The Complete Phylogeny of Pangolins: Scaling Up Resources for the Molecular Tracing of the Most Trafficked Mammals on Earth

• Published in: The Journal of heredity Vol. 109; no. 4; pp. 347 - 359
• Main Authors: Gaubert, Philippe, Antunes, Agostinho, Meng, Hao, Miao, Lin, Peigné, Stéphane, Justy, Fabienne, Njiokou, Flobert, Dufour, Sylvain, Danquah, Emmanuel, Alahakoon, Jayanthi, Verheyen, Erik, Stanley, William T, O’Brien, Stephen J, Johnson, Warren E, Luo, Shu-Jin
• Format: Journal Article
• Language: English
• Published: US Oxford University Press 11.05.2018; Oxford University Press (OUP)
• Subjects: Earth Sciences; Paleontology; Sciences of the Universe; Phatagininae subfam. nov; species delimitation; wildlife trade; diversification scenario; molecular phylogenetics; Pholidota
• ISSN: 0022-1503; 1465-7333; 1471-8505
• DOI: 10.1093/jhered/esx097

Abstract Pangolins, considered the most-trafficked mammals on Earth, are rapidly heading to extinction. Eight extant species of these African and Asian scale-bodied anteaters are commonly recognized, but their evolutionary relationships remain largely unexplored. Here, we present the most comprehensive phylogenetic assessment of pangolins, based on genetic variation of complete mitogenomes and 9 nuclear genes. We confirm deep divergence among Asian and African pangolins occurring not later than the Oligocene-Miocene boundary ca. 23 million years ago (Ma) (95% HPD = 18.7–27.2), limited fossil evidence suggesting dispersals from Europe. We recognize 3 genera including Manis (Asian pangolins), Smutsia (large African pangolins), and Phataginus (small African pangolins), which first diversified in the Middle-Upper Miocene (9.8–13.3 Ma) through a period of gradual cooling coinciding with a worldwide taxonomic diversification among mammals. Based on large mitogenomic distances among the 3 genera (18.3–22.8%) and numerous (18) morphological traits unique to Phataginus, we propose the subfamily Phatagininae subfam. nov. to designate small African pangolins. In contrast with the morphological-based literature, our results establish that the thick-tailed pangolin (Manis crassicaudata) is sister-species of the Sunda (Manis javanica) and Palawan (Manis culionensis) pangolins. Mitogenomic phylogenetic delineations supported additional pangolin species subdivisions (n = 13), including 6 African common pangolin (Phataginus tricuspis) lineages, but these patterns were not fully supported by our multi-locus approach. Finally, we identified more than 5000 informative mitogenomic sites and diagnostic variation from 5 nuclear genes among all species and lineages of pangolins, providing an important resource for further research and for effectively tracing the worldwide pangolin trade.