Advertisement

Conservation Genetics Resources

, Volume 4, Issue 3, pp 555–558 | Cite as

Development of twenty-four novel microsatellite markers for the freshwater crayfish, Geocharax gracilis, using next generation sequencing

  • Craig D. H. Sherman
  • Daniel Ierodiaconou
  • Annalise M. Stanley
  • Kim Weston
  • Michael G. Gardner
  • Mark B. Schultz
Technical Note

Abstract

The crayfish Geocharax gracilis is an important inhabitant of natural and agricultural drainage systems in south-eastern Australia. To investigate population structure, genetic diversity and patterns of connectivity in natural and human-altered ecosystems, we isolated and characterised 24 microsatellite loci using next generation sequencing. Loci were initially tested for levels of variation based on 12 individuals from across the species’ geographical range. A further 33 individuals from a single population were used to test for departures from Hardy–Weinberg equilibrium and linkage disequilibrium. We detected high to moderate levels of genetic variation across most loci with a mean allelic richness of 8.42 and observed heterozygosity of 0.629 (all samples combined). We found no evidence for linkage disequilibrium between any loci and only three loci (Geo01, Geo24 and Geo47) showed significant deviations from Hardy–Weinberg expectations. These same three loci, plus two additional loci (Geo06 and Geo28), also showed the presence of null alleles. These 24 variable markers will provide an important tool for future population genetic assessments in natural and human altered environments.

Keywords

Crustacean Dispersal Genetic structure Mating system Gene flow 

Notes

Acknowledgments

We would like to thank A. Miller and A. Fitch for technical assistance. A Deakin University Central Research Grant Scheme grant, awarded to DI, CDHS and MS, supported this research.

References

  1. Bilton DT, Freeland JR, Okamura B (2001) Dispersal in freshwater invertebrates. Ann Rev Ecol Syst 32:159–181CrossRefGoogle Scholar
  2. Casas JJ, Sanchez-Oliver JS, Sanz A, Furne M, Trenzado C, Juan M, Paracuellos M, Suarez MD, Fuentes F, Gallego I, Gil C, Ramos-Miras JJ (2011) The paradox of the conservation of an endangered fish species in a Mediterranean region under agricultural intensification. Biol Conserv 144:253–262CrossRefGoogle Scholar
  3. Crandall KA, Fetzner JW, Lawler SH, Kinnersley M, Austin CM (1999) Phylogenetic relationships among the Australian and New Zealand genera of freshwater crayfishes (Decapoda: Parastacidae). Aust J Zool 47:199–214CrossRefGoogle Scholar
  4. Gardner MG, Fitch AJ, Bertozzi T, Lowe AJ (2011) Rise of the machines—recommendations for ecologists when using next generation sequencing for microsatellite development. Mol Ecol Resour 11:1093–1101PubMedCrossRefGoogle Scholar
  5. Harvey MS (2002) Short-range endemism among the Australian fauna: some examples from non-marine environments. Invertebr Syst 16:555–570CrossRefGoogle Scholar
  6. Johnston K, Robson BJ (2009) Habitat use by five sympatric Australian freshwater crayfish species (Parastacidae). Freshw Biol 54:1629–1641CrossRefGoogle Scholar
  7. Jones JPG, Andriahajaina FB, Hockley NJ, Crandall KA, Ravoahangimalala OR (2007) The ecology and conservation status of Madagascar’s endemic freshwater crayfish (Parastacidae; Astacoides). Freshw Biol 52:1820–1833CrossRefGoogle Scholar
  8. Lada H, Neville C, Lacey B, Mac Nally R, Lake PS, Taylor AC (2010) Historic and current genetic population structure in two pond-dwelling macroinvertebrates in massively altered Australian woodland landscapes. Mar Freshw Res 61:1318–1326CrossRefGoogle Scholar
  9. March TS, Robson BJ (2006) Association between burrow densities of two Australian freshwater crayfish (Engaeus sericatus and Geocharax gracilis: Parastacidae) and four riparian land uses. Aquat Conserv Mar Freshw Ecosyst 16:181–191CrossRefGoogle Scholar
  10. 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 26:403–404PubMedCrossRefGoogle Scholar
  11. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295CrossRefGoogle Scholar
  12. Raymond M, Rousset F (1995) Genepop (version-1.2)—population-genetics software for exact tests and ecumenicism. J Hered 86:248–249Google Scholar
  13. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  14. Schultz MB, Smith SA, Richardson AMM, Horwitz P, Crandall KA, Austin CM (2007) Cryptic diversity in Engaeus erichson, Geocharax clark and Gramastacus riek (Decapoda: Parastacidae) revealed by mitochondrial 16S rDNA sequences. Invertebr Syst 21:569–587CrossRefGoogle Scholar
  15. Schultz MB, Ierodiaconou DA, Smith SA, Horwitz P, Richardson AMM, Crandall KA, Austin CM (2008) Sea-level changes and palaeo-ranges: reconstruction of ancient shorelines and river drainages and the phylogeography of the Australian land crayfish Engaeus sericatus Clark (Decapoda: Parastacidae). Mol Ecol 17:5291–5314PubMedCrossRefGoogle Scholar
  16. 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 4:535–538CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Craig D. H. Sherman
    • 1
  • Daniel Ierodiaconou
    • 2
  • Annalise M. Stanley
    • 1
  • Kim Weston
    • 1
  • Michael G. Gardner
    • 3
    • 4
  • Mark B. Schultz
    • 2
    • 5
  1. 1.School of Life and Environmental Sciences, Centre of Integrative EcologyDeakin UniversityWaurn PondsAustralia
  2. 2.School of Life and Environmental SciencesDeakin UniversityWarrnamboolAustralia
  3. 3.School of Biological SciencesFlinders UniversityAdelaideAustralia
  4. 4.School of Earth and Environmental Science, Australian Centre for Evolutionary Biology and BiodiversityUniversity of AdelaideAdelaideAustralia
  5. 5.Division of Infection and ImmunityWalter and Eliza Hall Institute of Medical ResearchParkvilleAustralia

Personalised recommendations