Publication Cover
Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
Volume 29, 2018 - Issue 1
267
Views
2
CrossRef citations to date
0
Altmetric
Research Article

Genetic variations and population structure in three populations of beardless barb, Cyclocheilichthys apogon (Valenciennes, 1842) inferred from mitochondrial cytochrome b sequences

, & ORCID Icon
Pages 82-90 | Received 01 Aug 2016, Accepted 26 Sep 2016, Published online: 14 Nov 2016

References

  • Arnason E. 2004. Mitochondrial cytochrome b DNA variation in the high-fecundity atlantic cod: trans-atlantic clines and shallow gene genealogy. Genetics. 166:1871–1885.
  • Avise JC. 2000. Phylogeography: the history and formation of species. Cambridge, Mass: Harvard University Press.
  • Avise JC. 2004. Molecular markers, natural history, and evolution. 2nd ed. Sunderland, Mass: Sinauer Associates.
  • Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16:37–48.
  • Begg GA, Friedland KD, Pearce JB. 1999. Stock identification and its role in stock assessment and fisheries management: an overview. Fish Res. 43:1–8.
  • Chakraborty A, Sakai M, Iwatsuki Y. 2006. Museum fish specimens and molecular taxonomy: a comparative study on DNA extraction protocols and preservation techniques. J Appl Ichthyol. 22:160–166.
  • Chauhan T, Lal KK, Mohindra V, Singh RK, Punia P, Gopalakrishnan A, Sharma PC, Lakra WS. 2007. Evaluating genetic differentiation in wild populations of the Indian major carp, Cirrhinus mrigala (Hamilton–Buchanan, 1882): evidence from allozyme and microsatellite markers. Aquaculture. 269:135–149.
  • Crandall KA, Posada D, Vasco D. 1999. Effective population sizes: missing measures and missing concepts. Anim Conserv. 2:317–319.
  • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792–1797.
  • Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 10:564–567.
  • Excoffier L, Smouse PE, Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 131:479–491.
  • Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:783.
  • Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147:915–925.
  • Gehrke PC, Gilligan DM, Barwick M. 2002. Changes in fish communities of the Shoalhaven River 20 years after construction of Tallowa Dam, Australia. River Res Appl. 18:265–286.
  • Grandjean F, Souty-Grosset C. 2000. Mitochondrial DNA variation and population genetic structure of the white-clawed crayfish, Austropotamobius pallipes pallipes. Conserv Genet. 1:309–319.
  • Grant W. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered. 89:415–426.
  • Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. 41:95–98.
  • Hamid MA, Mansor M, Hashim ZH, Mohammad MS. 2012. A comparative study of fish population in Temengor Reservoir and Bersia Reservoir, Perak, Malaysia. J Res Biol. 2:184–192.
  • Harpending HC. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol. 66:591–600.
  • Holsinger KE, Weir BS. 2009. Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat Rev Genet. 10:639–650.
  • Johns GC, Avise JC. 1998. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Mol Biol Evol. 15:1481–1490.
  • Kottelat M. 2001. Fishes of Laos. Colombo, Sri Lanka: WHT Publications.
  • Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.
  • Luhariya RK, Lal KK, Singh RK, Mohindra V, Punia P, Chauhan UK, Gupta A, Lakra WS. 2012. Genetic divergence in wild population of Labeo rohita (Hamilton, 1822) from nine Indian rivers, analyzed through MtDNA cytochrome b region. Mol Biol Rep. 39:3659–3665.
  • Mandal A, Mohindra V, Singh RK, Punia P, Singh AK, Lal KK. 2012. Mitochondrial DNA variation in natural populations of endangered Indian Feather-Back Fish, Chitala chitala. Mol Biol Rep. 39:1765–1775.
  • McGlashan DJ, Hughes JM. 2000. Reconciling patterns of genetic variation with stream structure, earth history and biology in the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae). Mol Ecol. 9:1737–1752.
  • McGlashan DJ, Hughes JM. 2001. Low levels of genetic differentiation among populations of the freshwater fish Hypseleotris compressa (Gobiidae: Eleotridinae): implications for its biology, population connectivity and history. Heredity. 86:222–233.
  • Meeuwig MH, Guy CS, Kalinowski ST, Fredenberg WA. 2010. Landscape influences on genetic differentiation among bull trout populations in a stream-lake network. Mol Ecol. 19:3620–3633.
  • Moritz C. 1994. Defining ‘Evolutionarily Significant Units’ for conservation. Trends Ecol Evol. 9:373–375.
  • Moritz C. 2004. Conservation units and translocations: strategies for conserving evolutionary processes. Hereditas. 130:217–228.
  • Penny D. 2001. A 40,000 year palynological record from north-east Thailand; implications for biogeography and palaeo-environmental reconstruction. Palaeogeogr Palaeoclimatol Palaeoecol. 171:97–128.
  • Perdices A, Cunha C, Coelho MM. 2004. Phylogenetic structure of Zacco platypus (Teleostei, Cyprinidae) populations on the upper and middle Chang Jiang (=Yangtze) drainage inferred from cytochrome b sequences. Mol Phylogenet Evol. 31:192–203.
  • Pereyra S, García G, Miller P, Oviedo S, Domingo A. 2010. Low genetic diversity and population structure of the narrownose shark (Mustelus schmitti). Fish Res. 106:468–473.
  • Posada D, Crandall KA. 2001. Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol. 16:37–45.
  • Rainboth WJ. 1996. Fishes of the Cambodian Mekong. Rome: Food and Agriculture Organization of the United Nations.
  • Ramos-Onsins SE, Rozas J. 2002. Statistical properties of new neutrality tests against population growth. Mol Biol Evol. 19:2092–2100.
  • Rogers AR. 1995. Genetic evidence for a pleistocene population explosion. Evolution. 49:608.
  • Rogers AR, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol. 9:552–569.
  • Ryman N. 1991. Conservation genetics considerations in fishery management. J Fish Biol. 39:211–224.
  • Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406–425.
  • Saraswat D, Lakra WS, Nautiyal P, Goswami M, Shyamakant K, Malakar A. 2014. Genetic characterization of Clupisoma garua (Hamilton 1822) from six Indian populations using mtDNA cytochrome b gene. Mitochondrial DNA. 25:70–77.
  • 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. 152:1079–1089.
  • Slatkin M, Hudson RR. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 129:555–562.
  • Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:585–595.
  • 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.
  • Tan HH, Kottelat M. 2009. The fishes of the Batang Hari drainage, Sumatra, with description of six new species. Ichthyol Explor Freshw. 20:13–69.
  • Tang KL, Agnew MK, Hirt MV, Sado T, Schneider LM, Freyhof J, Sulaiman Z, Swartz E, Vidthayanon C, Miya M, et al. 2010. Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Mol Phylogenet Evol. 57:189–214.
  • Templeton AR. 2006. Population genetics and microevolutionary theory. Hoboken, N.J: Wiley-Liss.
  • Templeton AR, Crandall KA, Sing CF. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics. 132:619–633.
  • Tsukagoshi H, Takeda K, Kariya T, Ozaki T, Takatsu T, Abe S. 2015. Genetic variation and population structure of marbled sole Pleuronectes yokohamae and cresthead flounder P. schrenki in Japan inferred from mitochondrial DNA analysis. Biochem Syst Ecol. 58:274–280.
  • Vidthayanon C. 2012. Cyclocheilichthys apogon (Beardless barb). Cyclocheilichthys apogon [Internet]. [cited 2015 Jul 14]. Available from: http://www.iucnredlist.org.
  • Voris HK. 2000. Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. J Biogeogr. 27:1153–1167.
  • Ward RD. 2000. Genetics in fisheries management. Hydrobiologia. 420:191–201.
  • Ward RD, Woodwark M, Skibinski OF. 1994. A comparison of genetic diversity levels in marine, freshwater and anadromous fishes. J Fish Biol. 44:213–232.
  • Wasko AP, Martins C, Oliveira C, Foresti F. 2003. Non-destructive genetic sampling in fish. An improved method for DNA extraction from fish fins and scales. Hereditas. 138:161–165.
  • Waters JM, Lintermans M, White RWG. 1994. Mitochondrial DNA variation suggests river capture as a source of vicariance in Gadopsis bispinosus (Pisces: Gadopsidae). J Fish Biol. 44:549–551.
  • Wofford JEB, Gresswell RE, Banks MA. 2005. Influence of barriers to movement on within-watershed genetic variation of coastal cutthroat trout. Ecol Appl. 15:628–637.
  • Woodruff DS. 2003. Neogene marine transgressions, paleogeography and biogeographic transitions on the Thai-Malay Peninsula: Seaways and Southeast Asian. J Biogeogr. 30:551–567.

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.