Publication Cover
Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
Volume 29, 2018 - Issue 7
329
Views
7
CrossRef citations to date
0
Altmetric
Research Article

Phylogeography and genetic population structure of the spadenose shark (Scoliodon macrorhynchos) from the Chinese coast

, , , &
Pages 1100-1107 | Received 07 May 2017, Accepted 01 Dec 2017, Published online: 11 Dec 2017

References

  • Avise JC. 2000. Phylogeography: the history and formation of species. Cambridge (MA): Harvard University Press.
  • Boomer JJ, Harcourt RG, Francis MP, Stow AJ. 2012. Genetic divergence, speciation and biogeography of Mustelus (sharks) in the central Indo-Pacific and Australasia. Mol Phylogenet Evol. 64:697–703.
  • Chen CA, Ablan MCA, McManus JW, Bell JD, Tuan VS, Cabanban AS, Shao KT. 2004. Population structure and genetic variability of six bar wrasse (Thallasoma hardwicki) in northern South China Sea revealed by mitochondrial control region sequences. Mar Biotechnol. 6:312–326.
  • Chen X, Peng X, Zhang P, Yang S, Liu M. 2014. Complete mitochondrial genome of the spadenose shark (Scoliodon macrorhynchos). Mitochondrial DNA. 25:91–92.
  • Clarke CR, Karl SA, Horn RL, Bernard AM, Lea JS, Hazin FH, Paulo AP, Shivji MS. 2015. Global mitochondrial DNA phylogeography and population structure of the silky shark, Carcharhinus falciformis. Mar Biol. 162:945–955.
  • Drummond AJ, Suchard MA, Xie D, Rambau A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. http://beast.bio.ed.ac.uk.
  • Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Mol Ecol. 11:2571–2581.
  • Earl DA. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour. 4:359–361.
  • Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 14:2611–2620.
  • Excoffier L, Lischer HEL. 2010. Arlequin suite version 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 10:564–567.
  • Féral JP. 2002. How useful are the genetic markers in attempts to understand and manage marine biodiversity? J Exp Mar Biol Ecol. 268:121–145.
  • Fu Y. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147:915–925.
  • 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. 89:415–426.
  • Han Z, Xu H, Shui B, Zhou Y, Gao T. 2015. Lack of genetic structure in endangered large yellow croaker Larimichthys crocea from China inferred from mitochondrial control region sequence data. Biochem Syst Ecol. 61:1–7.
  • Harpending HC. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol. 66:591–600.
  • Keeney DB, Heist EJ. 2006. Worldwide phylogeography of the blacktip shark (Carcharhinus limbatus) inferred from mitochondrial DNA reveals isolation of western Atlantic populations coupled with recent Pacific dispersal. Mol Ecol. 15:3669–3679.
  • Li Y, Chen G, Yu J, Wu S, Xiong D, Li X, Cui K, Li Y. 2016. Population genetics of Thamnaconus hypargyreus (Tetraodontiformes: Monacanthidae) in the South China Sea. Mitochondrial DNA A DNA Mapp Seq Anal. 27:798–805.
  • Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.
  • Liu JX, Gao TX, Wu SF, Zhang YP. 2007. Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck & Schlegel, 1845). Mol Ecol. 16:275–288.
  • Liu SYV, Huang IH, Liu MY, Lin HD, Wang FY, Liao TY. 2015. Genetic Stock Structure of Terapon jarbua in Taiwanese waters. Mar Coast Fish. 7:464–473.
  • Martin AP, Naylor GJP, Palumbi SR. 1992. Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature. 357:153.
  • McManus JW. 1985. Marine speciation, tectonics and sea-level changes in southeast Asia. Proceedings of the Fifth International Coral Reef Congress; Tahiti. Vol. 4. p. 133–138.
  • Mendonça FF, Oliveira C, Gadig OB, Foresti F. 2011. Phylogeography and genetic population structure of Caribbean sharpnose shark Rhizoprionodon porosus. Rev Fish Biol Fish. 21:799–814.
  • Mendonça FF, Oliveira C, Gadig OBF, Foresti F. 2009. Populations analysis of the Brazilian Sharpnose Shark Rhizoprionodon lalandii (Chondrichthyes: Carcharhinidae) on the São Paulo coast, Southern Brazil: inferences from mt DNA sequences. Neotrop Ichthyol. 7:213–216.
  • Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
  • Periasamy R, Chen X, Ingole B, Liu W. 2016. Complete mitochondrial genome of the Spadenose shark Scoliodon laticaudus (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA A. 27:3248–3249.
  • Pons O, Petit RJ. 1996. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics. 144:1237–1245.
  • Posada D. 2008. jModelTest: phylogenetic model averaging. Mol Biol Evol. 25:1253–1256.
  • Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945–959.
  • Qiu F, Li H, Lin H, Ding S, Miyamoto MM. 2016. Phylogeography of the inshore fish, Bostrychus sinensis, along the Pacific coastline of China. Mol Phylogenet Evol. 96:112–117.
  • Rambaut A, Suchard MA, Xie D, Drummond AJ. 2014. Tracer v1. 6. Computer program and documentation distributed by the author, website; [accessed 2014 July 27]. http://beast.bio.ed.ac.uk/Tracer.
  • Ramírez-Macías D, Vázquez-Juárez R, Galván-Magaña F, Munguía-Vega A. 2007. Variations of the mitochondrial control region sequence in whale sharks (Rhincodon typus) from the Gulf of California, Mexico. Fish Res. 84:87–95.
  • Ronquist F, Huelsenbeck JP. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–1574.
  • 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.
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876–4882.
  • Voris HK. 2000. Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. J Biogeogr. 27:1153–1167.
  • Wang C, Li C, Li S. 2008. Mitochondrial DNA-inferred population structure and demographic history of the mitten crab (Eriocheir sensu stricto) found along the coast of mainland China. Mol Ecol. 17:3515–3527.
  • Wang J, Tsang LM, Dong YW. 2015. Causations of phylogeographic barrier of some rocky shore species along the Chinese coastline. BMC Evol Biol. 15:114.
  • White WT, Last PR, Naylor GJ. 2010. Scoliodon macrorhynchos (Bleeker, 1852), a second species of spadenose shark from the Western Pacific (Carcharhiniformes: Carcharhinidae). Descriptions of New Sharks and Rays from Borneo, 61–76. In: Last PR, White WT, Pogonoski JJ, editors. Descriptions of new sharks and rays from Borneo. CSIRO Marine and Atmospheric Research Paper 032; p. 165.
  • Yin W, Fu CZ, Guo L, He QX, Li J, Jin BS, Wu QH, Li B. 2009. Species delimitation and historical biogeography of the genus Helice (Brachyura: Varunidae) in the northwestern Pacific. Zool Sci. 26:467–475.
  • Zhang JB, Cai ZP, Huang LM. 2006. Population genetic structure of crimson snapper Lutjanus erythropterus in East Asia, revealed by analysis of the mitochondrial control region. ICES J Mar Sci. 63:693–704.
  • Zhao L, Zhang J, Liu Z, Funk SM, Wei F, Xu M, Li M. 2008. Complex population genetic and demographic history of the Salangid, Neosalanx taihuensis, based on cytochrome b sequences. BMC Evol Biol. 8:201–219.

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.