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Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
Volume 30, 2019 - Issue 2
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Research Article

Evidence for intra-mitochondrial variation in population genetic structure of Platycephalus sp.1 In the Northwestern Pacific

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Pages 281-288 | Received 03 Apr 2018, Accepted 29 May 2018, Published online: 08 Sep 2018

References

  • Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders N. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst. 18:489–522.
  • Ballard JW, Kreitman M. 1995. Is mitochondrial DNA a strictly neutral marker? Trends Ecol. Evol. (Amst.) 10:485–488.
  • Ballard JWO, Pichaud N. 2014. Mitochondrial DNA: more than an evolutionary bystander. Funct Ecol. 28:218–231.
  • Ballard JWO, Whitlock MC. 2004. The incomplete natural history of mitochondria. Mol Ecol. 13:729–744.
  • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B. 57:289–300.
  • Bowen BW, Gaither MR, DiBattista JD, Iacchei M, Andrews KR, Grant WS, Toonen RJ, Briggs JC. 2016. Comparative phylogeography of the ocean planet. Proc Natl Acad Sci USA. 113:7962–7969.
  • Bryant D, Moulton V. 2004. Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol. 21:255–265.
  • Cowen RK, Sponaugle S. 2009. Larval dispersal and marine population connectivity. Ann Rev Mar Sci. 1:443–466.
  • Delport W, Poon AFY, Frost SDW, Kosakovsky Pond SL. 2010. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics. 26:2455–2457.
  • Dress AWM, Huson DH. 2004. Constructing Splits Graphs. IEEE/ACM Trans Comput Biol Bioinform. 1:109–115.
  • 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.
  • Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147:915–925.
  • Grant WS, Spies IB, Canino MF. 2006. Biogeographic evidence for selection on mitochondrial DNA in north Pacific walleye pollock Theragra chalcogramma. J Hered. 97:571–580.
  • Grant WS, Bowen BW. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered. 89:415–426.
  • Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23:254–267.
  • Imamura H. 1996. Phylogeny of the family Platycephalidae and related taxa (Pisces: Scorpaeniformes). Spec Divers. 1:123–233.
  • Jackson TM, Roegner GC, O’Malley KG. 2017. Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System. Mol Ecol. 27:352–368.
  • Jacobsen MW, da Fonseca RR, Bernatchez L, Hansen MM. 2016. Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.). Mol Phylogenet Evol. 95:161–170.
  • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772–780.
  • Kosakovsky Pond S, Muse SV. 2005. Site-to-site variation of synonymous substitution rates. Mol Biol Evol. 22:2375–2385.
  • Kosakovsky Pond SL, Frost SDW. 2005. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 22:1208–1222.
  • Kosakovsky Pond SL, Frost SDW, Grossman Z, Gravenor MB, Richman DD, Brown AJL. 2006. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol. 2:e62.
  • Kosakovsky Pond SL, Frost SDW, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 21:676–679.
  • Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD. 2006. GARD: a genetic algorithm for recombination detection. Bioinformatics. 22:3096–3098.
  • Lee YS, Markov N, Argunov A, Voloshina I, Bayarlkhagva D, Kim BJ, Min MS, Lee H, Kim KS. 2016. Genetic diversity and phylogeography of Siberian roe deer, Caproulus pygargus, in central and peripheral populations. Ecol Evol. 6:7286–7297.
  • Liu JY. 2013. Status of marine biodiversity of the China seas. PLoS One. 8:e50719.
  • Liu M, Lin LS, Gao TX, Yanagimoto T, Sakurai Y, Grant WS. 2012. What maintains the central north Pacific genetic discontinuity in Pacific herring? PLoS One. 7:e50340.
  • Lowe WH, Allendorf FW. 2010. What can genetics tell us about population connectivity? Mol Ecol. 19:3038–3051.
  • Murrell B, Moola S, Mabona A, Weighill T, Sheward D, Kosakovsky Pond SL, Scheffler K. 2013. FUBAR: a fast, unconstrained Bayesian approximation for inferring selection. Mol Biol Evol. 30:1196–1205.
  • Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. 2012. Detecting individual sites subject to episodic diversifying selection. PLoS Genet. 8:e1002764.
  • Nakabo T. 2002. Fishes of Japan with pictorial keys to the species, Kanagawa: Tokai University Press.
  • Ni G, Li Q, Kong LF, Yu H. 2014. Comparative phylogeography in marginal seas of the northwestern Pacific. Mol Ecol. 23:534–548.
  • Okonechnikov K, Golosova O, Fursov M. 2012. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 28:1166–1167.
  • Palumbi SR. 2003. Population genetics, demographic connectivity, and the design of marine reserves. Ecol Appl. 13:146–158.
  • Peakall R, Smouse PE. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics. 28:2537–2539.
  • Qin Y, Song N, Zou JW, Zhang ZH, Cheng GP, Gao TX, Zhang XM. 2013. A new record of a flathead fish (Teleostei: Platycephalidae) from China based on morphological characters and DNA barcoding. Chin. J Oceanol Limnol. 31:617–624.
  • Qin Y. 2014. Study of taxology, morphology and genetics of brownspot flathead [Master Thesis]. Qingdao: Ocean University of China.
  • Rollins LA, Woolnough AP, Fanson BG, Cummins ML, Crowley TM, Wilton AN, Sinclair R, Butler A, Sherwin WB. 2016. Selection on mitochondrial variants occurs between and within individuals in an expanding invasion. Mol Biol Evol. 33:995–1007.
  • Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC. 2004. Effects of purifying and adaptive selection on regional variation in human mtDNA. Science. 303:223–226.
  • Sexton JP, Hangartner SB, Hoffmann AA. 2014. Genetic isolation by environment or distance: which pattern of gene flow is most common? Evolution. 68:1–15.
  • Silva G, Lima FP, Martel P, Castilho R. 2014. Thermal adaptation and clinal mitochondrial DNA variation of European anchovy. Roy Soc Lond B: Biol Sci. 281:20141093.
  • Slatkin M, Hudson RR. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 129:555–562.
  • Song N, Zhang XM, Sun XF, Yanagimoto T, Gao TX. 2010. Population genetic structure and larval dispersal potential of spottedtail goby Synechogobius ommaturus in the north-west Pacific. J Fish Biol. 77:388–402.
  • Sun YB, Shen YY, Irwin DM, Zhang YP. 2011. Evaluating the roles of energetic functional constraints on teleost mitochondrial-encoded protein evolution. Mol Biol Evol. 28:39–44.
  • Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:585–595.
  • Tomasco IH, Lessa EP. 2011. The evolution of mitochondrial genomes in subterranean caviomorph rodents: adaptation against a background of purifying selection. Mol Phylogenet Evol. 61:64–70.
  • Wang IJ, Bradburd GS. 2014. Isolation by environment. Mol Ecol. 23:5649–5662.
  • Waples RS, Gaggiotti O. 2006. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol Ecol. 15:1419–1439.
  • Wright S. 1943. Isolation by distance. Genetics. 28:114–138.
  • Xu SY, Sun DR, Song N, Gao TX, Han ZQ, Shui BN. 2017. Local adaptation shapes pattern of mitochondrial population structure in Sebastiscus marmoratus. Environ Biol Fish. 100:763–774.
  • Yang ZH. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586–1591.
  • Zvychainaya EY, Danilkin AA, Kholodova MV, Sipko TP, Berber AP. 2011. Analysis of the variability of the control region and cytochrome b gene of mtDNA of Capreolus pygargus Pall. Biol Bull. 38:434–439.

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