1. Indices of morphological disparity seek to summarise the highly multivariate morphological variation across groups of species within clades, time bins or other groups. Morphological variation can be quantified using geometric morphometric, outline or surface-based methods. These are most effective when morphological differences are relatively modest and there are numerous ubiquitous landmarks and phase-aligned features of shape variation. The most disparate samples, such as those across classes and phyla, typically necessitate the use of discrete characters. Unfortunately, such characters are often compiled subjectively in a manner reflecting the level of morphological and taxonomic focus and the intensity of taxon sampling.

2. Sampling intensity is often highly variable within a single data set, especially in repurposed and amalgamated cladistic matrices. Here we propose indices of molecular disparity analogous to those of morphological disparity. Molecular sequence data can be obtained in a more objective, automated and scaleable manner than morphological data.

3. Comparisons of the morphological and molecular disparity of subclades in sixteen large data sets suggest that molecular disparity is less susceptible to sampling biases than morphological disparity. Moreover, distance matrices inferred from individual genes tend to correlate strongly with each other and with distances from all concatenated genes. By contrast, morphological and molecular disparity are typically not significantly correlated across subclades, such that comparisons for groups can help to give a fuller picture of their evolution. Within mammals, Afrotheria have conspicuously high morphological disparity but modest molecular disparity, suggesting unusually high morphological plasticity. Even more strikingly, the molecular disparity of rodents is over five times that for Artiodactyla, despite having only half of their morphological disparity. These contrasts suggest the differential operation of geometric, biomechanical, ontogenetic and environmental constraints on form.

4. Given the increasing abundance of total evidence data sets in the literature and the widespread and sometimes uncritical repurposing of discrete morphological characters, we propose the comparison of morphological and molecular disparity as a useful tool to understand subclade evolution more fully.  

This dataset was collated from 16 published total evidence datasets. Hereby we supply the molecular and morphological character data for each dataset as well as the associated phylogeny and GTR distance file in CSV format.

Discrete character and DNA alignment files can be opened with Mesquite (nexus format) or with the R packages Claddis and Ape.