Ancient DNA (aDNA) is increasingly being used to investigate questions such as the phylogenetic relationships and divergence times of extant and extinct species. If aDNA samples are sufficiently old, expected branch lengths (in units of nucleotide substitutions) are reduced relative to contemporary samples. This can be accounted for by incorporating sample ages into phylogenetic analyses. Existing methods that use tip (sample) dates infer gene trees rather than species trees, which can lead to incorrect or biased inferences of the species tree. Methods using a multispecies coalescent (MSC) model overcome these issues. We developed an MSC model with tip dates and implemented it in the program bpp. The method performed well for a range of biologically realistic scenarios, estimating calibrated divergence times and mutation rates precisely. Simulations suggest that estimation precision can be best improved by prioritizing sampling of many loci and more ancient samples. Incorrectly treating ancient samples as contemporary in analyzing simulated data, mimicking a common practice of empirical analyses, led to large systematic biases in model parameters, including divergence times. Two genomic datasets of mammoths and elephants were analyzed, demonstrating the method’s empirical utility.

中文翻译：

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多物种与古代 DNA 序列合并下的贝叶斯推理


古代 DNA （aDNA） 越来越多地用于研究现存和已灭绝物种的系统发育关系和分化时间等问题。如果 aDNA 样品足够古老，则相对于当代样品，预期的分支长度（以核苷酸替换为单位）会减少。这可以通过将样本年龄纳入系统发育分析来解释。使用 tip（样本）日期的现有方法推断的是基因树而不是物种树，这可能导致物种树的推断不正确或有偏差。使用多物种聚结 （MSC） 模型的方法克服了这些问题。我们开发了一个带有针尖日期的 MSC 模型，并在程序 bpp 中实施它。该方法在一系列生物学上真实的场景中表现良好，精确估计了校准的分歧时间和突变率。模拟表明，通过优先对许多基因座和更古老的样本进行采样，可以最好地提高估计精度。在分析模拟数据时，错误地将古代样本视为当代样本，模仿实证分析的常见做法，导致模型参数（包括发散时间）出现巨大的系统偏差。分析了猛犸象和大象的两个基因组数据集，证明了该方法的实证效用。