Phylogenetic relationships of the Chalcidoidea (Hymenoptera) inferred from secondary structural alignment of 18S and 28S rDNA

Molecular data was used to infer both sistergroup level relationships and phylogenetic relationships within Chalcidoidea. Sequences were obtained for 525 taxa representing all 19 families of Chalcidoidea (65 subfamilies and 267 genera) and five outgroup superfamilies (17 families and 51 genera). Molecular data included 18S and 28S D2 through D5 rDNA, which was manually aligned according to secondary structural models. Seventy-six regions of ambiguous alignment (RAA) sensu stricto were identified and removed from the dataset and a phylogeny was inferred from the non-ambiguously aligned conserved regions of the alignment. This hypothesis of relationships served as an input/guide tree for a MAFFT alignment of each of the isolated, independent RAAs. MAFFT aligned RAAs and structurally aligned conserved data were concatenated to produce a combined dataset for cladistic analyses. Both datasets demonstrated consistent support for many traditional taxon groupings at the family, subfamily, and tribal levels. Inclusion of MAFFT aligned RAAs demonstrated an improvement in the retention of monophyletic assemblages and within three RAAs, differences in motifs were seen between the ingroup and outgroups.