Abstract
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.
Highlights
Phylogenetic trees are vital for inferring patterns and rates of evolutionary change and for testing evolutionary hypotheses
That differences between classes of morphological data exist is problematic in and of itself, and those differences need to be recognized and accounted for. It is especially problematic in instances where those differences correspond with missing data biases; if only some selected subset of data is available for phylogenetic inference, and that subset is not representative of the complete phylogenetic data as a whole, the resultant trees will be systematically distorted
The incongruence relationship difference test (IRD) test is analogous to the incongruence length difference (ILD) in that it compares the original character partitions with repeatedly randomized partitions of equivalent size, but differs in that it uses tree-to-tree metrics rather than sums of tree lengths
Summary
Phylogenetic trees are vital for inferring patterns and rates of evolutionary change and for testing evolutionary hypotheses. We test whether any differences are distributed evenly or whether they are concentrated in particular animal clades These combined analyses constitute the first systematic and taxonomically inclusive exploration of differences in phylogenetic signal between fossilizable and less-fossilizable morphological characters. By systematically addressing these questions in a disparate and wide-ranging sample of groups at different taxonomic levels, our conclusions will be relevant to a large breadth of the metazoan fossil record rather than just a few limited case studies
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