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Articles

Phylogeography of the intertidal marine bivalve Lasaea hinemoa (Mollusca: Bivalvia) in New Zealand

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Pages 191-203 | Received 19 Jan 2021, Published online: 17 Aug 2021

References

  • Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology 215, 403–410.
  • Andrews, S. (2010) FastQC: a quality control tool for high throughput sequence data. Available online at https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ [Accessed on 6 August 2021].
  • Apte, S. & Gardner, J.P.A. (2002) Population genetic subdivision in the New Zealand greenshell mussel (Perna canaliculus) inferred from single-strand conformation polymorphism analysis of mitochondrial DNA. Molecular Ecology 11, 1617–1628.
  • Ayers, K.L. & Waters, J.M. (2005) Marine biogeographic disjunction in central New Zealand. Marine Biology 147, 1045–1052.
  • Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D., Pyshkin, A.V., Sirotkin, A.V., Vyahhi, N., Tesler, G., Alekseyev, M.A. & Pevzner, P.A. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19, 455–477.
  • Beauchamp, K.A. (1986) Reproductive ecology of the brooding, hermaphroditic clam Lasaea subviridis. Marine Biology 93, 225–235.
  • Booth, J.D. (1979) Common bivalve larvae from New Zealand: Leptonacea. New Zealand Journal of Marine and Freshwater Research 13, 241–254.
  • Bowman, M.J., Kibblewhite, A.C., Murtagh, R.A., Chiswell, S.M. & Sanderson, B.G. (1983) Circulation and mixing in greater Cook Strait, New Zealand. Oceanologica Acta 6, 383–391.
  • Brown, W.M., George, M. & Wilson, A.C. (1979) Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences, USA 76, 1967–1971.
  • Chatterji, S. & Pachter, L. (2006) Reference based annotation with GeneMapper. Genome Biology 7, R29.
  • Clement, M., Posada, D.C.K.A. & Crandall, K.A. (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology 9, 1657–1659.
  • Crow, J.F. (1992) An advantage of sexual reproduction in a rapidly changing environment. Journal of Heredity 83, 169–173.
  • Cumming, R.A., Nikula, R., Spencer, H.G. & Waters, J.M. (2016) Trans-Tasman genetic connectivity in the intertidal air-breathing slug Onchidella nigricans. Marine Ecology Progress Series 562, 93–100.
  • Domaneschi, O., Da Silva, J., Neto, L. & Passos, F. (2002). New perspectives on the dispersal mechanisms of the Antarctic brooding bivalve Mysella charcoti (Lamy, 1906). Polar Biology 25, 538–541.
  • Doyle, J.J. & Dickson, E.E. (1987) Preservation of plant samples for DNA restriction endonuclease analysis. Taxon 36, 715–722.
  • Drábková, L.Z., Kirschner, J., Štěpánek, J., Záveský, L. & Vlček, Č (2009) Analysis of nrDNA polymorphism in closely related diploid sexual, tetraploid sexual and polyploid agamospermous species. Plant Systematics and Evolution 278, 67–85.
  • Ekblom, R. & Galindo, J. (2011) Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107, 1–15.
  • Evanno, G., Regnaut, S. & Goudet, J. (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 2611–2620.
  • Excoffier, L., Smouse, P.E. & Quattro, J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479–491.
  • Excoffier, L. & Lischer, H.E. (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10, 564–567.
  • Faircloth, B.C. (2008) MSATCOMMANDER: Detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources 8, 92–94.
  • Francis, M.P. (1996) Geographic distribution of marine reef fishes in the New Zealand region. New Zealand Journal of Marine and Freshwater Research 30, 35–55.
  • Fraser, C.I., Nikula, R. & Waters, J.M. (2010) Oceanic rafting by a coastal community. Proceedings of the Royal Society B: Biological Sciences 278, 649–655.
  • Gardner, M.G., Fitch, A.J., Bertozzi, T. & Lowe, A.J. (2011) Rise of the machines–recommendations for ecologists when using next generation sequencing for microsatellite development. Molecular Ecology Resources 11, 1093–1101.
  • Godwin, L.S. (2003) Hull fouling of maritime vessels as a pathway for marine species invasions to the Hawaiian Islands. Biofouling 19, 123–131.
  • Guindon, S., Dufayard, J.F., 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. Systematic Biology 59, 307–321.
  • Hedgecock, D., Li, G., Hubert, S., Bucklin, K. & Ribes, V. (2004) Widespread null alleles and poor cross-species amplification of microsatellite DNA loci cloned from the Pacific oyster, Crassostrea gigas. Journal of Shellfish Research 23, 379–386.
  • Helmuth, B., Veit, R.R. & Holberton, R. (1994) Long-distance dispersal of a subantarctic brooding bivalve (Gaimardia trapesina) by kelp-rafting. Marine Biology 120, 421–426.
  • Highsmith, R.C. (1985) Floating and algal rafting as potential dispersal mechanisms in brooding invertebrates. Marine Ecology Progress Series 25, 169–179.
  • Jablonski, D. (1986) Larval ecology and macroevolution in marine invertebrates. Bulletin of Marine Science 39, 565–587.
  • Jackson, J.B.C. (1986) Modes of dispersal of clonal benthic invertebrates – consequences for species distributions and genetic structure of local populations. Bulletin of Marine Science 39, 588–606.
  • Jombart, T., Devillard, S. & Balloux, F. (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11, 94.
  • Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30, 772–780.
  • Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P. & Drummond, A. (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649.
  • Knox, G.A. (1975) Biogeography and Ecology in New Zealand. Springer, Dordrecht.
  • Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. (2018) MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution 35, 1547–1549.
  • Kuo, H.C., Chen, S.F., Fang, Y.P., Cotton, J.A., Parker, J.D., Csorba, G., Eger, J., Chen, C.H., Chou, C.H. & Rossiter, S.J. (2015) Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data. Molecular Ecology 24, 5910–5926.
  • Lanfear, R., Calcott, B., Ho, S.Y. & Guindon, S. (2012) PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29, 1695–1701.
  • Lanfear, R., Frandsen, P.B., Wright, A.M., Senfeld, T. & Calcott, B. (2016) PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution 34, 772–773.
  • Leigh, J.W. & Bryant, D. (2015) POPART: full-feature software for haplotype network construction. Methods in Ecology and Evolution 6, 1110–1116.
  • Li, J., Ó Foighil, D. & Park, J.K. (2013) Triton’s trident: cryptic Neogene divergences in a marine clam (Lasaea australis) correspond to Australia’s three temperate biogeographic provinces. Molecular Ecology 22, 1933–1946.
  • Li, Y.L. & Liu, J.X. (2018) StructureSelector: A web-based software to select and visualize the optimal number of clusters using multiple methods. Molecular Ecology Resources 18, 176–177.
  • Lynch, M. & Gabriel, W. (1990) Mutation load and the survival of small populations. Evolution 44, 1725–1737.
  • Martel, A. & Chia, F.S. (1991) Drifting and dispersal of small bivalves and gastropods with direct development. Journal of Experimental Marine Biology and Ecology 150, 131–147.
  • Miller, M.A., Pfeiffer, W. & Schwartz, T. (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: 2010 Gateway Computing Environments Workshop (GCE), 1–8. Institution of Electrical and Electronic Engineers. Available online at https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.9b00330. [Accessed on 6 August 2021.].
  • Moore, L.B. (1949) The marine algal provinces of New Zealand. Transactions of the Royal Society of New Zealand 77, 187–189.
  • Nelson, W.A. (1994) Distribution of macroalgae in New Zealand – an archipelago in space and time. Botanica Marina 37, 221–234.
  • Ó Foighil, D. (1989) Planktotrophic larval development is associated with a restricted geographic range in Lasaea, a genus of brooding, hermaphroditic bivalves. Marine Biology 103, 349–358.
  • Ó Foighil, D. & Smith, M.J. (1995) Evolution of asexuality in the cosmopolitan marine clam Lasaea. Evolution 49, 140–150.
  • Ó Foighil, D. & Thiriot-Quiévreux, C. (1999) Sympatric Australian Lasaea species (Mollusca: Bivalvia) differ in their ploidy levels, reproductive modes and developmental modes. Zoological Journal of the Linnean Society 127, 477–494.
  • Okamoto, A. & Arimoto, B. (1986) Chromosomes of Corbicula japonica, C. sandai and C. (Corbiculina) leana. Venus (Japanese Journal of Malacology) 45, 194–202.
  • Ponder, W.F. (1971) Some New Zealand and subantarctic bivalves of the Cyamiacea and Leptonacea with descriptions of new taxa. Records of the Dominion Museum 7, 119–141.
  • Ponder, W.F. & Taylor, J.D. (1992) Predatory shell drilling by two species of Austroginella (Gastropoda: Marginellidae). Journal of Zoology 228, 317–328.
  • Pritchard, J.K., Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945–959.
  • Pritchard, J.K., Wen, W. & Falush, D. (2003) Documentation for Structure Software: Version 2. Department of Human Genetics, University of Chicago, Chicago.
  • Rambaut, A., Drummond, A.J., Xie, D., Baele, G. & Suchard, M.A. (2018) Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 67, 901–904.
  • Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Hohna, S., Larget, B., Liu, L., Suchard, M.A. & Huelsenbeck, J.P. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61, 539–542.
  • Sánchez, J.A. & Dorado, D. (2008) Intragenomic ITS2 variation in Caribbean seafans. Proceedings of the 11th International Coral Reef Symposium 26, 1383–1387.
  • Sanmartín, I. & Ronquist, F. (2004) Southern Hemisphere biogeography inferred by event-based models: plant versus animal patterns. Systematic Biology 53, 278–298.
  • Schuelke, M. (2000) An economic method for the fluorescent labelling of PCR fragments. Nature Biotechnology 18, 233–234.
  • Shears, N.T., Smith, F., Babcock, R.C., Duffy, C.A. & Villouta, E. (2008) Evaluation of biogeographic classification schemes for conservation planning: Application to New Zealand’s coastal marine environment. Conservation Biology 22(2), 467–481.
  • Smith, S.D. (2002) Kelp rafts in the Southern Ocean. Global Ecology and Biogeography 11, 67–69.
  • Sponer, R. & Roy, M.S. (2002) Phylogeographic analysis of the brooding brittle star Amphipholis squamata (Echinodermata) along the coast of New Zealand reveals high cryptic genetic variation and cryptic dispersal potential. Evolution 56, 1954–1967.
  • Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690.
  • Strathmann, R.R. (1978) The evolution and loss of feeding larval stages of marine invertebrates. Evolution 4, 894–906.
  • Tamura, K. & Nei, M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10, 512–526.
  • Taylor, D.J. & Ó Foighil, D. (2000) Transglobal comparisons of nuclear and mitochondrial genetic structure in a marine polyploid clam (Lasaea, Lasaeidae). Heredity 84, 321–330.
  • Van Oosterhout, C., Hutchinson, W.F., Wills, D.P. & Shipley, P. (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4, 535–538.
  • Wade, C.M., Mordan, P.B. & Naggs, F. (2006) Evolutionary relationships among the pulmonate land snails and slugs (Pulmonata. Stylommatophora). Biological Journal of the Linnaean Society 87, 593–610.
  • Walls, K. (1995). The New Zealand experience in developing a marine biogeographic regionalisation. In Muldoon, J. (Ed.), Towards a Marine Regionalisation for Australia. Great Barrier Reef Marine Park Authority, Townsville, pp. 33–48.
  • Warham, J. & Johns, P.M. (1975) The University of Canterbury Antipodes Island expedition 1969. Journal of the Royal Society of New Zealand 5, 103–131.
  • Xu, Z., Guo, X., Gaffney, P.M. & Pierce, J.C. (2001) Chromosomal location of the major ribosomal RNA genes in Crassostrea virginica and Crassostrea gigas. The Veliger 44, 79–83.

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