Publication Cover
Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
Volume 29, 2018 - Issue 7
163
Views
3
CrossRef citations to date
0
Altmetric
Research Article

Analysis of sequence divergence in redfin (Cypriniformes, Cyprinidae, Tribolodon) based on mtDNA and nDNA markers with inferences in systematics and genetics of speciation

&
Pages 975-992 | Received 01 Feb 2017, Accepted 08 Nov 2017, Published online: 21 Nov 2017

References

  • Akaike H. 1973. Information theory and an extension of the maximum likelihood principle. Budapest (Hungary): Akademiai Kiado; p. 267–281.
  • Arnold ML, Fogarty ND. 2009. Reticulate evolution and marine organisms: the final frontier? Int J Mol Sci. 10:3836–3860.
  • Avise JC, Wollenberg K. 1997. Phylogenetics and the origin of species (allelic genealogies gene trees line ages mitochondrial DNA phylogeography). Proc Natl Acad Sci USA. 94:7748–7755.
  • Avise JC. 2000. Phylogeography—the history and formation of species. London, Cambridge (MA): Harvard University Press; p. 477.
  • Avise JC. 2001. Cytonuclear genetic signatures of hybridization phenomena: rationale, utility, and empirical examples from fishes and other aquatic animals. Rev Fish Biol Fish. 10:253–263.
  • Batishcheva NM, Kartavtsev YP, Bogutskaya NG. 2011. Phylogenetic analysis of Altai Osmans of the genus Oreoleuciscus (Pisces, Cyprinidae, Leuciscinae), based on the analysis of the cytochrome oxidase 1 gene (Co_1) sequence. Russ J Genet. 47:1335–1345.
  • Behrens-Chapuis S, Herder F, Esmaeili HR, Freyhof J, Hamidan NA, Özuluğ M, Šanda R, Geiger MF. 2015. Adding nuclear rhodopsin data where mitochondrial COI indicates discrepancies – can this marker help to explain conflicts in cyprinids? DNA Barcodes. 3:187–199.
  • Bogutskaya NG. 1990. Morphological principles of systematics of Cyprinid fishes from the subfamily of minnows (Leuciscinae, Cyprinidae). Vopr Ikhtiol. 30:920–933.
  • Borkin LJ, Litvinchuk SN. 2013. Animal hybridization, speciation and systematics. Proc Zool Inst Russ Acad Sci. 2:83–139.
  • Brykov VA, Polyakova NE, Semina AV. 2011. Phylogeographic analysis reveals two periods of divergence in large: scaled redfin tribolodon hakonensis (Pisces, Cyprinidae). Russ J Genet. 47:1491–1500.
  • Bushuev VP, Shitikova OY, Bogdanov LV. 1980. Biochemical differentiation of Pacific redfins of the genus Tribolodon Sauvage (Cyprinidae) from the Kievka river. J Ichthyol (Russia). 20:455–451.
  • Campton DE. 1987. Natural hybridization and introgression in fishes. Methods of detection and genetic interpretations. In: Ryman N, Utter F, editors. Population genetics and fishery management. Seattle (WA): Univ. of Washington Press; p. 161–192.
  • Chen WJ, Bonillo C, Lecointre G. 2003. Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa. Mol Phylogenet Evol. 26:262–288.
  • Chen WJ, Mayden RL. 2009. Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the world's largest clade of freshwater fishes: further evidence from six nuclear genes. Mol Phylogenet Evol. 52:544–549.
  • Chen WJ, Miya M, Saitoh K, Mayden RL. 2008. Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: the order Cypriniformes (Ostariophysi) as a case study. Gene. 432:125–134.
  • Clare EL, Lim BK, Engstrom MD, Eger JL, Hebert PDN. 2007. DNA barcoding of Neotropical bats: species identification and discovery within Guyana: barcoding. Mol Ecol Notes. 7:184–190.
  • Collins RA, Cruickshank RH. 2013. The seven deadly sins of DNA barcoding. Mol Ecol Resour. 13:969–975.
  • Dettai A, Lecointre G. 2005. Further support for the clades obtained by multiple molecular phylogenies in the acanthomorph bush. C R Biol. 328:674–689.
  • Doi A, Shinzawa H. 2000. Tribolodon nakamurai, a new cyprinid fish from the middle part of Honshu Island, Japan. Raffles Bull Zool. 48:241–247.
  • Gavrenkov YI, Ivankov VN. 1979. The taxonomic status and the biology of Pacific redfins from South Primorye. J Ichthyol. 19:1014–1023.
  • Gavrenkov YI, Sviridov VV. 2001. Breeding ecology of far eastern dace Tribolodon in rives of Primorsky region. V Y Levanidov’s Biennial Memorial Meet. 1:296–304.
  • Gavrenkov YI. 1982. Reproductive ecology of Pacific redfin, Tribolodon brandti (Dybowski), and large-scaled redfin, Tribolodon hakonensis (Gunther). J Ichthyol (Russia). 22:37–41.
  • Gavrenkov YI. 1989. Biology of Far Eastern dace of the genus Tribolodon as perspective object of aquaculture in the Southern part of Primorskii region. Moscow: Vseross. Nauchno-Issled. Inst. Rybn. Khoz. Okeanogr.; p. 25.
  • Gritsenko OF. 1972. On two varieties of Far-Eastern dace (Leuciscus) in the Sachalin rivers. J Zool (Russia). 51:388–392.
  • Gritsenko OF. 1974. Taxonomy of Pacific dace of the genus Tribolodon Sauvage 1883 (Leuciscus brandti (Dybowski)) (Cyprinidae). J Ichthyol (Russia). 14:782–795.
  • Gritsenko OF. 1990. Diadromous fishes of Sakhalin Island (systematics, ecology, and fishing). Moscow: Vseross. Nauchno-Issled. Inst. Rybn. Khoz. Okeanogr.; p. 42.
  • Hall E. 2000. Radiobiology for the radiologist. 5th ed. Philadelphia: Lippincott Williams and Wilkins; p. 608.
  • Hanzawa N, Taniguchi N, Numachi K-I. 1988. Geographical differentiation in populations of Japanese Dace Tribolodon hakonensis deduced from allozymic variation: ecology and taxonomy. Zool Sci. 5:449–461.
  • Hanzawa N, Taniguchi N, Shinzawa H. 1984. Genetic markers of the artificial hybrids between Tribolodon hakonensis and T. sp. (Ukekuchi-ugui). Otsuchi Mar Res Cent Rep Univ Tokyo. 10:11–17.
  • Hanzawa N, Yonekawa H, Numachi K-I. 1987. Variability of mitochondrial DNA in Japanese dace, Tribolodon hakonensis (Cyprinidae). Jpn J Genet. 62:27–38.
  • Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc Biol Sci R Soc. 270:313–321.
  • Hubbs C. 1961. Developmental temperature tolerances of four etheostomatine fishes occurring in Texas. Copeia. 1961:195–198.
  • Hudson RR, Boos DD, Kaplan NL. 1992. A statistical test for detecting geographic subdivision. Mol Biol Evol. 9:138–151.
  • Hudson RR. 2000. A new statistic for detecting genetic differentiation. Genetics. 155:2011–2014.
  • Hurvich C, Tsai C. 1989. Regression and time series model selection in small samples. Biometrika. 76:297–307.
  • Huson DH, Scornavacca C. 2012. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol. 61:1061–1067.
  • Imoto JM, Saitoh K, Sasaki T, Yonezawa T, Adachi J, Kartavtsev YPh, Miya M, Nishida M, Hanzawa N. 2013. Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis. Gene. 514:112–124.
  • Ivankov VN, Lukianov PE, Mostovaya NV, Rukhlova GF. 1984. Taxonomic value of morphological characters of two species of juvenile Pacific redfins. Russ J Mar Biol. 3:29–33.
  • Ivankov VN, Lukianov PE, Mostovaya NV. 1987. Hybridization of the two closely related species of Far Eastern dace the genus Tribolodon (Cyprinidae). J Hydrobiol (Russia). 23:35–39.
  • Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN. 2007. Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes. 7:544–548.
  • Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In: Munro HN, editor. Mammalian protein metabolism. New York: Academic Press; p. 21–123.
  • Kartavtsev YPh, Batischeva NM, Bogutskaya NG, Katugina AO, Hanzawa N. 2017. Molecular systematics and DNA barcoding of Altai osmans, oreoleuciscus (pisces, cyprinidae, and leuciscinae), and their nearest relatives, inferred from sequences of cytochrome b (Cyt-b), cytochrome oxidase c (Co-1). Mitochondrial DNA A. 28:502–517.
  • Kartavtsev YPh, Hanzawa N. 2007. Inferences in Leuciscinae (Pisces, Cyprinidae) phylogeny and taxonomy based on cytochrome b sequence distances and on enzyme loci diversity. Korean J Genet. 29:427–435.
  • Kartavtsev YPh, Sharina SN, Saitoh K, Imoto JM, Hanzawa N, Redin AD. 2014. Phylogenetic relationships of Russian far eastern flatfish (Pleuronectiformes, Pleuronectidae) based on two mitochondrial gene sequences, Co-1 and Cyt-b, with inferences in order phylogeny using complete mitogenome data. Mitochondrial DNA. 27:667–678.
  • Kartavtsev YPh, Sviridov VV, Sasaki T, Hanzawa N. 2002. Genetic divergence of far eastern dace belonging to the genus Tribolodon (Pisces, Cyprinidae) and closely related taxa: some insights in taxonomy and speciation. Russ J Genet. 38:1–14.
  • Kartavtsev YPh. 2011. Sequence divergence at mitochondrial genes in animals: applicability of DNA data in genetics of speciation and molecular phylogenetics. Mar Genom. 4:71–81.
  • Kartavtsev YPh. 2013. Some current concerns of Neo-Darwinism: gene introgression throughout a species border. J Phylogenet Evol Biol. 1:1–4.
  • Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16:111–120.
  • Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.
  • Lindberg GU, Legeza MI. 1965. Fishes of the Sea of Japan and adjacent parts of the Sea of Okhotsk and Yellow Sea. Part 2. Leningrad: Nauka; p. 391.
  • Marchetto F, Zaccara S, Muenzel F, Salzburger W. 2010. Phylogeography of the Italian vairone (Telestes muticellus, Bonaparte 1837) inferred by microsatellite markers: evolutionary history of a freshwater fish species with a restricted and fragmented distribution. BMC Evol Biol. 10:111.
  • Martin D, Rybicki E. 2000. RDP: detection of recombination amongst aligned sequences. Bioinformatics (Oxford, England). 16:562–563.
  • Mayr E. 1963. Animal species and evolution. Eugenics Rev. 55:226–228.
  • Nakabo T. 2002. Fishes of Japan with pictorial keys to the species. In: Nakabo, editor. Tokai University Press; p. 1749.
  • Nakamura M. 1963. Keys to the freshwater fishes of Japan fully illustrated in colors. Tokyo: Hokuryukan; p. 258.
  • Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. New York: Oxford University Press; p. 333.
  • Nei M, Miller JC. 1990. A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics. 125:873–879.
  • Nei M. 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA. 70:3321–3323.
  • Nei M. 1982. Evolution of human races at the gene level. Prog Clin Biol Res. 103:167–181.
  • Nei M. 1987. Molecular evolutionary genetics. Tempe (AZ): Arizona State University; p. 512.
  • Nelson JS. 2006. Fishes of the world. 4th ed. New York: John Wiley and Sons, Inc; p. 601.
  • Neznanova SY. 2012. Ultrastructural study of spermiogenesis in Far-eastern redfins of the genus Tribolodon (Pisces; Cyprinidae). Russ J Mar Biol. 38:144–152.
  • Okada Y. 1960. Studies on the freshwater fishes of Japan. Mie Prefecture, Japan: Prefectural University of Mie Tsu; p. 860.
  • Omelchenko VT, Polykova NE, Ivankov VN, Lukyanov PE. 1986. Genetico-biochemical and morphological characteristics of Pacific redfins Tribolodon brandti (Dybowski), Tribolodon hakonensis (Gunther) (Cyprinidae) and their hybrid progeny. J Ichthyol (Russia). 26:246–252.
  • Palandačić A, Zupančič P, Snoj A. 2010. Revised classification of former genus Phoxinellus using nuclear DNA sequences. Biochem Syst Ecol. 38:1069–1073.
  • Palumbi SR, Baker CS. 1994. Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales. Mol Biol Evol. 11:426–435.
  • Polyakova NE, Semina AV, Brykov VA. 2015. Analysis of mtDNA and nuclear markers points to homoploid hybrid origin of the new species of Far Eastern redfins of the genus Tribolodon (Pisces, Cyprinidae). Russ J Genet. 51:1075–1087.
  • Posada D. 2008. jModelTest: phylogenetic model averaging. Mol Biol Evol. 25:1253–1256.
  • Pravdin IF. 1966. In: Dryagin PA, editor. Guide to the study of fish (mostly from freshwater). 4th ed. Moscow: Food Industry; p. 374.
  • Puillandre N, Lambert A, Brouillet S, Achaz G. 2012. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol. 21:1864–1877.
  • Ratnasingham S, Hebert PDN. 2007. BOLD: the barcode of life data system (http://www.barcodinglife.org). Mol Ecol Notes. 7:355–364.
  • Ratnasingham S, Hebert PDN. 2013. A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS ONE. 8:1–16.
  • Ride WDL, Cogger HG, Dupuis C, Kraus O, Minelli A, Thompson FC, Tubbs PK. 2006. International code of Zoological Nomenclature. Fourth Edition. International Union of Biological Sciences; p. 223. (in Russian).
  • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–1574.
  • Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, Nishida M, Miya M. 2006. Mitogenomic evolution and interrelationships of the cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol. 63:826–841.
  • Saitoh T, Alström P, Nishiumi I, Shigeta Y, Williams D, Olsson U, Ueda K. 2010. Old divergences in a boreal bird supports long-term survival through the Ice Ages. BMC Evol Biol. 10:1–13.
  • Saitou N, Nei M. 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406–425.
  • Sakai H, Amano S. 2014. A new subspecies of Anadromous Far Eastern Dace, Tribolodon brandtii maruta subsp. nov. (Teleostei, Cyprinidae) from Japan. Bull Natl Mus Nat Sci A. 40:219–229.
  • Sakai H, Goto A, Jeon S-R. 2002. Speciation and dispersal of Tribolodon species (Pisces, Cyprinidae) around the Sea of Japan. Zool Sci. 19:1291–1303.
  • Sakai H, Hamada K. 1985. Electrophoretic discrimination of Tribolodon species (Cyprinidae) and the occurrence of their hybrids. Jap J Ichthyol. 32:216–224.
  • Sakai H, Ito Y, Shedko SV, Safronov SN, Frolov SV, Chereshnev IA, Jeon S-R, Goto A. 2006. Phylogenetic and taxonomic relationships of Northern Far Eastern Phoxinin Minnows, Phoxinus and Rhynchocypris (Pisces, Cyprinidae), as inferred from allozyme and mitochondrial 16S rRNA sequence analyses. Zool Soc Japan Zool Sci. 23:323–331.
  • Sambrook J. 1989. Molecular cloning. In: Sambrook J, Fritsch EF, Maniatis T, editors. A laboratory manual. New York: Cold Spring Harbor Lab. Press; p. 1626.
  • Sasaki T, Kartavtsev YPh, Chiba SN, Uematsu T, Sviridov VV, Hanzawa N. 2007. Genetic divergence and phylogenetic independence of Far Eastern species in subfamily Leuciscinae (Pisces: Cyprinidae) inferred from mitochondrial DNA analyses. Genes Genet Syst. 82:329–340.
  • Sauvage HE. 1883. Sur une collection de poissons recuellie dans le lac Biwako (Japon) par MF Steenackers. Bull De La Soc Philomáth Paris. 77:144–150.
  • Schindel DE, Miller SE. 2005. DNA barcoding a useful tool for taxonomists. Nature. 435:17.
  • Schulz-Mirbach T, Reichenbacher B, Yildirim MZ, Atalay MA. 2006. Otolith characteristics of species, subspecies, and populations of Aphanius Nardo, 1827 (Teleostei, Cyprinodontiformes) from Anatolia (Turkey). J Nat Hist. 40:1687–1705.
  • Semina A, Polyakova NE, Brykov VA. 2006. Genetic analysis reveals cryptic species of far easterm dace of the genus Tribolodon. Doklady Biol Sci. 407:571–573.
  • Semina AV, Polyakova NE, Brykov VA. 2007. Analysis of mitochondrial DNA: taxonomic and phylogenetic relationship in two fish taxa (Pisces: Mugilidae and Cyprinidae). Biochemistry (Moscow). 72:1651–1658.
  • Semina AV. 2008. Molecular evolution and phylogenetic relationship of two fish families Mugilidae and Cyprinidae. Vladivostok: A.V. Zhirmunsky Institute of Marine Biology FEB RAS; p. 178.
  • Shneyer VS. 2009. DNA barcoding of animal and plant species as an approach for their molecular identification and describing of diversity. J Gen Biol (Russia). 70:296–315.
  • Srivathsan A, Meier R. 2012. On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics. 28:190–194.
  • StaSoft Inc. 2005. StatSoft. Statistica Data analysis software system, version 7. http://www.statsoft.com/.
  • Steinke D, Hanner R. 2011. The FISH-BOL collaborators’ protocol. Mitochondrial DNA. 22:10–14.
  • Sviridov VV. 2002. Morphological and genetic divergence and geographic variation Far Eastern redfins of the genus Tribolodon. Vladivostok: Russian Federation Ministry of Education Far Eastern State University; p. 190.
  • Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics. 105:437–460.
  • Tajima F. 1993. Measurement of DNA polymorphism. In: Takahata N, Clark AG, editors. Mechanisms of molecular evolution. Sunderland (MA): Sinauer Associates Inc.; p. 37–59.
  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30:2725–2729.
  • Truett GE, Heeger P, Mynatt RL, Truett AA, Walker JA, Warman ML. 2000. Preparation of PCR-quality mouse genomic DNA with hot sodium hydroxide and tris (HotSHOT). BioTechniques. 29:52–54.
  • Turanov SV, Kartavtsev YPh. 2014. The taxonomic composition and distribution of sand lances from the genus Ammodytes (Perciformes: Ammodytidae) in the North Pacific. Russ J Mar Biol. 40:447–454.
  • Ward RD, Hanner R, Hebert PDN. 2009. The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol. 74:329–356.
  • Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B Biol Sci. 360:1847–1857.
  • Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 7:256–276.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.