Data from: The Strepsiptera Problem: Phylogeny of the Holometabolous Insect Orders Inferred from 18S and 28S Ribosomal DNA Sequences and Morphology

Phylogenetic relationships among the holometabolous insect orders were
inferred from cladistic analysis of nucleotide sequences of 18S ribosomal
DNA (rDNA) (85 exemplars) and 28S rDNA (52 exemplars) and morphological
characters. Exemplar outgroup taxa were Collembola (1 sequence),
Archaeognatha (1), Ephemerida (1), Odonata (2), Plecoptera (2), Blattodea
(1), Mantodea (1), Dermaptera (1), Orthoptera (1), Phasmatodea (1),
Embioptera (1), Psocoptera (1), Phthiraptera (1), Hemiptera (4), and
Thysanoptera (1). Exemplar ingroup taxa were Coleoptera: Archostemata (1),
Adephaga (2), and Polyphaga (7); Megaloptera (1); Raphidioptera (1);
Neuroptera (sensu stricto ;eq Planipennia): Mantispoidea (2),
Hemerobioidea (2), and Myrmeleontoidea (2); Hymenoptera: Symphyta (4) and
Apocrita (19); Trichoptera: Hydropsychoidea (1) and Limnephiloidea (2);
Lepidoptera: Ditrysia (3); Siphonaptera: Pulicoidea (1) and
Ceratophylloidea (2); Mecoptera: Meropeidae (1), Boreidae (1), Panorpidae
(1), and Bittacidae (2); Diptera: Nematocera (1), Brachycera (2), and
Cyclorrhapha (1); and Strepsiptera: Corioxenidae (1), Myrmecolacidae (1),
Elenchidae (1), and Stylopidae (3). We analyzed ~1 kilobase of 18S rDNA,
starting 398 nucleotides downstream of the 5' end, and ~400 bp of 28S
rDNA in expansion segment D3. Multiple alignment of the 18S and 28S
sequences resulted in 1,116 nucleotide positions with 24 insert regions
and 398 positions with 14 insert regions, respectively. All Strepsiptera
and Neuroptera have large insert regions in 18S and 28S. The secondary
structure of 18S insert 23 is composed of long stems that are GC rich in
the basal Strepsiptera and AT rich in the more derived Strepsiptera. A
matrix of 176 morphological characters was analyzed for holometabolous
orders. Incongruence length difference tests indicate that the 28S +
morphological data sets are incongruent but that 28S + 18S, 18S +
morphology, and 28S + 18S + morphology fail to reject the hypothesis of
congruence. Phylogenetic trees were generated by parsimony analysis, and
clade robustness was evaluated by branch length, Bremer support,
percentage of extra steps required to force paraphyly, and sensitivity
analysis using the following parameters: gap weights, morphological
character weights, methods of data set combination, removal of key taxa,
and alignment region. The following are monophyletic under most or all
combinations of parameter values: Holometabola, Polyphaga, Megaloptera +
Raphidioptera, Neuroptera, Hymenoptera, Trichoptera, Lepidoptera,
Amphiesmenoptera (Trichoptera + Lepidoptera), Siphonaptera, Siphonaptera +
Mecoptera, Strepsiptera, Diptera, and Strepsiptera + Diptera (Halteria).
Antliophora (Mecoptera + Diptera + Siphonaptera + Strepsiptera),
Mecopterida (Antliophora + Amphiesmenoptera), and Hymenoptera +
Mecopterida are supported in the majority of total evidence analyses.
Mecoptera may be paraphyletic because Boreus is often placed as sister
group to the fleas; hence, Siphonaptera may be subordinate within
Mecoptera. The 18S sequences for Priacma (Coleoptera: Archostemata),
Colpocaccus (Coleoptera: Adephaga), Agulla (Raphidioptera), and Corydalus
(Megaloptera) are nearly identical, and Neuropterida are monophyletic only
when those two beetle sequences are removed from the analysis. Coleoptera
are therefore paraphyletic under almost all combinations of parameter
values. Halteria and Amphiesmenoptera have high Bremer support values and
long branch lengths. The data do not support placement of Strepsiptera
outside of Holometabola nor as sister group to Coleoptera. We reject the
notion that the monophyly of Halteria is due to long branch attraction
because Strepsiptera and Diptera do not have the longest branches and
there is phylogenetic congruence between molecules, across the entire
parameter space, and between morphological and molecular data.