Conservation Genetics Resources

, Volume 3, Issue 3, pp 449–456 | Cite as

Twenty-nine microsatellite markers for two Australian freshwater turtles, Elseya albagula and Emydura macquarii krefftii: development from 454-sequence data and utility in related taxa

  • Erica ToddEmail author
  • David Blair
  • Mark Hamann
  • Dean Jerry
Technical Note


454 shotgun sequencing was used to identify thousands of in silico microsatellite loci from two Australian freshwater turtle species (Pleurodira, Chelidae), Elseya albagula and Emydura macquarii krefftii. Twenty-nine polymorphic microsatellites were subsequently developed and tested as markers, 15 for E. m. krefftii and 14 for E. albagula. The former marker set showed greater allelic richness (mean N A  = 7.7, range 3–15) than the latter (mean N A  = 4.4, range 2–8). Levels of expected heterozygosity were high for both marker suites (mean H E  = 0.718, range 0.177–0.875; and mean H E  = 0.567, range 0.317–0.827, respectively), indicating both are suitable for studies of population genetic structure, connectivity and mating systems in these taxa. Cross-species amplification in 12 other short-necked freshwater turtle taxa highlighted the potential utility of these markers in other species, notably Emydura spp., Rheodytes leukops and Elusor macrurus.


Testudines Chelidae 454 pyrosequencing Multiplex PCR Gene flow River regulation 



We thank Queensland Turtle Research and Jason Schaffer for providing tissue samples and fieldwork opportunities. Arthur Georges kindly provided many tissue samples for cross-species testing. Kyall Zenger provided helpful sequencing advice and assistance. Ivan Lawler, Dave Jones and Carolyn Smith-Keune also provided invaluable advice and support. This work was partially funded by research grants from the Wildlife Preservation Society of Queensland, Wildlife Preservation Society of Australia, and the Peter Rankin Trust Fund for Herpetology. Research was conducted under ethics permit no. A1444.


  1. Abdelkrim J, Robertson BC, Stanton JAL, Gemmell NJ (2009) Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. Biotechniques 46:185–192PubMedCrossRefGoogle Scholar
  2. Alacs EA, Hillyer MJ, Georges A, Fitzsimmons NN, Hughes JM (2009) Development of microsatellite markers in the Australasian snake-necked turtle Chelodina rugusa and cross-species amplification. Mol Ecol Resour 9:350–353PubMedCrossRefGoogle Scholar
  3. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B-Methodol 57:289–300Google Scholar
  4. Bodie JR (2001) Stream and riparian management for freshwater turtles. J Environ Manage 62:443–455PubMedCrossRefGoogle Scholar
  5. Buhlmann KA, Akre TSB, Iverson JB, Karapatakis D, Mittermeier RA, Georges A, Rhodin AGJ, van Dijk PP, Gibbons JW (2009) A global analysis of tortoise and freshwater turtle distributions with identification of priority conservation areas. Chelonian Conserv Biol 8:116–149CrossRefGoogle Scholar
  6. Clark NJ, Gordos MA, Franklin CE (2009) Implications of river damming: the influence of aquatic hypoxia on the diving physiology and behaviour of the endangered Mary River turtle. Anim Conserv 12:147–154CrossRefGoogle Scholar
  7. Csencsics D, Brodbeck S, Holderegger R (2010) Cost-effective, species-specific microsatellite development for the endangered dwarf Bulrush (Typha minima) using next-generation sequencing technology. J Hered 101:789–793PubMedCrossRefGoogle Scholar
  8. Georges A, Thomson S (2006) Evolution and zoogeography of Australian freshwater turtles. In: Merrick JR, Archer M, Hickey G, Lee MSY (eds) Evolution and biogeography of Australasian vertebrates. Australian Scientific Publishing, AUSCIPUB, Sydney, pp 291–308Google Scholar
  9. Georges A, Thomson S (2010) Diversity of Australasian freshwater turtles, with an annotated synonymy and keys to species. Zootaxa 2496:1–37Google Scholar
  10. Hamann M, Schauble CS, Limpus DJ, Emerick SP, Limpus CJ (2007) Management plan for the conservation of Elseya sp. [Burnett River] in the Burnett River Catchment. Queensland Environmental Protection Agency, BrisbaneGoogle Scholar
  11. Holleley CE, Geerts PG (2009) MULTIPLEX MANAGER 1.0: a cross-platform computer program that plans and optimizes multiplex PCR. Biotechniques 46:511–517PubMedCrossRefGoogle Scholar
  12. IUCN (2010) IUCN Red List of Threatened Species. Version 2010.3. Accessed 11 Nov 2010Google Scholar
  13. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106PubMedCrossRefGoogle Scholar
  14. Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380PubMedGoogle Scholar
  15. Meglecz 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
  16. 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
  17. Rousset F (2008) GENEPOP ‘ 007: a complete re-implementation of the GENEPOP software for windows and linux. Mol Ecol Resour 8:103–106PubMedCrossRefGoogle Scholar
  18. Saarinen EV, Austin JD (2010) When technology meets conservation: increased microsatellite marker production using 454 genome sequencing on the endangered Okaloosa Darter (Etheostoma okaloosae). J Hered 101:784–788PubMedCrossRefGoogle Scholar
  19. Shimizu M, Kosaka N, Shimada T, Nagahata T, Iwasaki H, Nagai H, Shiba T, Emi M (2002) Universal fluorescent labeling (UFL) method for automated microsatellite analysis. DNA Res 9:173–178PubMedCrossRefGoogle Scholar
  20. Thompson S, Georges A, Limpus C (2006) A new species of freshwater turtle in the genus Elseya (Testudines: Chelidae) from Central Coastal Queensland, Australia. Chelonian Conserv Biol 5:74–86CrossRefGoogle Scholar
  21. Tucker AD (1999) Cumulative impacts of dams and weirs on freshwater turtles: Fitzroy, Burnett and Mary Catchments. Queensland Parks and Wildlife Service. Unpublished report to Department of Natural ResourcesGoogle Scholar
  22. Tucker AD, Limpus CJ, Priest TE, Cay J, Glen C, Guarino E (2001) Home ranges of Fitzroy River turtles (Rheodytes leukops) overlap riffle zones: potential concerns related to river regulation. Biol Conserv 102:171–181CrossRefGoogle Scholar
  23. 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
  24. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Erica Todd
    • 1
    Email author
  • David Blair
    • 1
  • Mark Hamann
    • 2
  • Dean Jerry
    • 1
  1. 1.School of Marine and Tropical BiologyJames Cook UniversityTownsvilleAustralia
  2. 2.School of Earth and Environmental SciencesJames Cook UniversityTownsvilleAustralia

Personalised recommendations