New paper on pangolin phylogenomics and reference genome for the giant pangolin (Smutsia gigantea)
Rémi, Marie-Ka, and Frédéric participated in a work on the phylogeny and evolution of all living pangolin species now published in Molecular Biology and Evolution (doi:10.1093/molbev/msad190).
For this collaborative paper, we sequenced, assembled, and annotated the first reference genome for the giant pangolin (Smutsia gigantea) obtained using a hybrid assembly approach combining long Nanopore reads and short Illumina reads developed for the ConvergeAnt project. This resulted in a high quality reference genome for the only missing genus of living pangolins. Combining these data with four new draft genomes of additional species and previously available genomic data we assembled a phylogenomic dataset to assess the evolution of all eight extant pangolin species. Our phylogenomic reconstructions recovered the monophyly of the three genera (Manis, Phataginus, and Smutsia) and highlighted the existence of a yet undescribed species closely related to Southeast Asian pangolins. We also found signatures of admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, providing new insights into the early evolutionary history of the group. From the conservation point of view, demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. With this study, we provided a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade.
This paper was a collaboration with Sean Heighton and Philippe Gaubert (Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier, Toulouse, France) and Shu-Jin Luo (Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China).
Heighton S.P.*, Allio R.*, Murienne J., Salmona J., Meng H., Scornavacca C., Bastos A.D.S., Njiokou F., Pietersen D., Tilak M.-K., Luo S.-J.*, Delsuc F.* & Gaubert P.* (2023). Pangolin genomes offer key insights and resources for the world's most trafficked wild mammals. Molecular Biology and Evolution 40:msad190. doi:10.1093/molbev/msad190
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