Data from: Comparative and population mitogenomic analyses of Madagascar’s extinct, giant ‘subfossil’ lemurs

Humans first arrived on Madagascar only a few thousand years ago. Subsequent habitat destruction and hunting activities have had significant impacts on the island's biodiversity, including the extinction of megafauna. For example, we know of 17 recently extinct ‘subfossil’ lemur species, all of which were substantially larger (body mass ∼11–160 kg) than any living population of the ∼100 extant lemur species (largest body mass ∼6.8 kg). We used ancient DNA and genomic methods to study subfossil lemur extinction biology and update our understanding of extant lemur conservation risk factors by i) reconstructing a comprehensive phylogeny of extinct and extant lemurs, and ii) testing whether low genetic diversity is associated with body size and extinction risk. We recovered complete or near-complete mitochondrial genomes from five subfossil lemur taxa, and generated sequence data from population samples of two extinct and eight extant lemur species. Phylogenetic comparisons resolved prior taxonomic uncertainties and confirmed that the extinct subfossil species did not comprise a single clade. Genetic diversity estimates for the two sampled extinct species were relatively low, suggesting small historical population sizes. Low genetic diversity and small population sizes are both risk factors that would have rendered giant lemurs especially susceptible to extinction. Surprisingly, among the extant lemurs, we did not observe a relationship between body size and genetic diversity. The decoupling of these variables suggests that risk factors other than body size may have as much or more meaning for establishing future lemur conservation priorities.

人类首次抵达马达加斯加仅在数千年前。随后的栖息地破坏与狩猎活动对该岛的生物多样性造成了显著影响，其中包括巨型动物群（megafauna）的灭绝。例如，目前已知有17种近期灭绝的亚化石狐猴（subfossil lemur）物种，所有这些物种的体型均显著大于现存的约100种狐猴的任何种群：前者体重介于11至160千克，而现存狐猴的最大体重仅约6.8千克。
本研究借助古DNA（ancient DNA）与基因组学方法，探究亚化石狐猴的灭绝生物学，并更新我们对现存狐猴保护风险因子的认知，具体通过以下两项工作达成：其一，重建灭绝与现存狐猴的全面系统发育树；其二，验证低遗传多样性是否与体型大小及灭绝风险存在关联。
本研究从5个亚化石狐猴类群中获取了完整或近乎完整的线粒体基因组（mitochondrial genome），并从2种已灭绝狐猴与8种现存狐猴的种群样本中生成了序列数据。系统发育比较分析解决了此前的分类学悬案，并证实已灭绝的亚化石狐猴并非单系群（clade）。
两种被采样的已灭绝狐猴的遗传多样性估计值相对较低，这表明它们的历史种群规模偏小。低遗传多样性与种群规模偏小均为风险因子，这使得巨型狐猴尤其容易走向灭绝。令人意外的是，在现存狐猴类群中，我们未发现体型大小与遗传多样性之间存在关联。这些变量之间的解耦现象表明，除体型大小外的其他风险因子，在确立未来狐猴保护优先级时或许具有同等乃至更高的参考价值。