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Seizure samples reveal complex evolutionary dynamics among Southeast Asian pangolins

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Abstract

It is important to have clearly delineated taxonomic units informed by eco-evolutionary processes to ensure effective implementation of conservation efforts. For a group as threatened as Asian pangolins, a timely understanding and recognition of cryptic species is especially critical to inform policy and management decisions. Recent genomic investigations into the group have revealed genomic distinctions between currently recognised species and the putative Manis cf. mysteria, but only incorporate limited representation of the new lineage and its sister taxa, M. javanica and M. culionensis, which may obscure evolutionary inferences within the group and overlook important genetic variation at species boundaries. In this study, we broadly sample seizure materials to incorporate as holistic a representation of each lineage as possible so as to further verify genomic distinctions between the lineages, including new samples of M. cf. mysteria and M. culionensis, the latter of which was only genomically represented by one museum sample previously. We find that while M. cf. mysteria, M. javanica and M. culionensis do form distinct clades with deep divergences, new samples of M. cf. mysteria demonstrate mitonuclear discordance and admixture with M. javanica, illuminating more evolutionary complexity between the three lineages than previously reported. We also find much higher variation in individual heterozygosity within M. cf. mysteria than its sister taxa. Our findings highlight gaps in our understanding of the contemporary evolutionary dynamics of Southeast Asian pangolins, but also demonstrate the barriers these gaps create for practical and timely implementations of conservation effort trafficked taxa at large.

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Fig. 1: Deep divergence, admixture, and new haplotypes of the Manis cf. mysteria lineage shown by various analyses.
Fig. 2: Estimates of genetic divergence between lineages.
Fig. 3: Estimates of genetic diversity within each lineage.

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Data availability

Raw Illumina sequences along with associated metadata of each sample and assembled mitogenomes are deposited in the NCBI Sequence Read Archive and GenBank under BioProject PRJNA1289811.

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Acknowledgements

This work was supported by Research Impact Fund (R7021-20), University Grants Committee, Hong Kong Special Administrative Region (HKSAR). Seized pangolin tissues were donated for use in this study by AFCD and KFBG in Hong Kong, and DENR in the Philippines. Bioinformatic analyses were performed using research computing facilities offered by Information Technology Services, The University of Hong Kong (HKU). We would also like to acknowledge the valuable input from Dr. Simon Sin, Dr. Nina Therkildsen, and Dr. Lidane Noronha regarding the manuscript.

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Authors and Affiliations

  1. School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China

    Portia Y.-H. Wong, Ying Chen, Tracey-Leigh Prigge, Anmol Kanwal, Najeebah Ibnat Fayeeja, Lily Kam Ping Ng, Samuel Yeung, Paolo Momigliano & Timothy C. Bonebrake

  2. Department of Entomology, Cornell University, Ithaca, NY, USA

    Portia Y.-H. Wong

  3. Kadoorie Farm and Botanic Garden, Hong Kong SAR, China

    Huarong Zhang, Liz Rose-Jeffreys & Gary Ades

  4. Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines

    Mariano Roy M. Duya & Ian Kendrich C. Fontanilla

  5. State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China

    Tommy T. Y. Lam

  6. Department of Ecological and Biological Sciences, Tuscia University, Viterbo, Italy

    Paolo Momigliano

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Contributions

PYHW, YC, PM and TCB designed the research. PYHW, TLP, HZ, LRJ, GA, MRMD, IKCF and TCB facilitated and secured the donation of confiscated specimens. PYHW, TLP, AK, NIF, LKPN and SY processed specimens and collected DNA from samples. PYHW, YC, TLP and PM performed the research and conducted the data analysis. TTYL, PM and TCB advised on study design and bioinformatic analyses. PYHW, YC and TCB wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Paolo Momigliano or Timothy C. Bonebrake.

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Wong, P.YH., Chen, Y., Prigge, TL. et al. Seizure samples reveal complex evolutionary dynamics among Southeast Asian pangolins. Heredity (2026). https://doi.org/10.1038/s41437-026-00826-9

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