Seizure samples reveal complex evolutionary dynamics among Southeast Asian pangolins.

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.