Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions

Discrete character-taxon matrices are increasingly being used in an attempt to understand the pattern and tempo of morphological evolution; however, methodological sophistication and bespoke software implementations have lagged behind. In the present study, an attempt is made to provide a state-of-the-art description of methodologies and introduce a new R package (Claddis) for performing foundational disparity (morphologic diversity) and rate calculations. Simulations using its core functions show that: (1) of the two most commonly used distance metrics (Generalized Euclidean Distance and Gower's Coefficient), the latter tends to carry forward more of the true signal; (2) a novel distance metric may improve signal retention further; (3) this signal retention may come at the cost of pruning incomplete taxa from the data set; and (4) the utility of bivariate plots of ordination spaces are undermined by their frequently extremely low variances. By contrast, challenges to estimating morphol...