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For the morphological trees, it was never observed that lice from different microhabitat specializations, but from the same host group, were sister taxa, and this was well within the distribution of random trees.
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If we assume that the molecular tree reflects the true evolutionary species tree better than the morphological tree it becomes clear that some homology assessments of the morphological characters must be incorrect.
These results indicate that over the molecular tree, host group is strongly correlated with the phylogeny, while over the morphological tree it is not.
However, given the level of interest in the conflict between molecular and morphological trees [ 53, 54], it will be interesting to revisit the issue with new datasets in the future.
Overall, the Smerinthinae+Sphinginae lineage most closely matches the morphological trees of Rothschild and Jordan [1], and Nakamura [44], but as yet no definitive morphological synapomorphy is known.
For primates, carnivorans and cetaceans (excluding artiodactyls, which are not represented as well in this study) good morphological trees or super trees (combining molecular and morphological data) are available for comparison with the molecular data from this study [2], [5], [11], [30], [56] [66].
Creating morphological trees served multiple purposes in our module.
These randomizations suggest that over the morphological trees, microhabitat specialization was strongly correlated with the phylogeny.
We counted the number of times this occurred for both the molecular and morphological trees.
We then mapped these four character states over both the molecular and morphological trees using parsimony.
To make the molecular and morphological trees directly comparable, each morphological group was ascribed a single mtDNA sequence.
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