Abstract
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 practices or some complexities of empirical data as yet unaccounted for.
Highlights
Phylogenetic trees are vital for reconstructing evolutionary events
The metrics use the proportion of tree nodes that are stratigraphically congruent (SCI), or various relationships between the sum of unobserved ghost ranges and sum of observed ranges (RCI), or minimum possible ghost ranges (MSM*) and maximum possible ghost ranges (GER)
Adding the presence or the absence of a tree figure optimized to stratigraphic ranges in the original publication as an explanatory variable (Strat_Fig) increased the fit of the linear mixed-effect models (ANOVA p, 0.0001 for all four metrics); this variable was not significant, but its interaction with tree search method was ( p, 2 Â 10216 for all four metrics)
Summary
Phylogenetic trees are vital for reconstructing evolutionary events. Vital for reconstructing evolutionary history, but there is disagreement over which method is most appropriate. Homoplasy and non-independence of morphological characters are pervasive due to subjective and oversaturated character identification, and functional, ecological and developmental linkage [5,6,7,8]. These problematic phenomena are not evenly distributed across clades, characters and regions; differences exist between hard and soft characters [9,10], teeth and bones [11], and crania and post-crania [12]. By contrast, simulated characters are effectively homogeneous, because they are selected from the same underlying model
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