Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of Chalcidoid wasps

Chalcidoidea (Hymenoptera) are a megadiverse superfamily of wasps with
astounding variation in both morphology and biology. Most species are
parasitoids and important natural enemies of insects in terrestrial
ecosystems. In this study, we explored a transcriptome-based phylogeny of
Chalcidoidea and found that poorly resolved relationships could only be
marginally improved by adding more genes (a total of 5,591) and taxa (a
total of 65), proof-checking for errors of homology and contamination, and
decreasing missing data. Concatenation analyses consistently place
Mymaridae and Trichogrammatidae sister to remaining Chalcidoidea. However,
our coalescent analyses provide a different hypothesis with a grouping of
(Mymaridae (((Trichogrammatidae, Eulophidae), (Encyrtidae, Aphelinidae)),
remaining Chalcidoidea)). This hypothesis complicates our hypothesis of
egg parasitism as being ancestral in Chalcidoidea. At the deeper nodes,
the results uncovered a wide spectrum of gene discordance in the
transcriptomic markers and identified a strong signal of functional bias
in genes supporting alternative phylogenies. The basal nodes of the
phylogeny are thus strongly influenced by biased support from different
functional gene complexes. Shallower nodes showed similar gene
discordance, but without strong functional bias. Understanding and
identifying mechanisms that result in gene tree discordance may be
beneficial and even essential for sorting out backbone relationships,
especially for groups that have undergone extremely rapid radiation.