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

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

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 - - + + + + + +
  1. 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.