Conservation Genetics Resources

, Volume 10, Issue 2, pp 237–246 | Cite as

Stopping the spin cycle: genetics and bio-banking as a tool for addressing the laundering of illegally caught wildlife as ‘captive-bred’

  • Carolyn J. HoggEmail author
  • Siobhan Dennison
  • Greta J. Frankham
  • Meagan Hinds
  • Rebecca N. Johnson
Methods and Resources Article


The laundering of wild caught animals as ‘captive bred’ is an emerging trend in wildlife crime and the illegal pet trade. Enforcement of such activities requires accurate identification of laundered individuals, the development of validated genetic tools to investigate pedigrees, and the impetus of agencies involved in compliance to implement. The aim of this study was to assess the utility of 13 previously developed species-specific microsatellite loci in elucidating familial relationships in an endemic Australian snake species, the broad-headed snake (Hoplocephalus bungaroides), for which illegal activity had been identified as a threat to the species. We tested these genetic markers on a mix of captive animals held by zoos, privately owned individuals kept under licence, seized animals, and wild-sourced individuals. These loci contain sufficient variability to clearly discriminate the ‘zoo’ animals from the ‘wild’ and ‘privately’ held animals, however, considerable overlap between ‘wild’ and ‘private’ sample groups suggest recent gene flow between wild and privately-owned specimens. Inconsistent tracking of privately held animals makes it difficult to differentiate between legal and illegal acquisition, however the genetic patterns observed demonstrate that genetic markers can be used to elucidate between true captive bred animals in some scenarios. On the basis of our findings in this study, we recommend the implementation of genetic bio-banking for all legally traded wildlife to ensure that claimed captive-bred pedigree relationships can be validated and monitored long-term. These bio-banked samples can then be used to verify captive breeding in traded wildlife.


Microsatellites Wildlife trade Broad-headed snake Wildlife forensics Bio-banking 



The authors would like to thank the zoos (Zoos Victoria and Adelaide Zoo) and all the private holders who provided samples from their snakes for use in this study. Thanks also to the veterinarians who assisted in collection and P. Armstrong for her assistance. This work was initiated by the NSW Office of Environment and Heritage (OEH) and funded by the Australian Museum, OEH and BioPlatforms Australia.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

Samples collected for this study were done so under a management request from the NSW Office of Environment and Heritage. Samples were ethically collected by a veterinarian. Samples from zoo animals were collected under Zoos Victoria animal ethics permit number ZV15001.


  1. Alacs E, Georges A (2008) Wildlife across our borders: a review of the illegal trade in Australia Australian. J Forensic Sci 40:147–160Google Scholar
  2. Arèvalo E, Davis SK, Sites JW (1994) Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in central Mexico. Syst Biol 43:387–418CrossRefGoogle Scholar
  3. Blouin MS, M. P, Lotz S VL (1996) Use of microsatellite loci to classify individuals by relatedness. Mol Ecol 5:393–401CrossRefPubMedGoogle Scholar
  4. Clement MJ, Snell Q, Walker P, Posada D, Crandall KA (2002) TCS: estimating gene genealogies. In: ipdps, p 0184Google Scholar
  5. Conde DA et al (2013) Zoos through the lens of the IUCN red list: a global metapopulation approach to support conservation breeding programs. PLoS ONE. doi: 10.1371/journal.pone.0080311 CrossRefPubMedPubMedCentralGoogle Scholar
  6. Dawnay N, Ogden R, Thorpe RS, Pope LC, Dawson DA, McEwing R (2008) A forensic STR profiling system for the Eurasian badger: a framework for developing profiling systems for wildlife species. Forensic Sci Int Genet 2:47–53CrossRefPubMedGoogle Scholar
  7. Dennison S, Smith SM, Stow AJ (2012) Long-distance geneflow and habitat specificity of the rock-dwelling coppertail skink, Ctenotus taeniolatus. Austral Ecol 37:258–267CrossRefGoogle Scholar
  8. Dennison S, McAlpin S, Chapple DG, Stow AJ (2015) Genetic divergence among regions containing the vulnerable great desert skink (Liopholis kintorei) in the Australian arid zone. PLoS ONE 10:e0128874CrossRefPubMedPubMedCentralGoogle Scholar
  9. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRefPubMedGoogle Scholar
  10. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567CrossRefPubMedGoogle Scholar
  11. Frankham GJ, Hinds MC, Johnson RN (2015) Development of 16 forensically informative microsatellite loci to detect the illegal trade of broad headed snakes (Hoplocephalus bungaroides). Conserv Genet Resour 7:533CrossRefGoogle Scholar
  12. Gilbert D (2015) Broad-headed snake studbook. Zoo and Aquarium Association Australasia, MosmanGoogle Scholar
  13. Goncalves PFM, Oliveira-Marques AR, Matsumoto TE, Miyaki CY (2015) DNA barcoding identifies illegal parrot trade. J Hered 106:560–564. doi: 10.1093/jhered/esv035 CrossRefPubMedGoogle Scholar
  14. Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-Statistics. J Hered 86:485–486CrossRefGoogle Scholar
  15. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9. 3), pp 485–486Google Scholar
  16. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620CrossRefGoogle Scholar
  17. Hastie J, McCrea-Steele T (2014) Wanted-dead or alive: exposing online wildlife trade. International Fund for Animal Welfare, LondonGoogle Scholar
  18. Hulme PE (2015) Invasion pathways at a crossroad: policy and research challenges for managing alien species introductions. J Appl Ecol 52:1418–1424. doi: 10.1111/1365-2664.12470 CrossRefGoogle Scholar
  19. Jan C, Fumagalli L (2016) Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae). PeerJ 4:e2416. doi: 10.7717/peerj.2416 CrossRefPubMedPubMedCentralGoogle Scholar
  20. Johnson RN, Wilson-Wilde L, Linacre A (2014) Current and future directions of DNA in wildlife forensic science. Forensic Sci Int Genet 10:1–11. doi: 10.1016/j.fsigen.2013.12.007 CrossRefPubMedGoogle Scholar
  21. Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405CrossRefPubMedGoogle Scholar
  22. Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:1–15. doi: 10.1186/1471-2156-11-94 CrossRefGoogle Scholar
  23. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106CrossRefPubMedGoogle Scholar
  24. Kamvar ZN, Tabima JF, Grünwald NJ (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:e281CrossRefPubMedPubMedCentralGoogle Scholar
  25. Kisling VN (2001) Ancient collections and menageries. In: Kisling VN (ed) Zoo and aquarium history: ancient animal collections to zoological gardens. CRC Press, Boca RatonGoogle Scholar
  26. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452CrossRefPubMedGoogle Scholar
  27. Linacre AMT, Tobe SS (2013) Wildlife DNA analysis: applications in forensic science. Wiley-Blackwell, OxfordCrossRefGoogle Scholar
  28. Linacre A et al (2011) ISFG: recommendations regarding the use of non-human (animal) DNA in forensic genetic investigations. Forensic Sci Int Genet 5:501–505CrossRefPubMedGoogle Scholar
  29. Livingston B (1974) Animals, people, places. Arbor, New YorkGoogle Scholar
  30. Lynch M, Ritland K (1999) Estimation of pairwise relatedness with molecular markers. Genetics 152:1753–1766PubMedPubMedCentralGoogle Scholar
  31. Millins C, Howie F, Everitt C, Shand M, Lamm C (2014) Analysis of suspected wildlife crimes submitted for forensic examinations in Scotland. Forensic Sci Med Pathol 10:357–362. doi: 10.1007/s12024-014-9568-1 CrossRefPubMedGoogle Scholar
  32. Mucci N, Mengoni C, Randi E (2014) Wildlife DNA forensics against crime: Resolution of a case of tortoise theft. Forensic Sci Int Genet 8:200–202. doi: 10.1016/j.fsigen.2013.10.001 CrossRefPubMedGoogle Scholar
  33. Ogden R, Linacre A (2015) Wildlife forensic science: a review of genetic geographic origin assignment. Forensic Sci Int Genet 18:152–159CrossRefPubMedGoogle Scholar
  34. Petrossian GA, Piresb SF, van Uhmc DP (2016) An overview of seized illegal wildlife entering the United States. Global Crime 17:181–201CrossRefGoogle Scholar
  35. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  36. Queller DC, Goodnight KF (1989) Estimating relatedness using genetic markers. Evol Int J Org Evol 43:258–275CrossRefGoogle Scholar
  37. Shine R, Webb JK, Fitzgerald M, Sumner J (1998) The impact of bush-rock removal on an endangered snake species, Hoplocephalus bungaroides (Serpentes : Elapidae). Wildl Res 25:285–295. doi: 10.1071/WR97022 CrossRefGoogle Scholar
  38. Signorile AL, Reuman DC, Lurz PWW, Bertolino S, Carbone C, Wang J (2016) Using DNA profiling to investigate human-mediated translocations of an invasive species. Biol Conserv 195:97–105CrossRefGoogle Scholar
  39. Strehlow H (2001) Zoological gardens of Western Europe. In: Kisling VN (ed) Zoo and aquarium history: ancient animal collections to zoological gardens. CRC Press, Boca RatonGoogle Scholar
  40. Sumner J, Webb JK, Shine R, Keogh JS (2010) Molecular and morphological assessment of Australia’s most endangered snake, Hoplocephalus bungaroides, reveals two evolutionarily significant units for conservation. Conserv Genet 11:747–758. doi: 10.1007/s10592-009-9863-7 CrossRefGoogle Scholar
  41. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefPubMedPubMedCentralGoogle Scholar
  42. Temple-Smith P, Grant T (2002) Uncertain breeding: a short history of reproduction in monotremes. Reprod Fertil Dev 13:487–497. doi: 10.1071/RD01110 CrossRefGoogle Scholar
  43. UNEP, INTERPOL (2014) The environmental crime crisis: threats to sustainable development from illegal exploitation and trade in wildlife and forest resources. UNEP/GRID, ArendalGoogle Scholar
  44. United_Nations (2015) Tackling illicit trafficking in wildlife.
  45. Wang J (2002) An estimator for pairwise relatedness using molecular markers. Genetics 160:1203–1215PubMedPubMedCentralGoogle Scholar
  46. Wang J (2011) COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Mol Ecol Resour 11:141–145CrossRefPubMedGoogle Scholar
  47. Webb JK, Brook BW, Shine R (2002) Collectors endanger Australia’s most threatened snake, the broadheaded snake Hoplocephalus bungaroides. Oryx 36:170–181CrossRefGoogle Scholar
  48. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38(6):1358–1370PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  • Carolyn J. Hogg
    • 1
    • 2
    Email author
  • Siobhan Dennison
    • 3
  • Greta J. Frankham
    • 3
  • Meagan Hinds
    • 4
  • Rebecca N. Johnson
    • 3
  1. 1.The University of SydneySchool of Life and Environmental SciencesSydneyAustralia
  2. 2.Zoo and Aquarium Association AustralasiaMosmanAustralia
  3. 3.Australian Centre for Wildlife GenomicsAustralian Museum Research InstituteSydneyAustralia
  4. 4.Office of Environment and HeritageEcosystems and Threatened Species Greater Sydney RegionHurstvilleAustralia

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