What is the current extent of our systematic knowledge? A case study in synthesizing phylogenetic data for building large trees to advance phylogenetic research in Orobanchaceae

To date, no comprehensive phylogenetic analyses have been conducted in Orobanchaceae that include both a wide generic sampling and a large sampling of species. Here, we utilize a recently developed set of tools for synthesizing publicly available data, and apply these to assess where the gaps in our phylogenetic knowledge exist in the angiosperm clade Orobanchaceae. We then use the resulting timetree to investigate diversification dynamics in this clade of mostly parasitic plants. We used the PyPHLAWD pipeline and RAxML to assemble a supermatrix of >900 species and construct a comprehensive phylogenetic hypothesis of Orobanchaceae. Divergence times were estimated with penalized likelihood from a 'congruified' set of secondary calibrations, and diversification dynamics were investigated in both trait-independent and trait-dependent (parasitic habit) contexts with BAMM and HiSSE. We sampled 39.8% of described species from 80 of 108 genera, representing all eight primary clades of Orobanchaceae. Relationships and divergence time estimates were similar to previous, clade-specific studies; however, eight genera were recovered as non-monophyletic, and will require focused systematic attention. Ours is first Orobanchaceae wide study to use model based approach to assess diversification dynamics in the parasitic lineage. Our results reveal elevated diversification rates associated with hemiparasitic habit, and holoparasitic habit was revealed to be an absorbing state, meaning that lineages within Orobanchaceae tend towards a reduction in photosynthetic towards hemiparasitism and finally holoparasitism. Using a synthetic phylogenetic hypothesis in conjunction with a unified taxonomic framework, we are able to understand where our taxonomic and phylogenetic knowledge is incomplete or conflicting, and we predict that this approach will aid in identifying where to focus future systematic efforts in any clade of interest. For Orobanchaceae, our phylogeny reflects the most recent taxonomy, and provides a new, comprehensive temporal framework for the clade that can serve as a stepping-stone for future macroevolutionary studies.12_gene_7.3.3.part = partition file for RAxML RAxML_bipartitions.12_gene_7.3.3_rtPau.tre = Tree file rooted at Paulownia 12_gene_7.3.3.fasta = concatenated fasta Fu_oro_multiCalib.summed.dated.newick.tre = Tree calibrated from data From Fu et al. 2017 24_nov_bamm.Rmd = bamm analysis fu_500.zip = treepl analysis schneider_500.zip = treepl analysi