Supplementary material from "Differences between hard and soft phylogenetic data"

When building the tree of life, variability of phylogenetic signal is often accounted for by partitioning gene sequences and testing for differences. The same considerations, however, are rarely applied to morphological data, potentially undermining its use in evolutionary contexts. Here, we apply partition heterogeneity tests to 59 animal datasets to demonstrate that significant differences exist between the phylogenetic signal conveyed by ‘hard’ and ‘soft’ characters (bones, teeth and shells versus myology, integument etc). Furthermore, the morphological partitions differ significantly in their consistency relative to independent molecular trees. The observed morphological differences correspond with missing data biases, and as such their existence presents a problem not only for phylogeny reconstruction, but also for interpretations of fossil data. Evolutionary inferences drawn from clades in which hard, readily fossilizable characters are relatively less consistent and different from other morphology (mammals, bivalves) may be less secure. More secure inferences might be drawn from the fossil record of clades that exhibit fewer differences, or exhibit more consistent hard characters (fishes, birds). In all cases, it will be necessary to consider the impact of missing data on empirical data, and the differences that exist between morphological modules.