Data from: Assessing support for Blaberoidea phylogeny suggests optimal locus

Phylogenomics seeks to use next-generation data to robustly infer an
organism’s evolutionary history. Yet, the practical caveats of
phylogenomics motivates investigation of improved efficiency, particularly
when quality of phylogenies are questionable. To achieve improvements, one
goal is to maintain or enhance the quality of phylogenetic inference while
severely reducing dataset size. We approach this by assessing which kinds
of loci in phylogenomic alignments provide the majority of support for a
phylogenetic inference of cockroaches in Blaberoidea. We examine locus
substitution rate, saturation, evolutionary divergence, rate
heterogeneity, stabilizing selection, and a priori information content as
traits that may determine optimality. Our controlled experimental design
is based on 265 loci for 102 blaberoidean taxa and 22 outgroup species.
Loci with high substitution rate, low saturation, low sequence distance,
low rate heterogeneity, and strong stabilizing selection derive more
support for phylogenetic relationships. We found that some phylogenetic
information content estimators may not be meaningful for assessing
information content a priori. We use these findings to design concatenated
datasets with an optimized subsample of 100 loci. The tree inferred from
the optimized subsample alignment was largely identical to that inferred
from all 265 loci but with less evidence of long branch attraction,
improved statistical support, and potential 4-6x improvements to
computation time. Supported by phylogenetic and morphological evidence, we
erect three newly named clades (Anallactinae Evangelista & Wipfler
subfam. nov., Orkrasomeria tax. nov. Evangelista, Wipfler, &
Béthoux, and Hemithyrsocerini Evangelista tribe nov.) and propose other
taxonomic modifications. The diagnosis of Pseudophyllodromiidae
Grandcolas, 1996 is modified to accommodate Anallactinae and
Pseudophyllodromiinae Vickery & Kevan, 1983. The diagnosis of
Ectobiidae Brunner von Wattenwyl, 1865 is modified to add novel
morphological characters.