Synthesizing existing phylogenetic data to advance phylogenetic research in Orobanchaceae
Creators: name: Mortimer, Sebastian M. E.
name: Boyko, James
name: Beaulieu, Jeremy M.
name: Tank, David C.
Publisher: name: Zenodo
Year: 2021
Subjects: BAMM
diversification dynamics
HiSSE
holoparasitic
hemiparasitic
megaphylogeny
Orobanchaceae

description: To date, no comprehensive phylogenetic analyses have been conducted in Orobanchaceae that include both a wide generic sampling and a large sampling of species. In addition, a lack of fossil evidence in the clade precludes the use of primary fossil calibrations for divergence time estimation, preventing the establishment of a comprehensive temporal framework for use in macroevolutionary studies. Here, we use a recently developed set of tools for synthesizing publicly available data, apply these to reconstruct a comprehensive timetree for Orobanchaceae, and then investigate diversification dynamics in this clade of mostly parasitic plants using two model based methods. The assembled supermatrix included more than 900 species, representing approximately 40% of the known species diversity of the family, and the resulting phylogeny largely confirmed relationships revealed in earlier studies; however, we identified ten non-monophyletic genera that will require focused systematic attention to resolve. Diversification rate analyses found substantial support for character-dependent diversification, with elevated rates in hemiparasitic clades, and evidence for a number of speciation rate changes throughout the tree that are likely linked to other traits. Importantly, our multi-state HiSSE analysis revealed that transitions to a parasitic lifestyle only occur when there is a prior transition in an unobserved precursor state. For Orobanchaceae, our study provides a new comprehensive framework for the clade that can serve as a stepping-stone for future macroevolutionary studies.
description: mortimer_etal_2021_rpl32_cluster1284_10pclean.fasta 18.54 KB gene alignment mortimer_etal_2021_rps2_cluster1245_10pclean.fasta 150.73 KB gene alignment mortimer_etal_2021_rps16_cluster1224_10pclean.fasta 253.86 KB gene alignment mortimer_etal_2021_trnL_cluster1253_10pclean.fasta 975.23 KB gene alignment 10per_3-3alns.taxonomyUpdate_v2.treefile 47.25 KB ML tree Fu_Calibrated_0.1_dated.nexus.trees 18.81 MB Calibrated Tree Distribution Fu_Calibrated_0.1_target_summary_medianHts.tre 714.52 KB Summary Tree Fu_Calibrated_point_estimation_0.1_dated.nexus.tre 37.64 KB Point Estimate Tree Fu17_rerun_10pb_500Calibration.trees.format.nex 6.60 MB Trees from Fu et al. 2017 Fu17_rerun_10pb_combined_MCC.tre 109.31 KB Tree from Fu et al. 2017 Schneider_Calibrated_1k_dated.nexus.trees 18.80 MB Calibrated Tree Distribution Schneider_Calibrated_1k_target_summary_medianHts.tre 719.62 KB Summary Tree Schneider_Calibrated_point_estimation_1K_dated.nexus.tre 37.66 KB Point Estimate Tree FigureS5_Orobanchaceae_ML_tree.pdf 58.75 KB S5 ML tree FigureS8_2021_Bamm_mcmc.pdf 1.57 MB S8 mcmc FigureS9_2021_Bamm_post_prior.pdf 8.98 KB S9 prior/posterior FigureS10-S17_MuHiSSE_models.docx 2.17 MB S10 - S17 TableS1_2021.docx 33.67 KB S1 - sequences removed TableS2_2021.docx 15.78 KB S2 - subspecific tips TableS3_2021.docx 28.47 KB S3 - genus, clade, sampling, taxonomy, geography TableS4_2021.docx 13.46 KB S4 - name changes TableS6_2021.tsv 2.03 KB S6 - Fu et al. 2017 calibrated dates TableS7_2021.tsv 2.03 KB S7 - Schneider and Moore 2017 calibrated dates
description: pyphlawd mined genbank accessions.