Phylogeography of the Sunda pangolin, Manis javanica: implications for
taxonomy, conservation management and wildlife forensics
Abstract
Aim: The Sunda pangolin (Manis javanica) is the most widely distributed
Asian pangolin species. It is one of the most trafficked mammals in the
world, which not only negatively impacts wild Sunda pangolin
populations, but also poses a potential disease risk to other species,
including humans and livestock. Despite the imminent threat to the
species’ survival and its prevalence in the wildlife trade, the
phylogeography and evolution of the Sunda pangolin is not well
understood. We aimed to investigate the species’ phylogeography across
its distribution to improve our understanding of the species’
evolutionary history, elucidate any taxonomic uncertainties and enhance
the species’ conservation genetic management and wildlife forensics
applications. Location: Southeast Asia and southern China. Methods: We
sequenced mtDNA genomes from 23 wild Sunda pangolins from Borneo and
Peninsular Malaysia. We used these data in conjunction with previous
generated mtDNA and nuclear datasets from across the species’ range to
perform various phylogenetic and population genetic analyses. Results:
We identified an evolutionarily distinct mtDNA lineage in north Borneo,
which was estimated to be ~1.6 million years divergent
from lineages in west/south Borneo and the mainland, comparable to the
divergence time of the Palawan pangolin. There appeared to be
mitonuclear discordance, with no apparent genetic structure across
Borneo based on analysis of nuclear SNPs. Main conclusions: These
findings are consistent with the ‘out of Borneo hypothesis’, whereby
Sunda pangolins diversified in Borneo before subsequently migrating
throughout Sundaland, and/or a secondary contact scenario between
mainland and Borneo. We have elucidated possible taxonomic issues in the
Sunda/Palawan pangolin complex, and highlight the critical need for
additional georeferenced samples to accurately apportion its range-wide
genetic variation into appropriate taxonomic and conservation units.
Additionally, these data have improved forensic species identification
testing involving these species and permit the implementation of
geographic provenance testing in some scenarios.