PDF(Pubmed)
Abstract：
Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their 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 extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. 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. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome 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.
摘要：
穿山甲是一组有鳞的哺乳动物，它们的肉类和所谓的药用特性以创纪录的数量被贩运。尽管他们关心保护，对它们进化的了解受到缺乏基因组数据的限制。我们的目标是产生详尽的基因组资源，其中包括3,238个直系同源基因和全基因组多态性，以评估所有八个现存穿山甲物种的进化。强大的基于直系同源基因的系统发育恢复了三个属的单系，并强调了与东南亚穿山甲密切相关的未描述物种的存在。在已灭绝的人之间出现了中，中，上新世混合物的特征，可能是欧洲的,东南亚穿山甲的血统和祖先，为该群体的早期进化史提供新的见解。人口统计轨迹和全基因组杂合度估计揭示了大陆与岛屿种群和物种谱系之间的对比，建议保护规划应考虑种内模式。随着最近基因组多样性的预期损失，在穿山甲中尚未实现广泛的贩运，我们建议对人群进行基因调查，以预测非法贸易的任何有害影响。最后,我们生产了一套完整的基因组资源，这些资源将成为穿山甲未来保护管理和法医工作不可或缺的一部分，包括追踪他们的非法贸易.这些包括通过巨大穿山甲（Smutsiagigantea）的第一个参考基因组的杂交组装完成穿山甲的全基因组和四个其他物种的新基因组草案（43x-77x），以及具有超过340万个多态性位点的直系同源基因数据库。
