Data_Sheet_2_Ancient DNA From Museum Specimens and Next Generation Sequencing Help Resolve the Controversial Evolutionary History of the Critically Endangered Puebla Deer Mouse.PDF

Key insights into the evolutionary history of recently extinct or critically endangered species can be obtained through analysis of genomic data collected using high-throughput sequencing and ancient DNA from museum specimens, particularly where specimens are rare. For instance, the evolutionary history of the critically endangered Puebla deer mouse, Peromyscus mekisturus, remains unclear due to discordance between morphological and molecular phylogenetic analyses. However, previous molecular analyses were based on PCR and Sanger sequencing of only a few mitochondrial genes. Here, we used ancient DNA from historical museum specimens followed by target enrichment and high-throughput sequencing of several thousand nuclear ultraconserved elements and whole mitochondrial genomes to test the validity of the previous phylogenetic placement of P. mekisturus. Based on UCEs and mitogenomes, our results revealed that P. mekisturus forms a well-supported distinct lineage outside the clade containing all other members of the Peromyscus melanophrys group. Additionally, the mitogenome phylogeny further supports the placement of P. mekisturus as the sister species of the genus Reithrodontomys. This conflicts with the previous mtDNA phylogenetic reconstruction, in which P. mekisturus was nested within the species P. melanophrys. Our study demonstrates that high-throughput sequencing of ancient DNA, appropriately controlling for contamination and degradation, can provide a robust resolution of the evolutionary history and taxonomic status of species for which few or no modern genetic samples exist. In light of our results and pending further analysis with denser taxon sampling and the addition of morphological data, a re-evaluation of the taxonomy and conservation management plans of P. mekisturus is needed to ensure that the evolutionary distinctiveness of this species is recognized in future conservation efforts.

通过对利用高通量测序（high-throughput sequencing）和博物馆标本中古DNA（ancient DNA）获取的基因组数据开展分析，可获取新近灭绝或极度濒危物种演化历史的关键洞见，尤其在标本稀缺的场景下优势尤为突出。例如，极度濒危的普埃布拉鹿鼠（Peromyscus mekisturus）的演化历史至今仍不明确，原因是其形态学与分子系统发育分析结果存在冲突。既往分子研究仅基于聚合酶链式反应（PCR）与桑格测序（Sanger sequencing）技术，对少数线粒体基因开展分析。本研究采用历史博物馆标本中的古DNA，通过目标富集（target enrichment）与高通量测序，获得了数千个核超保守元件（ultraconserved elements, UCEs）以及完整线粒体基因组（mitogenomes），以此验证普埃布拉鹿鼠此前的系统发育定位是否合理。基于超保守元件与线粒体基因组的分析结果显示，普埃布拉鹿鼠构成了一个得到强力支持的独立演化支，其所处分支的外类群包含黑眼鹿鼠类群（Peromyscus melanophrys group）的所有其他成员。此外，线粒体基因组系统发育分析进一步支持普埃布拉鹿鼠作为美洲禾鼠属（Reithrodontomys）姐妹种的分类定位。这一结论与此前基于线粒体DNA的系统发育重建结果相悖，后者将普埃布拉鹿鼠归入黑眼鹿鼠（P. melanophrys）类群内部。本研究证实，在妥善控制污染与降解问题的前提下，对古DNA开展高通量测序，可为缺乏或几乎无现代遗传样本的物种提供可靠的演化历史与分类地位解析。结合本研究结果，并待未来开展更密集的类群采样与补充形态学数据分析后，需对普埃布拉鹿鼠的分类学与保护管理计划进行重新评估，以确保该物种的演化独特性在未来的保护工作中得到认可。