We present the most comprehensive morphological dataset on Ditrysia to date, consisting of over 500 morphological characters.
The placement of Brachydelphis inside Inioidea contrasts with an analysis of an earlier version of the morphological dataset utilized here [ 2]; the authors of that study reconstructed Brachydelphis as a stem platanistoid (sensu [ 56]).
More detailed information on characters and corresponding references are found in Additional file 5. We report the results of the maximum likelihood (ML) and parsimony (MP) analyses of the morphological dataset alone, and compare these results to those of the ML analysis of combined morphological and molecular data.
In order to make a morphological comparison between the two populations in this study, we reanalyzed a subset of the morphological dataset from Pavey et al. 2010 of 360 age 0 (meaning previous to first winter) juvenile sockeye with only the two current study populations [Table 1 in [ 27]].
For tracing evolutionary changes on the phenotypic level we used the most extensive morphological dataset presently available, including 356 characters of representatives of all holometabolan orders and of carefully selected outgroup taxa [ 15].
Blomberg's K and Pagel's λ statistics of phylogenetic signal and standard deviation for the damselfish morphological dataset in the posterior distributions of phylograms and chronograms.
Removing explicit character ordering and weighting from the parsimony analyses of the morphological dataset had modest effects.
The choice of Recent taxa for inclusion in this dataset is based on maximizing the overlap of the morphological dataset with the 19 nuclear and 3 mitochondrial gene dataset used by [ 9].
With this correction, and using either PAUP [ 23] or NONA [ 27] under the analytical defaults of POY 2.7 [ 28] (e.g., polymorphisms treated as missing data), the morphological dataset published in appendix 1 of [ 17] yields the reported 4 trees at 1088 steps.
