Data from: Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods

The increasing ability to extract and sequence DNA from non-contemporaneous tissue offers biologists the opportunity to analyze ancient DNA (aDNA) together with modern DNA (mDNA) to address the taxonomy of extinct species, evolutionary origins, historical phylogeography and biogeography. Perhaps more exciting are recent developments in coalescence-based Bayesian inference that offer the potential to use temporal information from aDNA and mDNA for the estimation of substitution rates and divergence dates as an alternative to fossil and geological calibration. This comes at a time of growing interest in the possibility of time dependency for molecular rate estimates. Here we provide a critical assessment of Bayesian MCMC analysis for the estimation of substitution rate using simulated samples of aDNA and mDNA. We conclude that the current models and priors employed in Bayesian MCMC analysis of heterochronous mtDNA are susceptible to an upward bias in the estimation of substitution rates due to model misspecification when the data comes from populations with less than simple demographic histories, including sudden short-lived population bottlenecks or pronounced population structure. However when model misspecification is only mild, then the 95% HPD intervals provide adequate frequentist coverage of the true rates.

从非同期组织中提取并测序DNA的技术能力不断增强，为生物学家提供了将古代DNA（aDNA）与现代DNA（mDNA）结合分析的契机，以解决灭绝物种分类学、演化起源、历史系统地理学及生物地理学相关问题。或许更令人振奋的是，基于溯祖理论的贝叶斯推断领域近期取得的进展，该方法可利用aDNA与mDNA携带的时序信息，估算分子替换速率与分化时间，作为化石与地质校准的替代方案。这一进展恰逢学界对分子速率估算的时间依赖性可能性关注度与日俱增之际。本研究通过模拟生成的aDNA与mDNA样本，对用于估算替换速率的贝叶斯马尔可夫链蒙特卡洛（Bayesian MCMC）分析展开批判性评估。研究表明，当数据来自非简单种群历史动态的类群（包括突发性短期种群瓶颈或显著种群结构）时，针对异时性线粒体DNA（mtDNA）的贝叶斯MCMC分析中所采用的现有模型与先验分布，易因模型误设导致替换速率估算出现正向偏倚。但当模型误设程度较轻时，95%最高后验密度（HPD）区间可对真实替换速率提供足够的频率学派覆盖度。