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Before the turn of the millenium the investigation of phylogenetic relationships was revolutionized by two major inputs, the use of molecular sequence data for phylogenetic reconstruction, paralleled by the sophistication of computer aided reconstruction methods. The ever growing number of data however did not only result in clarifications of open questions, but brought forth a number of new conflicting phylogenetic hypotheses. Sometimes they are wrongly referred to as conflicts between morphological and molecular approaches, which sporadically even culminated in the rejection of the usefulness of one of the two approaches (e.g. Scotland et al 2003). These scientists overlook the great advantage of having two a priori largely independent data sets (Wägele 2001) which in a synthetic way enable the greatest progress in phylogenetic research. However, solely putting data together will not suffice to choose among conflicting hypotheses. The increasing number of conflicts necessitates approaches that go beyond mere data congruence, but searching for the possible reasons of conflicts. In the present paper, problems in the reconstruction of the phylogenetic origin of Hexapoda, as well as of the early branchings within the Hexapoda, will exemplify approaches of critical re-evaluation and testing of data used in morphological data matrices for phylogenetic analyses. The early cladogenetic events of hexapods are especially suited for such a discussion for several reasons. The hexapods, as the most species-rich group of organisms, look back at a long and multi-faceted history of taxonomic and phylogenetic studies, culminating in a number of conflicting hypotheses. Triggered by incongruences with morphological analyses the reconstruction of the hexapodan roots likewise became a hot-spot of molecular research activities during^the last two decades. Furthermore the phylogenetic positions of the oldest lineages branching off within the hexapodan clade, the Diplura, Protura and Collembola, are in particular very difficult to reconstruct. While at least the latter two are well defined by morphological autapomorphies their phylogenetic position could not be reconstructed unambiguously, since their morphology seems highly derived with respect to the hexapodan ground pattern.
Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. In order to get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies using an extended transcriptome dataset.Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive datasets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we employed Four-cluster Likelihood-Mapping (FcLM) to measure the degree of congruence among genes of a dataset, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated with neither functional class assignment of these genes, nor with model misspecification due to unpartitioned analyses. The herein analyzed dataset is the currently largest dataset covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. While this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artefacts.