Conservation Genetics Resources

, Volume 5, Issue 2, pp 327–330 | Cite as

Molecular forensics in the precious Mediterranean red coral, Corallium rubrum: testing DNA extraction and microsatellite genotyping using dried colonies

  • Jean-Baptiste Ledoux
  • Didier Aurelle
  • Jean-Pierre Féral
  • Joaquim Garrabou
Technical Note

Abstract

Corallium rubrum is an overharvested precious coral submitted to strong environmental pressures. The development of new management tools such as assignment tests is crucial to assess the origin of traded colonies and to reinforce existing regulations in order to ultimately reduce poaching. As a starting point, we test the feasibility of DNA extractions and PCR amplifications of ten microsatellites using dried tissues such as those that can be obtained from traded or seized colonies. We genotype the same ten colonies conserved in alcohol and after five drying periods (from 7 days to 8 months) as well as ten dried colonies coming from a seizure conducted in 2009. Estimating the rate of negative PCRs through time, PCR repeatability and frequencies of null alleles, we demonstrate that dried colonies can be successfully genotyped. This study opens new avenues for the conservation of C. rubrum and other precious corals.

Keywords

Poaching Corallium rubrum Dried tissues Degraded DNA DNA extraction Microsatellites Genotyping 

References

  1. Aurelle D, Ledoux JB, Rocher C, Borsa P, Chenuil A, Féral JP (2011) Phylogeography of the red coral (Corallium rubrum): inferences on the evolutionary history of a temperate gorgonian. Genetica 139:855–869PubMedCrossRefGoogle Scholar
  2. Bruckner AW (2009) Rate and extent of decline in Corallium (pink and red coral) populations: existing data meet the requirements for a CITES Appendix II listing. Mar Ecol Prog Ser 397:319–332CrossRefGoogle Scholar
  3. Calderon I, Garrabou J, Aurelle A (2006) Evaluation of the utility of COI and ITS markers as tools for population genetic studies of temperate gorgonians. J Exp Mar Biol Ecol 336:184–197CrossRefGoogle Scholar
  4. Carlsson J (2008) Effects of microsatellite null alleles on assignment testing. J Hered 99:616–623PubMedCrossRefGoogle Scholar
  5. Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631PubMedCrossRefGoogle Scholar
  6. Costantini F, Abbiati M (2006) Development of microsatellite markers for the Mediterranean gorgonian coral Corallium rubrum. Mol Ecol Notes 6:521–523CrossRefGoogle Scholar
  7. Costantini F, Fauvelot C, Abbiatti M (2007) Genetic structuring of the temperate gorgonian coral (Corallium rubrum) across the western Mediterranean Sea revealed by microsatellites and nuclear sequences. Mol Ecol 16:5168–5182PubMedCrossRefGoogle Scholar
  8. Costantini F, Rossi S, Pintus E, Cerrano C, Gili JM, Abbiati M (2011) Low connectivity and declining genetic variability along a depth gradient in Corallium rubrum populations. Coral Reefs 30:991–1003CrossRefGoogle Scholar
  9. Garrabou J, Coma R, Bally M, Bensoussan N, Chevaldonné P, Cigliano M et al (2009) Mass mortality in northwestern Mediterranean rocky benthic communities: effects of the 2003 heat wave. Global Change Biol 15:1090–1103CrossRefGoogle Scholar
  10. Hoffman JI, Amos W (2005) Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Mol Ecol 14:599–612PubMedCrossRefGoogle Scholar
  11. Ledoux JB, Mokthar-Jamai K, Roby C, Feral JP, Garrabou J, Aurelle D (2010a) Genetic survey of shallow populations of the Mediterranean red coral [Corallium rubrum (Linnaeus, 1758)]: new insights into evolutionary processes shaping nuclear diversity and implications for conservation. Mol Ecol 19:675–690PubMedCrossRefGoogle Scholar
  12. Ledoux JB, Garrabou J, Bianchimani O, Drap P, Feral JP, Aurelle D (2010b) Fine-scale genetic structure and inferences on population biology in the threatened Mediterranean red coral, Corallium rubrum. Mol Ecol 19:4204–4216CrossRefGoogle Scholar
  13. Linares C, Garrabou J, Hereu B, Diaz D, Marschal C, Sala E, Zabala M (2012) Assessing the effectiveness of marine reserves on unsustainably harvested long-lived sessile invertebrates. Conserv Biol 26:88–96PubMedCrossRefGoogle Scholar
  14. Manel S, Berthier P, Luikart G (2002) Detecting wildlife poaching: identifying the origin of individuals with Bayesian assignment tests and multilocus génotypes. Conserv Biol 16:650–659CrossRefGoogle Scholar
  15. Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16:1215PubMedCrossRefGoogle Scholar
  16. Polato NR, Conception GT, Toonen RJ, Baums IB (2010) Isolation by distance across the Hawaiian Archipelago in the reef-building coral Porites lobata. Mol Ecol 19:4661–4677PubMedCrossRefGoogle Scholar
  17. Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors causes, consequences and solutions. Nat Rev Genet 6:847–859PubMedCrossRefGoogle Scholar
  18. Sefc KM, Payne RB, Sorenson MD (2003) Microsatellite amplification from museum feather samples: effects of fragment size and template concentration on genotyping errors. Auk 120:982–989CrossRefGoogle Scholar
  19. Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Lett 9:615–629PubMedCrossRefGoogle Scholar
  20. Tsounis G, Rossi S, Grigg R, Santangelo G, Bramanti L, Gili JM (2010) The exploitation and conservation of precious corals. Oceanogr Mar Biol 48:161–212CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • Jean-Baptiste Ledoux
    • 1
    • 2
    • 3
  • Didier Aurelle
    • 3
  • Jean-Pierre Féral
    • 3
  • Joaquim Garrabou
    • 1
    • 3
  1. 1.Institut de Ciències del MarCSICBarcelonaSpain
  2. 2.CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e AmbientalUniversidade do PortoPortoPortugal
  3. 3.UMR 7263 IMBE, CNRSAix-Marseille UniversityMarseilleFrance

Personalised recommendations