Single-copy nuclear genes resolve the phylogeny of the holometabolous insects

Table 2 Clade recovery results from maximum-likelihood analyses with varied taxon and character inclusion used to counter long-branch attraction.

Experiment	Clade recovery
Maximum likelihood	Coleoptera + Strepsiptera	Halteria	Basal Hymenoptera	Mecopterida	Neuropteroidea (with Strepsiptera)	Amphiesmenoptera	Antliophora	Neuropterida
Third position included	+	-	+	+	+	+	+	+
Amino acids	+	-	+	+	+	+	+	+
Strepsiptera removed	N/A	N/A	+	+	+	+	+	+
Out-groups removed	+	-	N/A	+	+	+	+	+
Third RY coded	+	-	+	+	+	+	+	+
First and third RY coded	-	-	+	+	+	+	+	+
Conservative alignment	+	-	+	+	+	+	+	+
Taxa with base composition bias excluded	-	-	+	+	+	+	+	+

These variations on taxon and character inclusion (with the exception of the inclusion of third positions) are cited as a means to rectify the effects of long-branch attraction. Clade recovery from these various methods is substantially in agreement with each other and with our final results.

ISSN: 1741-7007