The Complete Phylogeny of Pangolins: Scaling Up Resources for the Molecular Tracing of the Most Trafficked Mammals on Earth
The Complete Phylogeny of Pangolins: Scaling Up Resources for the Molecular Tracing of the Most Trafficked Mammals on Earth
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DOI：
10.1093/jhered/esx097
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发表时间：
2018-06-01
影响因子：
3.1
通讯作者：
Luo, Shu-Jin
中科院分区：
文献类型：
--
作者：
Gaubert, Philippe;Antunes, Agostinho;Luo, Shu-Jin
穿山甲被认为是地球上被贩卖最多的哺乳动物，现在正迅速走向灭绝。这些非洲和亚洲鳞状身体的食蚁兽中有8个现存物种被普遍认识，但它们的进化关系在很大程度上仍未被探索。在这里，我们提出了最全面的系统发育评估，基于完整的有丝分裂基因组和9个核基因的遗传变异。我们确认亚洲和非洲穿山甲之间的深度差异发生在大约2300万年前(95%HPD=18.7-27.2)之前的渐新世-中新世界线，有限的化石证据表明穿山甲从欧洲扩散。我们识别了包括Manis(亚洲穿山甲)、Smusia(大型非洲穿山甲)和Phataginus(非洲小型穿山甲)在内的3个属，它们最早在中新世中晚期(9.8-13.3 Ma)通过逐渐降温而多样化，与世界范围内哺乳动物的分类多样性相吻合。基于3个属之间较大的有丝分裂组距离(18.3-22.8%)和许多(18)形态特征，我们提出了Phataginae亚科。11月来指定小型非洲穿山甲。与基于形态的文献相比，我们的结果证实厚尾穿山甲(Mams Crassicaudata)是舜达穿山甲(Manis Javanica)和巴拉望穿山甲(Manis Culion Ensis)的姊妹种。有丝分裂组系统发育研究支持另外的穿山甲物种亚类(n=13)，包括6个非洲普通穿山甲(Phataginus Tricuspis)谱系，但这些模式并不完全被我们的多基因座方法支持。最后，我们在穿山甲的所有物种和谱系中确定了5000多个信息的有丝分裂基因组位点和5个核基因的诊断变异，为进一步研究和有效追踪全球穿山甲贸易提供了重要的资源。
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 (Mams 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.