Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia

Abstract

The use of genome-wide genetic markers is an emerging approach for informing evidence-based management decisions for highly threatened species. Pangolins are the most heavily trafficked mammals across illegal wildlife trade globally, but critically endangered Sunda pangolins (Manis javanica) have not been widely studied in insular Southeast Asia. We used > 12,000 single nucleotide polymorphic markers (SNPs) to assign pangolin seizures from illegal trade of unknown origin to possible geographic sources via genetic clustering with pangolins of known origin. Our SNPs reveal three previously unrecognized genetic lineages of Sunda pangolins, possibly from Borneo, Java and Singapore/Sumatra. The seizure assignments suggest the majority of pangolins were traded from Borneo to Java. Using mitochondrial markers did not provide the same resolution of pangolin lineages, and to explore if admixture might explain these differences, we applied sophisticated tests of introgression using > 2000 SNPs to investigate secondary gene flow between each of the three Sunda pangolin lineages. It is possible the admixture which we discovered is due to human-mediated movements of pangolins. Our findings impact a range of conservation actions, including tracing patterns of trade, repatriation of rescue animals, and conservation breeding. In order to conserve genetic diversity, we suggest that, pending further research, each pangolin lineage should as a precaution be protected and managed as an evolutionarily distinct conservation unit.

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Acknowledgements

All authors contributed equally to this work. All authors discussed the results and implications and commented on the manuscript at all stages. We thank the Indonesian Institute of Sciences (LIPI), Lee Kong Chian Natural History Museum (LKCNHM), Agri-Food & Veterinary Authority of Singapore (AVA), Wildlife Reserves Singapore (WRS), Department of Wildlife and National Parks Peninsular Malaysia (DWNP), Universiti Malaysia Terengganu (UMT) and Kadoorie Farm and Botanic Garden (KFBG) for assistance with sample collection and the arrangement of relevant permits and permissions. Special thanks are given to Yulianto (LIPI) and H. Zhang (KFBG) who helped to extract DNA, and S. Oh (WRS), A. Ali (WRS), S. Luz (WRS), P. Lee (WRS), C. F. Maosheng (LKCNHM), M. Chua (LKCNHM), R. Meier (LKCNHM), C.Y. Gwee (NUS), G. Ades (KFBG) and A. Grioni (KFBG). We also thank R. Asher (University of Cambridge) for his encouragement and advice, and the IUCN-SSC Pangolin Specialist Group and Singapore Pangolin Working Group who provided logistical support throughout this research. The Rheindt Lab at NUS shared a ddRADseq protocol. L. Wijedasa gave us base maps for the figures. S. Thompson helped with coding for fineRADstructure. Funding was provided by the Dennis Gould Foundation; H.C.N is supported by a SINGA PhD Research Scholarship at NUS; S.T.T is supported by a Royal Society University Research Fellowship (UF130573). We also acknowledge internal departmental funding at the Department of Biological Sciences at NUS; and the Research Center for Biology-LIPI Competitive Project 3400.001.002.021 SEAMEO BIOTROP DIPA 060.12/PSRP/SPK-PNLT/2014.

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Nash, H.C., Wirdateti, Low, G.W. et al. Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia. Conserv Genet 19, 1083–1095 (2018). https://doi.org/10.1007/s10592-018-1080-9

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Keywords

  • SNPs
  • Mitochondrial markers
  • Gene flow
  • Illegal wildlife trade
  • Population assignment
  • Conservation breeding