Genomic consequences of population decline in critically endangered pangolins and their demographic histories

Abstract

Pangolins are among the most critically endangered animals due to heavy poaching and world wild trafficking. However, their demographic histories and the genomic consequences of their recent population declines remain unknown. We generated high-quality de novo reference genomes for critically endangered Malayan (Manis javanica, MJ) and Chinese (M. pentadactyla, MP) pangolins and re-sequencing population genomic data from 74 MJs and 23 MPs. We recovered the population identities of illegally traded pangolins and previously unrecognized genetic populations that should be protected as evolutionarily distinct conservation units. Demographic reconstruction suggested environmental changes have resulted in population size fluctuation of pangolins. Additionally, recent population size declines due to human activities have resulted in an increase in inbreeding and genetic load.Deleterious mutations were enriched in genes related to cancer/diseases and cholesterol homeostasis, which may have increased their susceptibility to diseases and decreased their survival potential to adapt to environmental changes and high-cholesterol diet. This comprehensive study provides not only high-quality pangolin reference genomes, but also valuable information concerning the driving factors of long-term population size fluctuations and the genomic impact of recent population size declines due to human activities, which is essential for pangolin conservation management and global action planning.

Harbor porpoise losing its edges: genetic time series suggests a rapid population decline in Iberian waters over the last 30 years

“…Indeed, genome-wide data can provide further insights into the temporal dynamics of the Iberian population. For example, the reconstruction of historical demography based on genome-wide data (Liu & Fu, 2020;Schiffels & Wang, 2020;Terhorst et al, 2017) can be used to test whether these harbor porpoises, since their post-glacial emergence (Fontaine, 2016;Fontaine et al, 2014;Fontaine et al, 2010), maintained a longterm low Ne (Morin et al, 2020;Robinson et al, 2019) or if, on the contrary, they declined recently (Hu et al, 2020). A simulation framework, similar to the one developed by Robinson et al (2019), could be used to assess whether these porpoises managed to escape deleterious effects of the mutation load despite their current low Ne or not, as recently suggested for the vaquita (P. sinus; Morin et al, 2020;Robinson et al, 2019).…”

Genetic Diversity, Inbreeding Level, and Genetic Load in Endangered Snub-Nosed Monkeys (Rhinopithecus)

“…We found that genomic inbreeding coefficient (F ROH ) of the snub-nosed monkeys to be between 49.37 and 78.86% ( Figure 2B ). Compared with other critically endangered or endangered species, the genomic inbreeding levels of the snub-nosed monkeys was higher than in the eastern gorillas (F ROH = 34–39%) (Xue et al, 2015 ; Van Der Valk et al, 2019a ), vervets (F ROH = 6–12%) (Van Der Valk et al, 2019a ), and pangolins (F ROH = 12–42%) (Hu et al, 2020 ). These high levels of inbreeding of the snub-nosed monkeys are consistent with recent dramatic population decline (Zhou et al, 2016 ).…”

The high diversity of SARS-CoV-2-related coronaviruses in pangolins alters potential ecological risks

“…The DNA barcoding classification of four pangolin samples (MP20, MJ20, MJ57, and MJ54) was published previously ( Hu et al, 2020 ). An 829 bp region of the mitochondrial COI gene and a 790 bp region of the cyt b gene were sequenced for MJ18007 according to published protocols ( Hu et al, 2020 ; Nash et al, 2018 ). The COI sequence was queried using BLAST searches of GenBank to identify the pangolin species.…”

“…The COI sequence was queried using BLAST searches of GenBank to identify the pangolin species. Mitochondrial DNA clustering based on the COI and cyt b genes was performed according to the protocol used in a reported phylogeographic analysis of pangolins ( Hu et al, 2020 ). M. pentadactyla MP20 was classified into the MPB mt cluster, indicating that it likely originated in Myanmar ( Hu et al, 2020 ).…”