Journal of Genetics

, 98:11 | Cite as

Development and characterization of 20 polymorphic microsatellite loci in the deep sea squat lobster, Munida isos Ahyong and Poore, 2004 and cross-amplification in two congeneric species

  • Ruo-Jin YanEmail author
  • Kareen E. Schnabel
  • Xiang-Zhao Guo
  • Jonathan P. A. Gardner
Research Note


Munida isos is a deep sea squat lobster species that is widely distributed across the New Zealand and east Australian region, and is often associated with deep sea vulnerable marine ecosystems. To investigate its population genetic structure and patterns of regional connectivity, microsatellite loci were developed for M. isos from two genomic libraries using the Illumina HiSeq 2500 sequencing platform. Twenty-six loci amplified consistently in M. isos from the Tasman Sea, among which 20 were polymorphic and selectively neutral. Evidence of null alleles was observed at eight loci. Most loci exhibited moderate to high levels of polymorphism, with an average polymorphic information content value of 0.482. The mean number of alleles per locus was 7.45, with a mean expected heterozygosity of 0.520. Thirteen loci exhibited significant deviation from Hardy–Weinberg equilibrium, while only one locus pair was in linkage disequilibrium after false discovery rate correction for multiple testing (\(P < 0.05\)). Cross-species amplification tests revealed that the transferability of 14 loci (70%) was positive for the two congeners M. endeavourae and M. gracilis. The accessibility to new polymorphic microsatellite loci will facilitate population genetic studies and aid in developing conservation and management strategies for vulnerable marine ecosystems.


genetic diversity genetic connectivity management conservation south Pacific Ocean vulnerable marine ecosystems Munididae Munida isos 



Squat lobster specimens were supplied for genetic work by the National Institute of Water and Atmospheric (NIWA) Invertebrate Collection, Wellington, New Zealand and Museum Victoria, Melbourne, Australia. Particular special thanks to Ms Sadie Mills and Ms Diana Macpherson of the NIWA Invertebrate Collection and Dr Anna McCallum of the Museum Victoria, for their diligent assistance with loans. Sample collections were supported by funding from the former New Zealand Foundation for Research, Science and Technology, former New Zealand Ministry of Fisheries, Land Information New Zealand, Department of Conservation (New Zealand), GNS Science (New Zealand), Auckland University and Woods Hole Oceanographic Institute (USA). Dr Ashley Rowden of NIWA is thanked for his comments on the manuscript. This work was supported by funding from Victoria University of Wellington to J.P.A.G (SB80802).


  1. Ahyong S. T., Schnabel K. E. and Baba K. 2015 Southern high latitude squat lobsters: Galatheoidea and Chirostyloidea from Macquarie Ridge with description of a new species of Uroptychus. Rec. Aust. Mus. 67, 109–128.CrossRefGoogle Scholar
  2. Antao T., Lopes A., Lopes R. J., Beja-Pereira A. and Luikart G. 2008 LOSITAN: A workbench to detect molecular adaptation based on a \(F_{st}\)-outlier method. BMC Bioinformatics 9, 323.CrossRefGoogle Scholar
  3. Baba K., Macpherson E., Poore G. C. B., Ahyong S. T., Bermudez A., Cabezas P. et al. 2008 Catalogue of squat lobsters of the world (Crustacea: Decapoda: Anomura-families Chirostylidae, Galatheidae and Kiwaidae). Zootaxa 1905, 1–220.Google Scholar
  4. Bahassi E. M. and Stambrook P. J. 2014 Next-generation sequencing technologies: breaking the sound barrier of human genetics. Mutagenesis 29, 303–310.CrossRefGoogle Scholar
  5. Benjamini Y. and Hochberg Y. 1995 Controlling the false discovery rate, a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Stat. Methodol. 57, 289–300.Google Scholar
  6. Benson D. A., Cavanaugh M., Clark K., Karsch-Mizrachi I., Ostell J., Pruitt K. D. et al. 2017 GenBank. Nucleic Acids. Res. 46, D41–D47.CrossRefGoogle Scholar
  7. Boyle E. A., Thaler A. D., Jacobson A., Plouviez S. and Van Dover C. L. 2013 Characterization of 10 polymorphic microsatellite loci in Munidopsis lauensis, a squat-lobster from the southwestern Pacific. Conserv. Genet. Resour. 5, 647–649.CrossRefGoogle Scholar
  8. Coykendall D. and Morrison C. 2013 Polymorphic microsatellite markers developed from 454 pyro-sequencing in the cold water coral-associated squat lobster species, Eumunida picta (Chirostylidae: Eumunididae). Conserv. Genet. Resour. 5, 495–498.CrossRefGoogle Scholar
  9. Excoffier L. and Lischer H. E. 2010 Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564–567.CrossRefGoogle Scholar
  10. Frankham R., Ballou J. D. and Briscoe D. A. 2002 Introduction to conservation genetics. Cambridge University Press, Cambridge.CrossRefGoogle Scholar
  11. Guo S. W. and Thompson E. A. 1992 Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48, 361–372.CrossRefGoogle Scholar
  12. Jenkins T. L. and Stevens J. R. 2018 Assessing connectivity between MPAs: Selecting taxa and translating genetic data to inform policy. Mar. Policy 94, 165–173.CrossRefGoogle Scholar
  13. Kalinowski S. T., Taper M. L. and Marshall T. C. 2007 Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16, 1099–1106.CrossRefGoogle Scholar
  14. Molecular Ecology Resources Primer Development Consortium: Andris M., Aradottir G. I., Arnau G., Audzijonyte A., Bess E. C, Bonadonna F. et al. 2010 Permanent genetic resources added to molecular ecology resources database 1 June 2010–31 July 2010. Mol. Ecol. Resour. 10, 1106–1108.Google Scholar
  15. Nakajima Y., Shinzato C., Khalturina M., Nakamura M., Watanabe H. K., Nakagawa S. et al. 2018 Isolation and characterization of novel polymorphic microsatellite loci for the deep-sea hydrothermal vent limpet, Lepetodrilus nux, and the vent-associated squat lobster, Shinkaia crosnieri. Mar. Biodivers. 48, 677–684.CrossRefGoogle Scholar
  16. Peakall R. and Smouse P. E. 2012 GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537–2539.CrossRefGoogle Scholar
  17. Raymond M. and Rousset F. 1995 GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered. 86, 248–249.CrossRefGoogle Scholar
  18. Roterman C. N., Copley J. T., Linse K. T., Tyler P. A. and Rogers A. D. 2013 Development of polymorphic microsatellite loci for three species of vent-endemic megafauna from deep-sea hydrothermal vents in the Scotia Sea, Southern Ocean. Conserv. Genet. Resour. 5, 835–839.CrossRefGoogle Scholar
  19. Rousset F. 2008 Genepop’007: a complete re-implementation of the Genepop software for Windows and Linux. Mol. Ecol. Resour. 8, 103–106.CrossRefGoogle Scholar
  20. Schnabel K. E. 2009 Squat lobsters (Crustacea: Anomura: Galatheidae and Chirostylidae) of New Zealand: diversity, phylogeny and biogeography. PhD dissertation. University of Otago, Otago.Google Scholar
  21. Selkoe K. A. and Toonen R. J. 2006 Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol. Lett. 9, 615–629.CrossRefGoogle Scholar
  22. van Oosterhout C., Hutchinson W. F., Wills D. P. and Shipley P. 2004 MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Resour. 4, 535–538.CrossRefGoogle Scholar
  23. Waples R. S. 2015 Testing for Hardy-Weinberg proportions: have we lost the plot? J. Hered. 106, 1–19.CrossRefGoogle Scholar
  24. Zeng C., Rowden A. A., Clark M. R. and Gardner J. P. A. 2017 Population genetic structure and connectivity of deep-sea stony corals (Order Scleractinia) in the New Zealand region: Implications for the conservation and management of vulnerable marine ecosystems. Evol. Appl. 10, 1040–1054.CrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  1. 1.School of Biological SciencesVictoria University of WellingtonWellington 6140New Zealand
  2. 2.National Institute of Water and Atmospheric ResearchWellington 6140New Zealand

Personalised recommendations