Data from: Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse
Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher
plants) represent perhaps the oldest and most diverse lineage of
carnivorous plants. However, despite numerous studies seeking to elucidate
their evolutionary relationships, the early-diverging relationships remain
unresolved. METHODS: To explore the utility of phylogenomic data sets for
resolving relationships among the carnivorous Caryophyllales, we sequenced
10 transcriptomes, including all the carnivorous genera except those in
the rare West African liana family Dioncophyllaceae. We used a variety of
methods to infer the species tree, examine gene tree conflict, and infer
paleopolyploidy events. KEY RESULTS: Phylogenomic analyses supported the
monophyly of the carnivorous Caryophyllales, with a crown age of 68–83
million years. In contrast to previous analyses, we recovered the
remaining noncore Caryophyllales as nonmonophyletic, although the node
supporting this relationship contained a significant amount of gene tree
discordance. We present evidence that the clade contains at least seven
independent paleopolyploidy events, previously unresolved nodes from the
literature have high levels of gene tree conflict, and taxon sampling
influences topology even in a phylogenomic data set, regardless of the use
of coalescent or supermatrix methods. CONCLUSIONS: Our data demonstrate
the importance of carefully considering gene tree conflict and taxon
sampling in phylogenomic analyses. Moreover, they provide a remarkable
example of the propensity for paleopolyploidy in angiosperms, with at
least seven such events in a clade of less than 2500 species.