Phenotypic characters of static homology increase phylogenetic stability under direct optimization of otherwise dynamic homology characters

Abstract

Direct optimization of unaligned sequence characters provides a natural framework to explore the sensitivity of phylogenetic hypotheses to variation in analytical parameters. Phenotypic data, when combined into such analyses, are typically analyzed with static homology correspondences unlike the dynamic homology sequence data. Static homology characters may be expected to constrain the direct optimization and thus, potentially increase the similarity of phylogenetic hypotheses under different cost sets. However, whether a total-evidence approach increases the phylogenetic stability or not remains empirically largely unexplored. Here, I studied the impact of static homology data on sensitivity using six empirical data sets composed of several molecular markers and phenotypic data. The inclusion of static homology phenotypic data increased the average stability of phylogenetic hypothesis in five out of the six data sets. To investigate if any static homology characters would have similar effect, the analyses were repeated with randomized phenotypic data, and with one of the molecular markers fixed as static homology characters. These analyses had, on average, almost no effect on the phylogenetic stability, although the randomized phenotypic data sometimes resulted in even higher stability than empirical phenotypic data. The impact was related to the strength of the phylogenetic signal in the phenotypic data: higher average jackknife support of the phenotypic tree correlated with stronger stabilizing effect in the total-evidence analysis. Phenotypic data with a strong signal made the total-evidence trees topologically more similar to the phenotypic trees, thus, they constrained the dynamic homology correspondences of the sequence data. Characters that increase phylogenetic stability are particularly valuable for phylogenetic inference. These results indicate an important role and additive value of phenotypic data in increasing the stability of phylogenetic hypotheses in total-evidence analyses.