Using DNA barcoding and phylogenetics to identify Antarctic invertebrate larvae: Lessons from a large scale study

Austerlitz, 2009, DNA barcode analysis: a comparison of phylogenetic and statistical classification methods, BMC Bioinform., 13, 1 Barber, 2006, Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae, Proc. R. Soc. Lond. B Biol., 273, 2053, 10.1098/rspb.2006.3540 Bergmann, 2009, Character-based DNA barcoding: a superior tool for species classification, Berl. Munch. Tierarztl., 122, 446 Bertolazzi, 2009, Learning to classify species with barcodes, BMC Bioinform., 12, 1 Blaxter, 2005, Defining operational taxonomic units using DNA barcode data, Philos. Trans. R. Soc. B, 360, 1935, 10.1098/rstb.2005.1725 Brandt, 2007, The biodiversity of the deep Southern Ocean benthos, Philos. Trans.-R. Soc. B, 362, 39, 10.1098/rstb.2006.1952 Bucklin, 2010, DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition, Deep-Sea Res. Part II, 57, 40, 10.1016/j.dsr2.2009.08.005 Buhay, 2009, “COI-Like” Sequences are becoming problematic in molecular systematic and DNA barcoding studies, J. Crustac. Biol., 29, 96, 10.1651/08-3020.1 Clarke, 2003, Antarctic marine benthic diversity, Oceanogr. Mar. Biol., 41, 47 Deagle, 2003, Development and evaluation of a PCR-based test for detection of Asterias (Echinodermata:Asteroidea) larvae in Australian plankton samples from ballast water, Mar. Freshwater Res., 54, 709, 10.1071/MF03031 Drummond, 2009, Geneious Ewing, 1998, Base-calling of automated sequencer traces using phred. II. Error probabilities, Genome Res., 8, 186, 10.1101/gr.8.3.186 Ewing, 1998, Base-calling of automated sequencer traces using phred. I. Accuracy assessment, Genome Res., 8, 175, 10.1101/gr.8.3.175 Folmer, 1994, DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates, Mol. Mar. Biol. Biotechnol., 3, 294 Goetze, 2010, Species discovery in marine planktonic invertebrates through global molecular screening, Mol. Ecol., 19, 952, 10.1111/j.1365-294X.2009.04520.x Govindarajan, 2005, Mitochondrial evolution and phylogeography in the hydrozoan Obelia geniculata (Cnidaria), Mar. Biol., 146, 213, 10.1007/s00227-004-1434-3 Grant, 2009, Barcoding Antarctic Biodiversity: current status and the CAML initiative, a case study of marine invertebrates, Polar Biol., 32, 1629, 10.1007/s00300-009-0662-x Hare, 2000, Single-step species identification of bivalve larvae using multiplex polymerase chain reaction, Mar. Biol., 137, 953, 10.1007/s002270000402 Hart, 2003, Patiriella pseudoexigua (Asteroidea: Asterinidae): a cryptic species complex revealed by molecular and embryological analyses, J. Mar. Biol. Assoc. U.K., 83, 1109, 10.1017/S002531540300835Xh Heimeier, 2010, Molecular species identification of Astrotoma agassizii from planktonic embryos: further evidence for a cryptic species complex, J. Heredity, 101, 775, 10.1093/jhered/esq074 Howard-Williams, 2006, Measuring ecosystem response in a rapidly changing environment: the Latitudinal Gradient Project, Antarct. Sci., 18, 465, 10.1017/S0954102006000514 Janosik, 2008, Life history of the Antarctic sea star Labidiaster annulatus (Asteroidea : Labidiasteridae ) revealed by DNA barcoding, Mar. Biol., 20, 563 Kirby, 2007, Climate effects and benthic-pelagic coupling in the North Sea, Mar. Ecol. Prog. Ser., 330, 31, 10.3354/meps330031 Kirby, 2008, Climate-induced effects on the meroplankton and the benthic-pelagic ecology of the North Sea, Limnol. Oceanogr., 53, 1805, 10.4319/lo.2008.53.5.1805 Kuksa, 2009, Efficient alignment-free DNA barcode analytics, BMC Bioinform., 18, 1 Larsen, 2005, Single-step nested multiplex PCR to differentiate between various bivalve larvae, Mar. Biol., 146, 1119, 10.1007/s00227-004-1524-2 Little, 2008, A comparison of algorithms for identification of specimens using DNA barcodes: examples from gymnosperms, Cladistics, 24, 91 MacBride, 1920, Echinoderma (Part II.) and Enteropneusta. Larvae of Echinoderma and Enteropneusta. Natural History Report of the British Antarctic Terra Nova Expedition 1910, Zoology, 3, 83 MacBride, 1908, 4, 1 Machida, 2009, Zooplankton diversity analysis through single-gene sequencing of a community sample, BMC Genomics, 7, 1 Mahon, 2009, DNA uncovers Antarctic nemertean biodiversity and exposes a decades-old cold case of asymmetric inventory, Polar Biol., 33, 193, 10.1007/s00300-009-0696-0 Mortensen, 1921 Munch, 2008, Fast phylogenetic DNA barcoding, Philos. Trans. R. Soc. B, 363, 3997, 10.1098/rstb.2008.0169 Murray, 1895, General Observations on the Distribution of Marine Organisms, 1431 Olson, 1991, Whose larvae?, Nature, 351, 357, 10.1038/351357b0 Palumbi, 1996, Nucleic Acids II: The Polymerase Chain Reaction, 205 Pearse, 1991, Reproduction of Antarctic benthic marine-invertebrates-tempos, modes, and timing, Am. Zool., 31, 65, 10.1093/icb/31.1.65 Peck, 1993, Larval development in the Antarctic nemertean Parborlasia corrugatus (Heteronemertea: Lineidae), Mar. Biol., 116, 301, 10.1007/BF00350020 Peck, 1994, Pelagic larval development in the brooding Antarctic brachiopod Liothyrella uva, Mar. Biol., 120, 279, 10.1007/BF00349689 Puillandre, 2009, An integrative approach to species delimitation in Benthomangelia (Mollusca: Conoidea), Biol. J. Linn. Soc., 96, 696, 10.1111/j.1095-8312.2008.01143.x Rach, 2008, Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata, Proc. R. Soc. Lond., B Biol., 275, 237, 10.1098/rspb.2007.1290 Ross, 2008, Testing the reliability of genetic methods of species identification via simulation, Syst. Biol., 57, 216, 10.1080/10635150802032990 Sambrook, 1998 Sarkar, 2008, CAOS software for use in character-based DNA barcoding, Mol. Ecol. Resour., 8, 1256, 10.1111/j.1755-0998.2008.02235.x Sewell, 2005, Examination of the meroplankton community in the south-western Ross Sea, Antarctica, using a collapsible plankton net, Polar Biol., 28, 119, 10.1007/s00300-004-0670-9 Sewell, 2006, The meroplankton community of the northern Ross Sea: a preliminary comparison with the McMurdo Sound region, Antarct. Sci., 18, 595, 10.1017/S0954102006000630 Sewell, 2009, Desalination plants as plankton sampling devices in temporal studies: proof-of-concept and suggestions for the future, Limnol. Oceanogr. Methods, 7, 363, 10.4319/lom.2009.7.363 Sewell, 2006, Whose larva is that? Molecular identification of planktonic larvae of the Ross Sea, 3, 1 Shanks, 2001 Siddall, 2009, Barcoding bamboozled by Bacteria: convergence to metazoan mitochondrial primer targets by marine microbes, Syst. Biol., 58, 445, 10.1093/sysbio/syp033 Staley, 2009, Universal species concept: pipe dream or a step toward unifying biology?, J. Ind. Microbiol. Biotech., 36, 1331, 10.1007/s10295-009-0642-8 Stanwell-Smith, 1999, The distribution, abundance and seasonality of pelagic marine invertebrate larvae in the maritime Antarctic, Philos. Trans. R. Soc. B, 354, 471, 10.1098/rstb.1999.0398 Steinke, 2005, TaxI — a software for DNA barcoding using distance methods, Philos. Trans. R. Soc. B, 360, 1975, 10.1098/rstb.2005.1729 Tamura, 2007, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0, Mol. Biol. E., 24, 1596, 10.1093/molbev/msm092 Thompson, 1828, On the metamorphoses of the Crustacea, and on the zoea, exposing their singular structure, and demonstrating that they are not, as has been supposed, a peculiar genus, but the larva of Crustacea, 1 Webb, 2006, DNA barcoding: a molecular tool to identify Antarctic marine larvae, Deep-Sea Res. Part II, 53, 1053, 10.1016/j.dsr2.2006.02.013 Werle, 1994, Convenient single-step, one tube purification of PCR products for direct sequencing, Nucleic Acids Res., 22, 4354, 10.1093/nar/22.20.4354 Winsor, 1976 Xia, 2001, DAMBE: software package for data analysis in molecular biology and evolution, Comput. Notes, 371 Zhang, 2008, Inferring species membership using DNA sequences with back-propagation, Syst. Biol., 57, 202, 10.1080/10635150802032982