Abstract
We characterized a set of new hypervariable microsatellite loci for the barred sand-bass (Paralabrax nebulifer), a marine fish that supports important recreational and artisanal fisheries in California, USA and the west coast of the Baja California Peninsula, Mexico. We performed a shotgun genome sequencing with the 454 XL titanium chemistry and used bioinformatics to search for microsatellite loci with perfect repeats. We selected 40 primer pairs that were synthesized and genotyped in an ABI PRISM 3730XL DNA sequencer in 32 individuals from San Juanico, Baja California Sur. We estimated levels of genetic diversity, deviations from linkage and Hardy–Weinberg equilibrium, the frequency of null alleles and the probability of individual identity for the new markers. We successfully scored 24 microsatellite loci (13 tetranucleotides and 11 dinucleotides). The average number of alleles per locus was 12.5 (range 4–23). The average observed and expected heterozygosities were 0.779 (range 0.313–0.969) and 0.774 (range 0.350–0.939), respectively. We detected significant linkage disequilibrium in two pairs of loci. Genotype frequencies at seven loci showed significant deviations from the expectations of Hardy–Weinberg equilibrium and had estimated null allele frequencies ≥10%. The probability of individual identity for the new loci was 8.5−36. The new markers will be useful for investigating patterns of fine-scale genetic structure and diversity to estimate larval dispersal and assess metapopulation dynamics, information necessary for the sustainable management of P. nebulifer fisheries at the west coast of the Baja California Peninsula.
References
Allen LG, Block HE (2012) Planktonic larval duration, settlement, and growth rates of the young-of-the-year of two sand basses (Paralabrax nebulifer and P. maculatofasciatus: fam. Serranidae) from Southern California. Bull S Calif Acad Sci 111:15–21. doi:10.3160/0038-3872-111.1.15
Amos W, Hoffman JI, Frodsham A, Zhang L, Best S, Hill AVS (2007) Automated binning of microsatellite alleles: problems and solutions. Mol Ecol Notes 7:10–14. doi:10.1111/j.1471-8286.2006.01560.x
CONAPESCA (2016) Comisión Nacional de Acuacultura y Pesca. SAGARPA. http://www.sagarpa.gob.mx/quienesomos/datosabiertos/conapesca/Paginas/default.aspx. Accessed 13 September 2016
Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631. doi:10.1093/molbev/msl191
Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc Ser B 39:1–38
Erisman BE, Allen LG, Claisse JT, Pondella DJ, Miller EF, Murray JH, Walters C (2011) The illusion of plenty: hyperstability masks collapses in two recreational fisheries that target fish spawning aggregations. Can J Fish Aquat Sci 68:1705–1716. doi:10.1139/f2011-090
Goudet J (1995) FSTAT (Version 1.2): A computer program to calculate F-statistics. J Hered 86:485–486
Hastings P, Walker HJ, Galland GR (2014) Fishes: a guide to their diversity. University of California Press, Berkeley
Heemstra PC (1995) Meros, serranos, guasetas, enjambres, baquetas, indios, loros, gallinas, cabrillas, garropas. In: Fisher W, Krupp F, Scheneider W, Sommer C, Carpenter KE, Niem VH (eds) Guía FAO para la identitifcación de especies para los fines de la pesca. Pacífico centro-oriental, vol III. FAO, Roma, pp 1565–1613
Hovey CB, Allen LG, Hovey TE (2002) The reproductive pattern of barred sand bass (Paralabrax nebulifer) from southern California. CalCOFI Rep 43:174–181
Jarvis ET, Linardich C, Valle CF (2010) Spawning-related movements of barred sand bass, Paralabrax nebulifer, in Southern California: interpretations from two decades of historical tag and recapture data. Bull S Calif Acad Sci 109:123–143
Jarvis ET, Loke-Smith KA, Evans K, Kloppe RE, Young KA, Valle CF (2014) Reproductive potential and spawning periodicity in barred sand bass (Paralabrax nebulifer) from the San Pedro Shelf, southern California. Calif Fish Game 100:289–309
Karlsson S, Mork J (2005) Deviation from Hardy–Weinberg equilibrium, and temporal instability in allele frequencies at microsatellite loci in a local population of Atlantic cod. ICES J Mar Sci 62:1588–1596. doi:10.1016/j.icesjms.2005.05.009
Meglécz E, Costedoat C, Dubut V, Gilles A, Malausa T, Pech N, Martin JF (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
Munguia-Vega A, Saenz-Arroyo A, Greenley AP, Espinoza-Montes JA, Palumbi SR, Rossetto M, Micheli F (2015) Marine reserves help preserve genetic diversity after impacts derived from climate variability: lessons from the pink abalone in Baja California. Global Ecol Cons 4:264–276. doi:10.1016/j.gecco.2015.07.005
Paterson CN, Chabot CL, Robertson JM, Erisman B, Cota-Nieto JJ, Allen LG (2015) The genetic diversity and population structure of barred sand bass, Paralabrax nebulifer: a historically important fisheries species off southern and Baja California. CalCOFI Rep 56:97–109
Peakall R, Smouse PE (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
Raymond M, Rousset F (1995) GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249
Saenz-Agudelo P, Jones GP, Thorrold SR, Planes S (2009) Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios. Mol Ecol 18:1765–1776. doi:10.1111/j.1365-294X.2009.04109.x
Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotech 18:233–234. doi:10.1038/72708
Selkoe KA, D’Aloia CC, Crandall ED, Iacchei M, Liggins L, Puritz JB, von der Heyden S, Toonen RJ (2016) A decade of seascape genetics: contributions to basic and applied marine connectivity. Mar Ecol Prog Ser 554:1–19. doi:10.3354/meps11792
Selkoe KA, Toonen RJ (2011) Marine connectivity: a new look at pelagic larval duration and genetic metrics of dispersal. Mar Ecol Prog Ser 436:291–305. doi:10.3354/meps09238
Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538. doi:10.1111/j.1471-8286.2004.00684.x
Acknowledgements
We acknowledge the personnel from the Programa Escama at the Centro Regional de Investigación Pesquera - La Paz and the fishermen who helped us collecting the samples, including Laura Cynthia Zuñiga Pacheco, Ibeth and Yolitzia Bareño Higuera, Francisco Lucero Romero AKA Japo and Rolando Sanchez. Karla Vargas and Stacy L. Sotak helped us at various stages during microsatellite genotyping at the University of Arizona. This work was partially funded by The David and Lucile Packard Foundation grant #2015-62798 supporting the PANGAS Science Coordinator, Fondo Mexicano para la Conservación de la Naturaleza - Fondo Golfo de California grant M-1304-004 to Pronatura Noroeste A.C. and The Walton Family Foundation grant 2016-475 to SmartFish Rescate de Valor, A.C.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by K. Kocot
Rights and permissions
About this article
Cite this article
Domínguez-Contreras, J.F., Munguia-Vega, A., Castillo-Lopez, A. et al. Characterization by next-generation sequencing of 24 new microsatellite loci for the barred sand-bass, Paralabrax nebulifer (Girard, 1854), from the Baja California Peninsula, Mexico. Mar Biodiv 48, 2207–2210 (2018). https://doi.org/10.1007/s12526-017-0687-2
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12526-017-0687-2