Characterisation of 30 microsatellite loci for the Tehuelche scallop, Aequipecten tehuelchus (d’Orbigny, 1842) and their use for estimating demographic parameters relevant to fisheries management

References

• Amoroso, R.O. (2012) Dinámica poblacional de una metapoblación explotada y sus implicancias para el desarrollo de estrategias robustas de manejo: el caso de la vieira tehuelche (Aequipecten tehuelchus) del golfo San José (Chubut, Argentina). Universidad Nacional del Comahue, Ph.D Thesis.
   Google Scholar
• Amoroso, R.O. & Gagliardini, D.A. (2010) Inferring complex hydrographic processes using remote-sensed images: turbulent fluxes in the Patagonian gulfs and implications for scallop metapopulation dynamics. Journal of Coastal Research 26, 320–332. doi: 10.2112/08-1095.1
   Web of Science ®Google Scholar
• Amos, W., Hoffman, J.I., Frodsham, A., Zhang, L., Best, S. & Hill, A.V.S. (2007) Automated binning of microsatellite alleles: problems and solutions. Molecular Ecology Notes 7, 10–14. doi: 10.1111/j.1471-8286.2006.01560.x
   Web of Science ®Google Scholar
• Brownlow, R.J., Dawson, D.A., Horsburgh, G.J., Bell, J.J. & Fish, J.D. (2008) A method for genotype validation and primer assessment in heterozygote-deficient species, as demonstrated in the prosobranch mollusc Hydrobia ulvae. BMC Genetics 9, 55. doi: 10.1186/1471-2156-9-55
   PubMed Web of Science ®Google Scholar
• Chapuis, M.P. & Estoup, A. (2007) Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution 24, 621–631. doi: 10.1093/molbev/msl191
   PubMed Web of Science ®Google Scholar
• Dempster, A.P., Laird, N.M. & Rubin, D.B. (1977) Maximum likelihood from incomplete data via the EM algorithm. Journal of the Royal Statistical Society: Series B 39, 1–38.
   Google Scholar
• Di Rienzo, A., Peterson, A.C., Garza, J.C., Valdes, A.M., Slatkin, M. & Freimer, N.B. (1994) Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences USA 91, 3166–3170. doi: 10.1073/pnas.91.8.3166
   PubMed Web of Science ®Google Scholar
• Do, C., Waples, R.S., Peel, D., Macbeth, G.M., Tillett, B.J. & Ovenden, J.R. (2014) NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources 14, 209–214. doi: 10.1111/1755-0998.12157
   PubMed Web of Science ®Google Scholar
• Ekblom, R. & Galindo, J. (2011) Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107, 1–15. doi: 10.1038/hdy.2010.152
   PubMed Web of Science ®Google Scholar
• Estoup, A., Rousset, F., Michalakis, Y., Cornuet, J.M., Adriamanga, M. & Guyomard, R. (1998) Comparative analysis of microsatellite and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta). Molecular Ecology 7, 339–353. doi: 10.1046/j.1365-294X.1998.00362.x
   PubMed Web of Science ®Google Scholar
• Fiorda, P., Trobbiani, G. & Parma, A.M. (2013) Relevamiento de bancos de vieira tehuelche en el golfo San José- SANJO 2013. CENPAT-CONICET, Puerto Madryn, Argentina. Reporte No 29.
   Google Scholar
• Garza, J.C. & Williamson, E.G. (2001) Detection of reduction in population size using data from microsatellite loci. Molecular Ecology 10, 305–318. doi: 10.1046/j.1365-294x.2001.01190.x
   PubMed Web of Science ®Google Scholar
• Goudet, J. (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. Journal of Heredity 86, 485–486. doi: 10.1093/oxfordjournals.jhered.a111627
   Web of Science ®Google Scholar
• Hedgecock, D. & Pudovkin, A.I. (2011) Sweepstakes reproductive success in highly fecund marine fish and shellfish: a review and commentary. Bulletin of Marine Science 87, 971–1002. doi: 10.5343/bms.2010.1051
   Web of Science ®Google Scholar
• Jarne, P. & Lagoda, P.J. (1996) Microsatellites, from molecules to populations and back. Trends in Ecology and Evolution 11, 424–429. doi: 10.1016/0169-5347(96)10049-5
   PubMed Web of Science ®Google Scholar
• Jones, O.R. & Wang, J. (2010) COLONY: a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources 10, 551–555. doi: 10.1111/j.1755-0998.2009.02787.x
   PubMed Web of Science ®Google Scholar
• Kenchington, E.L., Patwary, M.U., Zouros, E. & Bird, C.J. (2006) Genetic differentiation in relation to marine landscape in a broadcast-spawning bivalve mollusc (Placopecten magellanicus). Molecular Ecology 15, 1781–1796. doi: 10.1111/j.1365-294X.2006.02915.x
   PubMed Web of Science ®Google Scholar
• Lemer, S., Rochel, E. & Planes, S. (2011) Correction method for null alleles in species with variable microsatellite flanking regions, a case study of the black-lipped pearl oyster Pinctada margaritifera. Journal of Heredity 102, 243–246. doi: 10.1093/jhered/esq123
   PubMed Web of Science ®Google Scholar
• Lowe, W.H. & Allendorf, F.W. (2010) What can genetics tell us about population connectivity? Molecular Ecology 19, 3038–3051. doi: 10.1111/j.1365-294X.2010.04688.x
   PubMed Web of Science ®Google Scholar
• Meglécz, E., Costedoat, C., Dubut, V., Gilles, A., Malausa, T., Pech, N. & Martin, J.F. (2010) QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26, 403–404. doi: 10.1093/bioinformatics/btp670
   PubMed Web of Science ®Google Scholar
• Narvarte, M.A. & Pascual, M.S. (2003) Fertilization, larval rearing and post-larval growth of the Tehuelche scallop Aequipecten tehuelchus D’Orb., 1846. Aquaculture 217, 259–274. doi: 10.1016/S0044-8486(02)00269-7
   Web of Science ®Google Scholar
• Orensanz, J.M., Parma, A.M., Ciocco, N. & Cinti, A. (2007) Achievements and setbacks in the commercial diving fishery of San José Gulf, Argentine Patagonia. In: McClanahan, T.R. & Castilla, J.C. (Eds), Fisheries Management: Progress Towards Sustainability. Blackwell Publishing Ltd., Oxford, UK, pp. 68–87.
   Google Scholar
• Orensanz, J.M., Parma, A.M. & Smith, S.J. (2016) Dynamics, assessment, and management of exploited natural scallop populations. In: Sandra, E.S. & Parsons, G.J. (Eds), Developments in Aquaculture and Fisheries Science. Elsevier, pp. 611–695.
   Google Scholar
• Peakall, R. & Smouse, P.E. (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28, 2537–2539. doi: 10.1093/bioinformatics/bts460
   PubMed Web of Science ®Google Scholar
• Picallo, T.S. (1980) Sobre bancos de mariscos de explotación potencialmente rentable en el Golfo San José. CENPAT–CONICET, Puerto Madryn, Argentina. Comunicación N° 39.
   Google Scholar
• Pinsky, M.L. & Palumbi, S.R. (2014) Meta-analysis reveals lower genetic diversity in overfished populations. Molecular Ecology 23, 29–39. doi: 10.1111/mec.12509
   PubMed Web of Science ®Google Scholar
• Piry, S., Luikart, G. & Cornuet, J.M. (1999) Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data. Journal of Heredity 90, 502–503. doi: 10.1093/jhered/90.4.502
   Web of Science ®Google Scholar
• Pisoni, J.P., Rivas, A.L. & Piola, A.R. (2015) On the variability of tidal fronts on a macrotidal continental shelf, Northern Patagonia, Argentina. Deep Sea Research Part II: Topical Studies in Oceanography 119, 61–68. doi: 10.1016/j.dsr2.2014.01.019
   Web of Science ®Google Scholar
• Queller, D.C. & Goodnight, K.F. (1989) Estimating relatedness using genetic markers. Evolution 43, 258–275. doi: 10.1111/j.1558-5646.1989.tb04226.x
   PubMed Web of Science ®Google Scholar
• Raymond, M. & Rousset, F. (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity 86, 248–249. doi: 10.1093/oxfordjournals.jhered.a111573
   Web of Science ®Google Scholar
• Real, L.E., Julio, N., Gardenal, N.C. & Ciocco, N.F. (2004) Genetic variability of Tehuelche scallop, Aequipecten tehuelchus, populations from the Patagonian coasts (Argentina). Journal of the Marine Biological Association of the UK 84, 235–238. doi: 10.1017/S0025315404009099h
   Web of Science ®Google Scholar
• Rice, R.W. (1989) Analyzing tables of statistical tests. Evolution 43, 223–225. doi: 10.1111/j.1558-5646.1989.tb04220.x
   PubMed Web of Science ®Google Scholar
• Schuelke, M. (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18, 233–234. doi: 10.1038/72708
   PubMed Web of Science ®Google Scholar
• Silva, C.N. & Gardner, J.P. (2015) Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae. Molecular Ecology 24, 5379–5393. doi: 10.1111/mec.13404
   PubMed Web of Science ®Google Scholar
• Soria, G., Orensanz, J.M., Morsán, E.M., Parma, A.M. & Amoroso, R.O. (2016) Scallops biology, fisheries, and management in Argentina. In: Sandra, E.S. & Parsons, G.J. (Eds.), Developments in Aquaculture and Fisheries Science. Elsevier, Amsterdam, pp. 1019–1046.
   Google Scholar
• Tonini, M.H., Palma, E.D. & Piola, A.R. (2013) A numerical study of gyres, thermal fronts and seasonal circulation in austral semi-enclosed gulfs. Continental Shelf Research 65, 97–110. doi: 10.1016/j.csr.2013.06.011
   Web of Science ®Google Scholar
• Van Oosterhout, C., Hutchinson, W.F., Wills, D.P.M. & Shipley, P. (2004) MICROCHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4, 535–538. doi: 10.1111/j.1471-8286.2004.00684.x
   Web of Science ®Google Scholar
• Wang, J. (2009) A new method for estimating effective population sizes from a single sample of multilocus genotypes. Molecular Ecology 18, 2148–2164. doi: 10.1111/j.1365-294X.2009.04175.x
   PubMed Web of Science ®Google Scholar
• Waples, R.S. (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics 7, 167–184. doi: 10.1007/s10592-005-9100-y
   Web of Science ®Google Scholar