Fig. 2 Alternative hypotheses for ecdysozoan relationships based on molecular data from expressed sequence tags (after Dunn et al. 2008), depicting Panarthropoda as variably having multiple evolutionary origins (a tardigrades within Cycloneuralia) or a single evolutionary origin (b tardigrades sister to Onychophora + Arthropoda).
Though recent studies of higher-level avian relationships based on molecular data have begun to converge on robust support for a Fregata + Suloidea clade [27], [29], this remains slightly incongruent with morphological phylogenetic analyses.
Analyses of higher-level squamate relationships based on molecular data have so far included relatively few (less than 200) species, and none have included representatives from all described families and subfamilies [ 17- 20, 23, 24].
Given our results, major taxonomic rearrangements within Teiidae seem problematic at present, especially with the extensive paraphyly of many traditional and re-defined teiid genera, the lack of strong resolution of many of these relationships based on molecular and morphological data, and incomplete taxon sampling in all studies so far.
Other proposed groups within Polyneoptera are not widely accepted due to the lack of convincing morphological synapomorphies and contradictory or only poorly resolved relationships based on molecular data sets, for example, Orthopterida (=Orthoptera + Phasmatodea) and Eukinolabia (=Phasmatodea + Embioptera) (but see Letsch et al. 2012).
Inter-generic and inter-subgeneric ingroup-only relationships based on the molecular matrix employed by Metzgar et al. (reproduced here in Fig. 10) indeed receive nearly unambiguous support from the concatenated gene matrix.
Since the 1960's, molecular phylogeneticists have sought to reconstruct organismal relationships based on gene and protein trees [ 1].
In all analyses, the reconstructed clades were remarkably similar to currently accepted vertebrate relationships based on morphological and molecular analyses.
Most importantly, relationships based on LFY2int2-N were congruent to previous studies based on morphological and molecular marker data.
Instead of calculating the protein relationships based on their biological process GO terms, we focused on their relationships based on the GO terms in "Molecular Function" category.
