Conservation Genetics Resources

, Volume 6, Issue 1, pp 143–146 | Cite as

Development, characterisation and cross-species amplification of 16 novel microsatellite markers for the endangered Black-throated Finch (Poephila cincta) in Australia

  • Lei Tang
  • Carolyn Smith-Keune
  • Michael G. Gardner
  • Britta Denise Hardesty
Microsatellite Letters


The Black-throated Finch (Southern) (Poephila cincta cincta) is threatened by the substantial landscape changes in northern Australia. We developed 16 polymorphic microsatellite markers using 454-shotgun whole-genome sequencing technology. We identified an average of 4.7 alleles per locus based on 63 wild caught individuals from Townsville, Queensland. Thirteen and 9 markers were also successfully cross-amplified in two confamilial species, the Double-barred Finch (Taeniopygia bichenovii) and the chestnut-breasted Mannikin (Lonchura castaneothorax) with 11 and 5 were polymorphic, respectively. These markers will help understand the population genetic structure of the endangered Black-throated Finch and determine genetic consequences of landscape changes for the species.


Black-throated Finch Poephila cincta Microsatellite Conservation genetics Next generation sequencing 



We especially thank Dr Tony Grice and Dr James Moloney for their valuable help and comments throughout this work. Juliana Rechetelo, Dr April Reside, Troy Countryman, Matthew McIntosh and other volunteers assisted with the fieldwork. We are also grateful to Blanche D’Anastasi, Erica Todd, Georgia McDougall and Alison Fitch for their general laboratory assistance and advice. The development of these primers was conducted within the Molecular Ecology & Evolutionary Laboratory (James Cook University) and funded by the Black-throated Finch Trust and School of Earth & Environmental Sciences at James Cook University.


  1. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate—a practical and powerful approach to multiple testing. J Roy Stat Soc B Met 57(1):289–300Google Scholar
  2. Franklin DC, Whitehead PJ, Pardon G, Matthews J, McMahon P, McIntyre D (2005) Geographic patterns and correlates of the decline of granivorous birds in northern Australia. Wildlife Research 32:399–408. doi: 10.1071/WR05052 CrossRefGoogle Scholar
  3. 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(6):1093–1101. doi: 10.1111/j.1755-0998.2011.03037.x PubMedCrossRefGoogle Scholar
  4. Holleley CE, Geerts PG (2009) Multiplex manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR. Biotechniques 46(7):511–517. doi: 10.2144/000113156 PubMedCrossRefGoogle Scholar
  5. 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(3):403–404. doi: 10.1093/bioinformatics/btp670 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Lei Tang
    • 1
    • 2
    • 3
    • 8
  • Carolyn Smith-Keune
    • 3
  • Michael G. Gardner
    • 4
    • 5
    • 6
  • Britta Denise Hardesty
    • 7
  1. 1.School of Earth and Environmental SciencesJames Cook UniversityTownsvilleAustralia
  2. 2.CSIRO Ecosystem SciencesTownsvilleAustralia
  3. 3.School of Marine and Tropical BiologyJames Cook UniversityTownsvilleAustralia
  4. 4.School of Biological SciencesFlinders UniversityAdelaideAustralia
  5. 5.Australian Centre for Evolutionary Biology and BiodiversityUniversity of AdelaideAdelaideAustralia
  6. 6.Evolutionary Biology UnitSouth Australian MuseumAdelaideAustralia
  7. 7.CSIRO Marine and Atmospheric ResearchHobartAustralia
  8. 8.Australian Tropical Science and Innovation PrecinctJames Cook UniversityTownsvilleAustralia

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