Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees

Reconstructing evolutionary histories requires accurate phylogenetic trees. Recent simulation studies suggest that probabilistic phylogenetic analyses of morphological data are more accurate than traditional parsimony techniques. Here we use empirical data to compare Bayesian and parsimony phylogenies in terms of their congruence with the distribution of age ranges of the component taxa. Analysis of 167 independent morphological data matrices of fossil tetrapods finds that Bayesian trees exhibit significantly lower stratigraphic congruence than the equivalent parsimony trees. As such, taking stratigraphic data as an independent benchmark indicates that parsimony analyses are more accurate for phylogenetic reconstruction of morphological data. The discrepancy between simulated and empirical studies may result from historic data peaking practises or some complexities of empirical data as yet unaccounted for.

重建演化历史离不开精准的系统发育树（phylogenetic tree）。近期的模拟研究表明，针对形态学数据的概率型系统发育分析，其准确性要优于传统的简约法（parsimony）分析技术。本研究采用实证数据，以各组成类群（taxon）的时限分布作为参照，对比贝叶斯系统发育树与简约法系统发育树的一致性表现。通过对167组独立的化石四足动物形态学数据矩阵开展分析，结果显示贝叶斯系统发育树的地层一致性（stratigraphic congruence）显著低于对应的简约法系统发育树。据此，若以地层数据作为独立基准，则可证明简约法分析在形态学数据的系统发育重建任务中具备更高准确性。模拟研究与实证研究间的结论差异，可能源于历史数据峰值处理实践的局限，抑或是实证数据中存在尚未被纳入考量的复杂特性。