化石年代的贝叶斯系统发育估计
Bayesian phylogenetic estimation of fossil ages
摘要：
最近的进展允许形态化石证据和分子序列被集成到一个单一的组合推理的分歧日期下的贝叶斯概率的规则。特别是，离散形态进化的离散化的出生-死亡树先验和Lewis-Mk模型允许的分歧时间和化石和现存类群之间的系统发育关系的估计。我们利用这一统计框架，调查这些模型的内部一致性，通过产生系统发育估计的年龄，每个化石反过来，在两个丰富的和良好的特征数据集的化石和现存物种（企鹅和犬科动物）。结果表明，两组数据的化石年龄估计精度普遍较高，可信区间不排除真实年龄，相对误差中位数分别为5.7%和13.2%。中位相对标准误差（RSD）分别为9.2%和7.2%，表明良好的精密度，但有一些离群值。事实上，在我们分析的两个数据集中，化石年龄的系统发育估计平均< 2 My，从它被挖掘的地质地层的中点年龄。在我们的分析中发现的高水平的内部一致性表明，贝叶斯统计模型采用的是一个足够适合的地质和形态数据，并提供证据，从真实的数据，所使用的框架可以准确地模拟离散的形态特征的进化编码化石和现存的类群。我们预计，这种方法将有不同的应用超出分歧的时间约会，包括约会化石的时间不受约束，测试的“形态时钟”，并发现潜在的模型错误和/或数据错误时，有争议的系统发育假说的基础上结合分歧约会分析。
英文摘要：
Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized data sets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two data sets of 5.7% and 13.2% respectively. The median relative standard error (RSD) was 9.2% and 7.2% respectively, suggesting good precision, although with some outliers. In fact in the two data sets we analyze the phylogenetic estimates of fossil age is on average < 2 My from the midpoint age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the "morphological clock", and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.
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