Data from: Resolving the phylogenetic position of Darwin’s extinct ground sloth (Mylodon darwinii) using mitogenomic and nuclear exon data

Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first discovered its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12,880 year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient sub-fossil, likely the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA with 22% of the assembled metagenomic contigs assigned to Xenarthra. Additionally, we enriched over 15 kilobases of sequence data from seven nuclear exons, using target sequence capture designed against a wide xenarthran dataset. Phylogenetic and dating analyses of the mitogenomic dataset including all extant species of xenarthrans and the assembled nuclear supermatrix unambiguously place Mylodon darwinii as the sister-group of modern two-fingered sloths from which it diverged around 22 million years ago. These congruent results from both the mitochondrial and nuclear data support the diphyly of the two modern sloths lineages, implying the convergent evolution of their unique suspensory behaviour as an adaption to arboreality. Our results offer promising perspectives for whole genome sequencing of this emblematic extinct taxon.

达尔文大地懒（Mylodon darwinii）是一种已灭绝的巨型大地懒，其名称源自查尔斯·达尔文——达尔文最早在南美洲发现了该物种的遗骸。本研究通过对采自智利迈洛顿洞穴（Mylodon Cave）中一块距今12880年的骨碎片进行Illumina鸟枪测序，成功获得了覆盖度达99倍的高质量线粒体基因组。该样本的DNA损伤水平极低，表明作为一件古代亚化石，它的保存状态异常完好，这大概率得益于洞穴内持续的干燥寒冷环境。据此，对本研究的鸟枪宏基因组数据进行分类学评估显示，内源DNA占比极高，组装得到的宏基因组重叠群（contigs）中有22%被归类到异关节总目（Xenarthra）。此外，本研究利用针对广谱异关节类数据集设计的靶向序列捕获技术，从7个核外显子中富集了超过15千碱基对的序列数据。对包含所有现生异关节类物种的线粒体基因组数据集以及组装得到的核超级矩阵开展的系统发育与定年分析明确显示：达尔文大地懒是现代二趾树懒的姊妹群，二者的分化时间约为2200万年前。线粒体与核基因组数据得到的这些一致结果，支持了现代树懒两个支系的双系类群属性，表明二者为适应树栖生活而演化出的独特悬挂行为属于趋同演化。本研究结果为这一标志性已灭绝类群的全基因组测序提供了极具前景的研究方向。