Web of Science ®Google Scholar
• Elp M, Şen F, Atıcı AA. 2014. The Distribution Area of Tarek (Alburnus tarichi (Guldenstaedtii, 1814)) in the Van Lake Basin. Yüzüncü Yıl Univ J Agric Sci. 24:228–232.
   Google Scholar
• Elp M, Şen F, Çetinkaya O. 2006. The problems encountered by fish populations living in Lake Van basin and their possible solutions. Ege Univ J Fish Aquat Sci. 23(1/3):407–412.
   Google Scholar
• Elp M. 2002. A Study on the Capoeta capoeta (Guldenstaedt, 1772) and Chalcalburnus tarichi (pallas, 1811) populations living in the Koçköprü dam lake [PhD Thesis]. Istanbul, Turkey: University of Istanbul.
   Google Scholar
• Excoffier L. 2004. Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Ecol. 13(4):853–864.
   PubMed Web of Science ®Google Scholar
• Excoffier L, Laval G, Schneider S. 2005. Arlequin ver. 3.0: An in tegrated software package for population genetics data analysis. Evol Bioinform Online. 1:117693430500100–117693430500150.
   Web of Science ®Google Scholar
• FAO 2021. Fishery and Aquaculture Statistics. Global capture production 1950–2019 (FishStatJ). FAO Fisheries Division, Rome; [accessed 2021 May] https://www.fao.org/fishery/statisticssoftware/fishstatj/en..
   Google Scholar
• Farris JS, Kallersjo M, Kluge AG, Bult C. 1995. Constructing a significance test for incongruence. Syst Biol. 44(4):570–572.
   Web of Science ®Google Scholar
• Ferreri M, Qu W, Han BO. 2011. Phylogenetic networks: a tool to display character conflict and demographic history. Afr J Biotechnol. 10(60):12799–12803.
   Google Scholar
• Forster P, Torroni A, Renfrew C, Röhl A. 2001. Phylogenetic star contraction applied to Asian and Papuan mtDNA evolution. Mol Biol Evol. 18(10):1864–1881.
   PubMed Web of Science ®Google Scholar
• Freeland JR, Kirk H, Peterson SD. 2011. Molecular Ecology. 2nd ed. UK: Wiley-Blackwell, p. 449.
   Google Scholar
• Freyhof J. 2014. Alburnus tarichi. IUCN Red List Threat Species. 2014:e.T4375A19222678.
   Google Scholar
• Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147(2):915–925.
   PubMed Web of Science ®Google Scholar
• Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics. 133(3):693–709.
   PubMed Web of Science ®Google Scholar
• Geldiay R, Balık S. 2002. Türkiye Tatlısu Balıkları (Freshwater Fishes in Turkey). Izmir: Ege University Faculty of Fisheries Publications. p. 532.
   Google Scholar
• Grant WAS, Bowen BW. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered. 89(5):415–426.
   Web of Science ®Google Scholar
• Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52(5):696–704.
   PubMed Web of Science ®Google Scholar
• Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 41:95–98.
   Google Scholar
• Harpending HC. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol. 591–600.
   PubMed Web of Science ®Google Scholar
• Kempe S, Kazmierczak J, Landmann G, Konuk T, Reimer A, Lipp A. 1991. Largest known microbialites discovered in Lake Van, Turkey. Nature. 349(6310):605–608.
   Web of Science ®Google Scholar
• Ketmaier V, Finamore F, Largiadèr C, Milone M, Bianco PG. 2009. Phylogeography of bleaks Alburnus spp. (Cyprinidae) in Italy, based on cytochrome b data. J Fish Biol. 75(5):997–1017.
   PubMed Web of Science ®Google Scholar
• Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16(2):111–120.
   PubMed Web of Science ®Google Scholar
• Kocabaş M. 1999. Studies on the structure, growth, reproduction and foods of the Chalcalbumus tarichi population in the Lake Nazik (Ahlat-Bitlis, Turkey) [MSc Thesis]. Van, Turkey: Yüzüncü Yıl University.
   Google Scholar
• Kocher TD, Thomas WK, Meyer A, Edwards SV, Pääbo S, Villablanca FX, Wilson AC. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci U S A. 86(16):6196–6200.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 35(6):1547–1549.
   PubMed Web of Science ®Google Scholar
• Kuru M. 1980. A new fish species from Lake Van (Cyprinidae) (Description). Hacettepe Univ Bull Nat Sci Eng. 9:97–102.
   Google Scholar
• Kuru M, Yerli S, Mangıt F, Ünlü E, Alp A. 2014. Fish biodiversity in inland waters of Turkey. J Acad Doc Fish Aquacult. 1: 93–120.
   Google Scholar
• Lande R, Barrowdough G. 1987. Effective population size, genetic variation, and their use in population management. In: Soule ME, editor. Viable populations for conservation. Cambridge: Cambridge University Press, p. 87–124.
   Google Scholar
• Leigh JW, Bryant D. 2015. PopART: Full-feature software for haplotype network construction. Methods Ecol Evol. 6(9):1110–1116.
   Web of Science ®Google Scholar
• Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25(11):1451–1452.
   PubMed Web of Science ®Google Scholar
• Lippe C, Dumont P, Bernatchez L. 2006. High genetic diversity and no inbreeding in the endangered copper redhorse, Moxostoma hubbsi (Catostomidae, Pisces): the positive sides of a long generation time. Mol Ecol. 15(7):1769–1780.
   PubMed Web of Science ®Google Scholar
• Luan S, Chiang TY, Gong X. 2006. High genetic diversity vs. low genetic differentiation in Nouelia insignis (Asteraceae), a narrowly distributed and endemic species in China, revealed by ISSR fingerprinting. Ann Bot. 98(3):583–589.
   PubMed Web of Science ®Google Scholar
• Lynch M, Crease TJ. 1990. The analysis of population survey data on DNA sequence variation. Mol Biol Evol. 7(4):377–394.
   PubMed Web of Science ®Google Scholar
• Mangit F, Yerli SV. 2018. Systematic evaluation of the genus Alburnus (Cyprinidae) with description of a new species. Hydrobiologia. 807(1):297–312.
   Web of Science ®Google Scholar
• Melis R, Vacca L, Cuccu D, Mereu M, Cau A, Follesa MC, Cannas R. 2018. Genetic population structure and phylogeny of the common octopus Octopus vulgaris Cuvier, 1797 in the western Mediterranean Sea through nuclear and mitochondrial markers. Hydrobiologia. 807(1):277–296.
   Web of Science ®Google Scholar
• Moritz C. 1994. Defining ‘Evolutionarily Significant Units’ for conservation. Trends Ecol Evol. 9(10):373–375.
   PubMed Web of Science ®Google Scholar
• Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press, p. 512.
   Google Scholar
• Okello JBA, Nyakaana S, Masembe C, Siegismund HR, Arctander P. 2005. Mitochondrial DNA variation of the common hippopotamus: evidence for a recent population expansion. Heredity. 95(3):206–215.
   PubMed Web of Science ®Google Scholar
• Oyar A, Cetinkaya O. 2000. Researches on the salinity tolerance of the cyprinid (Chalcalburnus tarichi, Pallas, 1811). Fourth East Anatolian Fisheries Symposium, Erzurum (Turkey), 28–30 June. Ataturk University, Faculty of Agriculture, p. 389–402.
   Google Scholar
• Parmaksız A, Eksi E. 2017. Genetic diversity of the cyprinid fish Capoeta trutta (Heckel, 1843) populations from Euphrates and Tigris rivers in Turkey based on mtDNA COI sequences. Indian J Fish. 64(1):18–22.
   Web of Science ®Google Scholar
• Posada D. 2008. jModelTest: phylogenetic model averaging. Mol Biol Evol. 25(7):1253–1256.
   PubMed Web of Science ®Google Scholar
• Rambaut A. 2018. FigTree v1. 4.2, a graphical viewer of phylogenetic trees. [accessed 2018 November 26]. http://tree.bio.ed.ac.uk/software/figtree.
   Google Scholar
• Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 67(5):901–904.
   PubMed Web of Science ®Google Scholar
• Ray N, Currat M, Excoffier L. 2003. Intra-deme molecular diversity in spatially expanding populations. Mol Biol Evol. 20(1):76–86.
   PubMed Web of Science ®Google Scholar
• Rogers AR, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol. 9(3):552–569.
   PubMed Web of Science ®Google Scholar
• Ronquist F, Klopfstein S, Vilhelmsen L, Schulmeister S, Murray DL, Rasnitsyn AP. 2012. A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst Biol. 61(6):973–999.
   PubMed Web of Science ®Google Scholar
• Sarı M. 1997. Selectivity of Nets Used in Pearl Mullet (Chalcalburnus tarichi, Pallas 1811) Fishing. Mediterranean Fisheries Congress, Izmir (Turkey), 9–11 April 1997. Izmir, p. 93–102.
   Google Scholar
• Sarı M. 2001. Van Gölü İnci Kefalı (Chalcalburnus tarichi, Pallas 1811) Stok Miktarının Tahmini ve Balıkçılık Yönetim Esaslarının Belirlenmesi. (The stock assessment of Chalcalburnus tarichi (Pallas 1811) in the Lake Van and the determination of the basis of fishery management). Istanbul: Çekul Scientific series, p. 150.
   Google Scholar
• Sarı M. 2008. Threatened fishes of the world: Chalcalburnus tarichi (Pallas 1811) (Cyprinidae) living in the highly alkaline Lake Van, Turkey. Environ Biol Fishes. 81:21–23.
   Web of Science ®Google Scholar
• Schneider S, Excoffier L. 1999. Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics. 152(3):1079–1089.
   PubMed Web of Science ®Google Scholar
• Schwarz G. 1978. Estimating the dimension of a model. Ann Stat. 6:461–464.
   Web of Science ®Google Scholar
• Şen F, Paruğ ŞŞ, Elp M. 2015. Projections on Past, Present and Future of Tarek (Alburnus tarichi, Güldenstädt,1814). Yuzuncu Yil Univ J Agric Sci. 25:347–356.
   Google Scholar
• Sharma IK, Jones DL, French CJ. 2003. Unusually high genetic variability revealed through allozymic polymorphism of an endemic and endangered Australian orchid, Pterostylis aff. picta (Orchidaceae). Biochem Syst Ecol. 31(5):513–526.
   Web of Science ®Google Scholar
• Simonsen KL, Churchill GA, Aquadro CF. 1995. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics. 141 (1):413–429.
   PubMed Web of Science ®Google Scholar
• Slatkin M. 1993. Isolation by distance in equilibrium and non‐equilibrium populations. Evolution. 47(1):264–279.
   PubMed Web of Science ®Google Scholar
• Slatkin M, Hudson RR. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 129(2):555–562.
   PubMed Web of Science ®Google Scholar
• Swofford DL. 1998. PAUP* Phylogenetic Analysis Using Parsimony (*and other methods). Version 4 beta 10. Sunderland (MA): Sinauer.
   Google Scholar
• Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123 (3):585–595.
   PubMed Web of Science ®Google Scholar
• Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22):4673–4680.
   PubMed Web of Science ®Google Scholar
• Ünal G, Türkoğlu V, Oğuz AR, Kaptaner B. 2007. Gonadal histology and some biochemical characteristics of Chalcalburnus tarichi (Pallas, 1811) having abnormal gonads. Fish Physiol Biochem. 33(2):153–165.
   Web of Science ®Google Scholar