Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of de novo mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation-rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprises nearly half of the primate clade. Using high-coverage linked-read sequencing for a focal quartet of gray mouse lemurs (Microcebus murinus), we estimated the mutation rate to be among the highest calculated for a mammal at 1.52 × 10^–8 (95% credible interval: 1.28 × 10⁻⁸–1.78 × 10⁻⁸) mutations/site/generation. Further, we found an unexpectedly low count of paternal mutations, and only a modest overrepresentation of mutations at CpG sites. Despite the surprising nature of these results, we found both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria. We also sequenced a technical replicate to estimate a false-negative and false-positive rate for our data and show that any point estimate of a de novo mutation rate should be considered with a large degree of uncertainty. For validation, we conducted an independent analysis of context-dependent substitution types for gray mouse lemur and five additional primate species for which de novo mutation rates have also been estimated. These comparisons revealed general consistency of the mutation spectrum between the pedigree-based and the substitution-rate analyses for all species compared.

突变是进化起作用的原材料，了解突变的频率和基因组分布对于理解进化如何在长和短时间尺度上运作至关重要。目前，已经在相对较少的谱系中直接表征了从头突变的速率和谱。我们的研究首次对链球菌（即狐猴和懒猴）的突变率进行了直接估计，链球菌几乎占灵长类进化枝的一半。通过对灰鼠狐猴（ Microcebus murinus ）的四个焦点进行高覆盖率的连锁读测序，我们估计突变率是哺乳动物中计算出的最高突变率之一，为 1.52 × 10 ^–8 （95% 可信区间：1.28 × 10 ⁻⁸ –1.78 × 10 ⁻⁸ ) 突变/位点/代。此外，我们发现父系突变数量出乎意料地低，并且 CpG 位点的突变仅适度高表达。尽管这些结果令人惊讶，但我们发现速率和频谱对于各种计算过滤标准的操作都是稳健的。我们还对技术重复进行了测序，以估计我们数据的假阴性和假阳性率，并表明对从头突变率的任何点估计都应考虑很大程度的不确定性。为了验证，我们对灰鼠狐猴和其他五种灵长类动物的上下文相关替代类型进行了独立分析，还估计了这些物种的从头突变率。这些比较揭示了所有比较物种的基于谱系的分析和替代率分析之间的突变谱的总体一致性。