Diversity of marine planktonic ostracods in South China Sea: a DNA taxonomy approach

References

• Angel MV, Blachowiak-Samolyk K, Drapun I, Castillo R. 2007. Changes in the composition of planktonic ostracod populations across a range of latitudes in the North-east Atlantic. Prog Oceanogr. 73:60–78.
   Web of Science ®Google Scholar
• Angel MV. 1983. A review on the progress of research on halocyprid and other oceanic planktonic ostracods1972–1982. In: Maddocks RF, editor. Applications of Ostracoda. Houston (TX): Geoscience Department, University of Houston; p. 529–548.
   Google Scholar
• Angel MV. 1993. Marine planktonic ostracods: keys and notes for identification of the species. Synopses of the British Fauna (New Series). London: The Linnean Society of London and the Estuarine and Coastal Sciences Association; 240 pp.
   Google Scholar
• Barrett RDH, Hebert PDN. 2005. Identifying spiders through DNA barcodes. Can J Zool. 83:481–491.
   Web of Science ®Google Scholar
• Blanco-Bercial L, Cornils A, Copley NJ, Bucklin A. 2014. DNA Barcoding of marine copepods: assessment of analytical approaches to species identification. PLoS Curr Tree Life. 6. doi:10.1371/currents.tol.cdf8b74881f87e3b01d56b43791626d2.
   PubMedGoogle Scholar
• Bode SN, Adolfsson S, Lamatsch DK, Martins MJ, Schmit O, Vandekerkhove J, Mezquita F, Namiotko T, Rossetti G, Schön I, et al. 2010. Exceptional cryptic diversity and multiple origins of parthenogenesis in a freshwater ostracod. Mol Phylogenet Evol. 54:542–552.
   PubMed Web of Science ®Google Scholar
• Brandão SN, Sauer J, Schön I. 2010. Circumantarctic distribution in southern ocean benthos? A genetic test using the genus Macroscapha (Crustacea, Ostracoda) as a model. Mol Phylogenet Evol. 55:1055–1069.
   PubMed Web of Science ®Google Scholar
• Bucklin A, Ortman BD, Jennings RM, Nigro LM, Sweetman CJ, Copley NJ. 2010. A “Rosetta Stone” for zooplankton: DNA barcode analysis of holozooplankton diversity of the Sargasso Sea (Northwest Atlantic Ocean). Deep-Sea Res II. 57:34–47.
   Web of Science ®Google Scholar
• Bucklin A, Wiebe PH, Smolenack SB, Copley NJ, Beaudet JG, Bonner KG, Farber-Lorda J, Pierson JJ. 2007. DNA barcodes for species identification of euphausiids (Euphausiacea, Crustacea). J Plankton Res. 29:483–493.
   Web of Science ®Google Scholar
• Chen RX, Lin JH. 1987. Spinoecia crassispina (nov. sp.), a new species of planktonic Ostracoda. Acta Oceonal Sin. 6:153–158.
   Google Scholar
• Chen RX, Lin JH. 1995. Planktonic Ostracoda in China Seas. Beijing: China Ocean Press (in Chinese).
   Google Scholar
• Chen RX, Lin JH. 1994. Paraconchoecia diacanthus (nov. sp.), a new species of planktonic Ostracoda. Acta Oceonal Sin. 13:269–274.
   Google Scholar
• Chen RX, Lin JH. 1997. Diversity of species and ecological groups of planktonic Ostracoda. Chin Biodivers. 5:257–262 (in Chinese with English Abstract).
   Google Scholar
• Chen RX, Lin JH. 1998. Large-scale ecological study on planktonic Ostracoda in China seas and adjacent waters. Correlation between planktonic Ostracoda and water systems. Acta Oceonal Sin. 20:96–101 (in Chinese with English Abstract).
   Google Scholar
• Cheng FP, Wang MX, Sun S, Li C, Zhang Y. 2013. DNA barcoding of Antarctic marine zooplankton for species identification and recognition. Adv Polar Sci. 24:19–27.
   Google Scholar
• Costa FO, DeWaard JR, Boutillier J, Ratnasingham S, Dooh RT, Hajibabaei M, Hebert PDN. 2007. Biological identifications through DNA barcodes: the case of the Crustacea. Can J Fish Aquat Sci. 64:272–295.
   Web of Science ®Google Scholar
• Drummond AJ, Suchard MA, Xie D, Rambautm A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 29:1969–1973.
   PubMed Web of Science ®Google Scholar
• Elías-Gutiérrez M, Jerónimo FM, Ivanova NV, Valdez-Moreno M, Hebert PDN. 2008. DNA barcodes for Cladocera and Copepoda from Mexico and Guatemala, highlights and new discoveries. Zootaxa. 1839:1–42.
   Google Scholar
• Ezard THG, Fujisawa T, Barraclough TG. 2009. Splits: SPecies’ LImits by threshold statistics. http://R-Forge.R- project.org/projects/splits/
   Google Scholar
• Fang G, Fang W, Fang Y, Wang K. 1998. A survey of studies on the south china sea upper ocean circulation. Acta Oceanogr Taiwan. 37:1–16.
   Google Scholar
• Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol. 3:294–299.
   PubMedGoogle Scholar
• Fujisawa T, Barraclough TG. 2013. Delimiting species using single-locus data and the generalized mixed Yule coalescent (GMYC) approach: a revised method and evaluation on simulated datasets. Syst Biol. 62:707–724.
   PubMed Web of Science ®Google Scholar
• Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood Phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307–321.
   PubMed Web of Science ®Google Scholar
• Hajibabaei M, DeWaard JR, Ivanova NV, Ratnasingham S, Dooh R, Kirk SL, Mackie PM, Hebert PDN. 2005. Critical factors for assembling a high volume of DNA barcodes. Philos Trans R Soc Lond B Biol Sci. 360:1959–1967.
   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. Nucl Acids Symp Ser. 41:95–98.
   Google Scholar
• Hebert PDN, Cywinska A, Ball SL, DeWaard JR. 2003. Biological identifications through DNA barcodes. Proc Biol Sci. 270:313–321.
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. 2004. Identification of birds through DNA barcodes. PLoS Biol. 2:e312.
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17:754–755.
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294:2310–2314.
   PubMed Web of Science ®Google Scholar
• Janzen DH, Hajibabaei M, Burns JM, Hallwachs W, Remigio E, Hebert PDN. 2005. Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Philos Tran R Soc Lond B Biol Sci. 360:1835–1845.
   PubMed Web of Science ®Google Scholar
• Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McLnerney JO. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 6:29.
   PubMed Web of Science ®Google Scholar
• Koenders A, Martens K, Halse S, Schön I. 2012. Cryptic species of the Eucypris virens, species complex (Ostracoda, Crustacea) from Europe have invaded western Australia. Biol Invasions. 14:2187–2201.
   Web of Science ®Google Scholar
• Kornicker LS. 1961. Ecology and taxonomy of recent Bairdiinae (Ostracoda). Micropaleontology. 7:55–70.
   Google Scholar
• Kornicker LS. 1979. Ostracoda. In: Fairbridge RW, Jablonski D, editors. The encyclopedia of paleontology. Stroudsburg: Dowden, Hutchinson and Ross, Inc.; p. 99–104.
   Google Scholar
• Kumar S, Dudley J, Nei M, Tamura K. 2008. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinformatics. 9:299–306.
   PubMed Web of Science ®Google Scholar
• Lanave C, Preparata G, Saccone C, Serio G. 1984. A new method for calculating evolutionary substitution rates. J Mol Evol. 20:86–93.
   PubMed Web of Science ®Google Scholar
• Martens K, Schön I, Meisch C, Horne DJ. 2008. Global diversity of ostracods (Ostracoda, Crustacea) in freshwater. Hydrobiologia. 595:185–193.
   Web of Science ®Google Scholar
• Matzen da Silva J, Creer S, dos Santos A, Costa AC, Cunha MR, Costa FO, Carvalho GR. 2011. Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca). PLoS One. 6:e19449.
   PubMed Web of Science ®Google Scholar
• Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B. 2011. How many species are there on earth and in the ocean? PLoS Biol. 9:e1001127.
   PubMed Web of Science ®Google Scholar
• Morton B, Blackmore G. 2001. South China Sea. Mar Pollut Bull. 42:1236–1263.
   PubMed Web of Science ®Google Scholar
• Myers N, Mittermeier RA, Mittermeier CG, Fonseca GAB, Kent J. 2000. Biodiversity hotspots for conservation priorities. Nature. 403:853–858.
   PubMed Web of Science ®Google Scholar
• Nigro LM, Angel MV, Blachowiak-Samolyk K, Hopcroft RR, Bucklin A. 2016. Identification, discrimination, and discovery of species of marine planktonic ostracods using DNA barcodes. PLoS One. 11:e0146327.
   PubMed Web of Science ®Google Scholar
• Nylander JAA. 2004. MrModeltest v2. Program distributed by the author. Sweden: Evolutionary Biology Centre, Uppsala University.
   Google Scholar
• Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK. 2012. Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement, and pancrustacean phylogeny. Mol Biol Evol. 30:215–233.
   PubMed Web of Science ®Google Scholar
• Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, Vogler AP. 2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol. 55:595–609.
   PubMed Web of Science ®Google Scholar
• Puillandre N, Lambert A, Brouillet S, Achaz G. 2012. ABGD, automatic barcode gap discovery for primary species delimitation. Mol Ecol. 21:1864–1877.
   PubMed Web of Science ®Google Scholar
• Radulovici AE, Archambault P, Dufresne F. 2010. DNA barcodes for marine biodiversity: moving fast forward? Diversity. 2:450–472.
   Google Scholar
• Ratnasingham S, Hebert PDN. 2007. BOLD: the Barcode of life data system (http://www.barcodinglife.org). Mol Ecol Notes. 7:355–364.
   PubMed Web of Science ®Google Scholar
• Raupach MJ, Radulovici AE. 2015. Looking back on a decade of barcoding crustaceans. ZooKeys. 539:53–81.
   Web of Science ®Google Scholar
• Ruppert EE, Fox RS, Barnes RD. 2004. Crustacea. In: Rose N, editor. Invertebrate zoology a functional evolutionary approach. 7th ed. Belmont (CA): Brooks/Cole, Cengage Learning; p. 687–690.
   Google Scholar
• Schön I, Pinto RL, Halse S, Smith AJ, Martens K, Birky CW Jr. 2012. Cryptic species in putative ancient asexual darwinulids (Crustacea, Ostracoda). PLoS One. 7:e39844.
   PubMed Web of Science ®Google Scholar
• Sites JW, Marshall JC. 2003. Delimiting species: a Renaissance issue in systematic biology. Trends Ecol Evol. 18:462–470.
   Web of Science ®Google Scholar
• Smith MA, Fisher BL, Hebert PDN. 2005. DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Philos Tran R Soc Lond B Biol Sci. 360:1825–1834.
   PubMed Web of Science ®Google Scholar
• Spalding MD, Fox HE, Allen GR, Davidson N, Ferdana ZA, Finlayson M, Halpern BS, Jorge MA, Lombana AL, Lourie SA, et al. 2007. Marine ecoregions of the world: a bioregionalization of coastal and shelf areas. Bioscience. 57:573–583.
   Web of Science ®Google Scholar
• Tanaka H, Ohtsuka S. 2015. Historical biogeography of the genus Polycopissa (Ostracoda: Myodocopa: Cladocopina), with the description and DNA barcode of the second Indo-Pacific species from the Seto Inland Sea. Mar Biodivers. 46:625–640.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Yang H, Liu Q, Liu Z, Wang D, Liu X. 2002. A general circulation model study of the dynamics of the upper ocean circulation of the South China Sea. J Geophys Res-Oceans. 107:22-1–22-14.
   Web of Science ®Google Scholar
• Yin JQ, Chen QC. 1991. Planktonic Ostracoda in Nansha archipelago (1984–1988). Zooplankton in Nansha archipelago and adjacent waters research study. 2nd ed. Beijing: Ocean Press; p. 64–134 (in Chinese).
   Google Scholar