Data from: Phylogeny of Trichoptera (caddisflies): characterization of signal and noise within multiple datasets
Kjer, Karl M.; Blahnik, Roger J.; Holzenthal, Ralph W. (2009), Data from: Phylogeny of Trichoptera (caddisflies): characterization of signal and noise within multiple datasets, Dryad, Dataset, https://doi.org/10.5061/dryad.694
Trichoptera are holometabolous insects with aquatic larvae that, together with the Lepidoptera, comprise the Amphiesmenoptera. Despite extensive previous morphological work, there has been little phylogenetic agreement over the relationship among the three suborders: Annulipalpia, Spicipalpia, and Integripalpia, and conflict over the monophyly of Spicipalpia. In an effort to resolve this conflict, we sequenced fragments of the large and small subunit nuclear ribosomal RNAs (1078 nts; D1, D3, V4-5), the nuclear Elongation factor 1α gene (1098 nts), and a fragment of mitochondrial COI (411 nts). Seventy adult and larval morphological characters were re-analyzed and added to molecular data in a combined analysis. We evaluated signal and homoplasy in each of the molecular datasets, and attempted to rank the particular datasets according to how approriate they were for inferring relationhip among suborders. This evaluation included testing for conflict among datasets, comparing tree lengths among alternative hypotheses, measuring the left-skew of tree-length distributions from maximally divergent sets of taxa, evaluating the recovery of expected clades, visualizing whether or not substitutions were accumulating with time, and estimating nucleotide compositional bias. All these measures cast doubt on the reliability of the deep-level signal coming from the nucleotides of the COI and EF-1α genes, yet these data could still be included in combined analyses without overturning the results from the most conservative marker; the rRNA. The different datasets were found to be evolving under extremely different rates. A site-specific likelihood method for dealing with combined data when parameters are non-overlapping was proposed, and a similar weighting scheme under parsimony was evaluated. Among our phylogenetic conclusions, we found Annulipalpia to be the most basal of the three suborders, with Spicipalpia and Integripalpia forming a clade. Monophyly of Annulipalpia and Integripalpia was confirmed, while the relationships among spicipalpians remain equivocal.