Data from: Multiple molecular data sets suggest independent origins of highly eusocial behavior in bees (Hymenoptera:Apinae)

Different views of the pattern of social evolution among the highly
eusocial bees have arisen as a result of discordance between past
molecular and morphology-based phylogenies. Here we present new data and
taxa for four molecular data sets and reassess the morphological
characters available to date. We show that there is no significant
character incongruence between four molecular data sets (two nuclear and
two mitochondrial) but that there is highly significant character
incongruence, which leads to topological incongruence, between the
molecular and morphological data. We investigate the effects of using
different outgroup combinations to root the estimated tree. We also
consider various ways in which biases in the sequence data could be
misleading, employing several maximum likelihood models, LogDet
corrections, and spectral analyses. Ultimately, we concede that there is
strong discordance between the molecular and morphological data
partitions, and that the conditional combination approach is appropriately
applied in this case. We also find for the molecular trees that there are
two equally well supported placements of the root, one supported by 16S
and 28S sequences, the other supported by cyt b and opsin. The strength of
the evidence leads us to accept two equally well supported hypotheses
based on analyses of the molecular data sets. These are the most
rigorously supported hypotheses of corbiculate bee relationships at this
time, and frame our argument that highly eusocial behavior within the
corbiculate bees evolved twice independently.