PS 22-56 - Increased genetic diversity identified within lineage of potential fifth Asian pangolin species

Abstract: Identifying and resolving cryptic diversity has important implications for biodiversity conservation and our understanding of biogeographical and evolutionary processes. For species groups that are already threatened, this is particularly critical as it can influence the delineation of conservation and management units, ultimately affecting strategies for effective conservation. Pangolins (Order Pholidota) are the most trafficked mammals in the world and a highly endangered group, but a lot of cryptic diversity within the clade remains unresolved and understudied. Specifically, unique haplotypes based on mitochondrial markers were identified in pangolin scales confiscated by authorities in Hong Kong. This has led to speculation of a potential fifth Asian pangolin species represented by the haplotypes, despite the lack of live specimens bearing the haplotypes or support from genome-wide information. We’ve addressed this knowledge gap by expanding our sampling effort and implementing genome-wide analyses. We sampled Asian pangolin scales from seizures in Hong Kong from 2012 to 2018, on top of sampling the original specimens containing the unique haplotypes. Our approach begins with identifying scales bearing these haplotypes by sequencing the CytB and COI regions of all samples, then proceeding with whole-genome sequencing to obtain genomic information in order to compare with genomes of existing Asian pangolin species. From the 16 sampled seizures, eight scales were found to match the unique haplotypes (n = 3 from 2012, n = 1 from 2013, and n = 4 from 2018), with one scale branching off slightly within the clade in the CytB tree. This suggests that there is more diversity within this clade of pangolins than expected. It remains possible that these scales belong to an undiscovered species that is well distinguished from other species, or that the genetic diversity of Asian pangolins is more complex than currently understood. The fact that scales bearing the haplotypes were found in a 2018 seizure, six years after the original samples were seized, also suggests that this clade, whether a new species or not, continues to exist in the wild and remains exploited, possibly indiscriminately from other Asian pangolin species. Ultimately, these results highlight that these haplotypes are more widespread than expected, as well as the fact that more field sampling and extensive genomic sampling is necessary to fully understand the phylogeny of Asian pangolins and ensure effective conservation of these animals.