The order in which the three groups of winged insects diverged from their common ancestor has important implications for understanding the origin of insect flight. But despite this importance, the split between the Odonata (dragonflies and damselflies), Ephemeroptera (mayflies) and Neoptera (the other winged orders) remains very much unresolved. Indeed, previous studies have obtained strong apparent support for each of the three possible branching patterns. Here, we present a systematic reinvestigation of the basal pterygote split. Our results suggest that outgroup choice and limited taxon sampling have been major sources of systematic error, even for datasets with a large number of characters (e.g., in phylogenomic datasets). In particular, a dataset of 113 taxa provides consistent support for the Palaeoptera hypothesis (the grouping of Odonata with Ephemeroptera), while results from datasets with fewer taxa give inconsistent results, and are highly sensitive to minor changes in data and methods. We also focus on recent methods that exploit temporal information, combined with additional assumptions about the evolutionary process, and so reduce the influence of outgroup choice. These methods are shown to provide more consistent results, for example, supporting Palaeoptera, even for datasets that previously supported other hypotheses. Together, these results have implications for understanding insect origins and for resolving other problematic splits in the tree of life.

Dataset1Nexus file for Dataset 1, 113-taxon datasetDataset2Nexus file for Dataset 2, 38-taxon dataset.Supplementary Table 1Supplementary Table 1Thomas_et_al_10-10-12.SuppTable1.pdfSupplementary Table 2Supplementary Table 2Thomas_et_al_10-10-12.SuppTable2.pdfSupplementary Table 3Supplementary Table 3Thomas_et_al_10-10-12.SuppTable3.pdfSupplementary Table 4Supplementary Table 4Thomas_et_al_10-10-12.SuppTable4.pdfSupplementary Table 5Supplementary Table 5Thomas_et_al_10-10-12.SuppTable5.pdfSupplementary Table 6Supplementary Table 6Thomas_et_al_10-10-12.SuppTable6.pdf