Population genomics and illegal trade of critically endangered Asian pangolins

Abstract

Illegal wildlife trade is recognized as one of the key global threats to biodiversity, as it not only causes serious population decline, it can also lead to evolutionary change and ecosystem-level effects. While taxa threatened by wildlife trade are a conservation priority, collecting data for taxa that are understudied can be difficult, especially when they are already threatened in the wild. The use of conservation genomics methods on seizure materials can circumvent these difficulties by obtaining ecological and evolutionary information through molecular methods, as well as reveal mechanisms and dynamics of trade. Asian pangolins (genus Manis) are a clade of mammals that are highly threatened by wildlife trade, but are also understudied. In this thesis, I use conservation genomics on seizure materials of Asian pangolins to fill in gaps in population structure and evolutionary information of the clade, as well as better understand the associated trade dynamics in Southeast Asia. In my first data chapter, I use broadly sampled Sunda pangolin (Manis javanica) seizure scales to construct a comprehensive picture of the species’ population structure using whole genome information. Using whole genomes from 125 individuals, my results show four distinct genetic populations across its range, identifying a distinct population in Java not previously recognized. Additionally, by comparing seizure location and population origin of these seized pangolins, I identified two distinct trafficking routes for the species that can be targeted to halt future trafficking efforts. In my second data chapter, I use whole genome data and broadly sampled Asian pangolin scales to verify whether the putative “fifth Asian pangolin species” harbours a genomic signal distinct from the Sunda pangolin. From whole genomes of 12 “fifth Asian pangolin species” individuals and 16 Sunda pangolin individuals, my results show that while these two putative species are genomically distinct, divergence may be recent and that there may be ongoing gene flow between the two clades. Additionally, I found evidence through broad sampling of seizures that there is previously undocumented but considerable diversity within the clade, and that its associations with the Sunda pangolin trade may be the key to finding the putative species in the wild. As a whole, my thesis adds to the growing database of genomic information on Asian pangolins, but it also shows the incredible utility of conservation genomics methods on seizure materials for both eco-evolutionary and conservation questions.