Genetic connectivity of the endangered brown sea cucumber Isostichopus fuscus in the northern Gulf of California revealed by novel microsatellite markers


  • José Miguel Ochoa-Chávez Centro de Investigación Científica y de Educación Superior de Ensenada
  • Miguel Ángel Del Río-Portilla Centro de Investigación Científica y de Educación Superior de Ensenada
  • Luis Eduardo Calderón-Aguilera Centro de Investigación Científica y de Educación Superior de Ensenada
  • Axayácatl Rocha-Olivares Biological Oceanography Department > CICESE


Palabras clave:

Holothurid, Fisheries, Conservation genetics, Next generation sequencing, Genome sequencing


Isostichopus fuscus is an economically important sea cucumber that has been highly exploited along its distribution range in the eastern Pacific. The significant population decline is responsible for its listing as endangered in the IUCN Red List. Despite its importance for management and conservation, information about its population genetic structure
is unavailable, largely due to the lack of suitable genetic markers. Here we develop species-specific microsatellite markers and use them to assess the genetic connectivity between populations in the Gulf of California. Next generation sequencing (Illumina) was used to shotgun-sequence the genome of 2 sea cucumbers. From these data, we identified
and characterized 19 polymorphic microsatellite loci; which were tested in organisms from Bahía de los Ángeles, on the western shore of the Gulf of California. The number of alleles ranged from 5 to 22, observed heterozygosity from 0.35 to 1, and 4 loci deviated from Hardy-Weinberg equilibrium. We determined high levels of genetic connectivity between this locality and San Felipe, in the upper gulf (Amova φst = 0.002; p > 0.05) with a subset of 8 markers. The newly designed microsatellites are suitable for multiplexing panels and will be useful for the future genetic assessment of this important tropical sea cucumber.

Biografía del autor/a

José Miguel Ochoa-Chávez, Centro de Investigación Científica y de Educación Superior de Ensenada

Departamento de Oceanografía Biológica

Miguel Ángel Del Río-Portilla, Centro de Investigación Científica y de Educación Superior de Ensenada

Departamento de Acuicultura

Luis Eduardo Calderón-Aguilera, Centro de Investigación Científica y de Educación Superior de Ensenada

Departamento de Ecología Marina

Axayácatl Rocha-Olivares, Biological Oceanography Department > CICESE

Departamento de Oceanografía Biológica


Excoffier, L., G. Laval and S. Schneider. 2005. Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50.

Faircloth, B. C. 2008. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources, 8, 92-94.

Gardner, M. G., A. J. Fitch, T. Bertozzi and A. J. Lowe. 2011. Rise of the machines - recommendations for ecologists when using next generation sequencing for microsatellite development. Molecular Ecology Resources, 11, 1093-1101.

Holland, M. M. and W. Parson. 2011. GeneMarker ® HID: A Reliable Software Tool for the Analysis of Forensic STR Data. Journal of Forensic Sciences, 56, 29-35.

Hong, Y. K., S. D. Kim, M. Polnefuller and A. O. Gibor. 1995. DNA extraction conditions from Porphyra perforata using LiCl. Journal of Applied Phycology, 7, 101-107.

Ibarra, A. A. and G. R. Soberón. 2002. Economic reasons, ecological actions and social consequences in the Mexican sea cucumber fishery. SPC Beche-de-Mer Information Bulletin, 17(October), 33–36.

Lavín, M. F. and S. G. Marinone. 2003, An overview of the physical oceanography of the Gulf of California. In O. Velasco-Fuentes, J. Sheinbaum and J. Ochoas (Eds.), Nonlinear Processes in Geophysical Fluid Dynamics (pp. 173-204). Dordrecht, Netherlands, Springer.

Lohr, H. R. 2003. Genetic variation among geographically isolated populations of the commercially important sea cucumber, Isostichopus fuscus, in the Eastern Pacific. M. S. Thesis, San Francisco State University, 112 pp.

Maluf, L. Y. 1988. Composition and distribution of the central eastern Pacific echinoderms. Natural History Museum of Los Angeles County, Los Angeles, Calif. 241 pp.

Park, S. 2001. MStools v 3 (Excel spreadsheet toolkit for data conversion). Smurfit Institute of Genetics. Trinity College, Dublin.

Rousset, F. 2008. GENEPOP ' 007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources, 8, 103-106.

Schuelke, M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology, 18, 233-234.

Toral-Granda, V. 2008, Population status, fisheries and trade of sea cucumbers in Latin America and the Caribbean. In V. Toral-Granda, A. Lovatelli and M. Vasconcelloss (Eds.), Sea Cucumbers. A Global Review of Fisheries and Trade. FAO Fisheries and Aquaculture Technical Paper (pp. 213–229). Rome, FAO.

Van Oosterhout, C., W. F. Hutchinson, D. P. M. Wills and P. Shipley. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535-538.


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