Scientific publications
2023PreprintEnglishOpen access
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Scientific publications
Sean P. Heighton* (Corresponding author)
Other affiliations: Université Toulouse III - Paul Sabatier · Evolution et Diversité Biologique · Institut de Recherche pour le Développement
Rémi Allio
Other affiliations: Université de Montpellier · Institut des Sciences de l'Evolution de Montpellier · Institut de Recherche pour le Développement
Jérôme Murienne
Other affiliations: Université Toulouse III - Paul Sabatier · Evolution et Diversité Biologique · Institut de Recherche pour le Développement
Jordi Salmona
Other affiliations: Université Toulouse III - Paul Sabatier · Evolution et Diversité Biologique · Institut de Recherche pour le Développement
Céline Scornavacca
Other affiliations: Université de Montpellier · Institut des Sciences de l'Evolution de Montpellier · Institut de Recherche pour le Développement
Marie‐Ka Tilak
Other affiliations: Université de Montpellier · Institut des Sciences de l'Evolution de Montpellier · Institut de Recherche pour le Développement
Frédéric Delsuc* (Corresponding author)
Other affiliations: Université de Montpellier · Institut des Sciences de l'Evolution de Montpellier · Institut de Recherche pour le Développement
Philippe Gaubert* (Corresponding author)
Other affiliations: Université Toulouse III - Paul Sabatier · Universidade do Porto · Evolution et Diversité Biologique · Institut de Recherche pour le Développement
Hao Meng
Other affiliations: Center for Life Sciences
Shu‐Jin Luo* (Corresponding author)
Other affiliations: Center for Life Sciences
Armanda D. S. Bastos
Darren W. Pietersen
bioRxiv (Cold Spring Harbor Laboratory)
Summary Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and medicinal properties. Despite their great conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3 238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera of pangolins, and highlighted the existence of an undescribed species closely related to South-East Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of South-East Asian pangolins, provides new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental vs . island populations and species lineages, suggesting that conservation planning should consider intra-specific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet been realized in pangolins, we recommend that populations are genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors required for conserving pangolins, including tracing their illegal trade. These include the completion of whole-genomes for pangolins through the first reference genome with long reads for the giant pangolin ( Smutsia gigantea ) and new draft genomes (~43x–77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.