Synthesizing existing phylogenetic data to advance phylogenetic research in Orobanchaceae
Data files
Sep 06, 2021 version files 50.38 MB
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10per_3-3alns.taxonomyUpdate_v2.treefile
47.25 KB
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Appendix1_genbank_accessions.csv
55.78 KB
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Fu_Calibrated_0.1_dated.nexus.trees
18.81 MB
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Fu_Calibrated_0.1_target_summary_medianHts.tre
714.52 KB
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Fu_Calibrated_point_estimation_0.1_dated.nexus.tre
37.64 KB
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Fu17_rerun_10pb_500Calibration.trees.format.nex
6.60 MB
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Fu17_rerun_10pb_combined_MCC.tre
109.31 KB
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mortimer_etal_2021_ETS_cluster1159_10pclean.fasta
32.39 KB
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mortimer_etal_2021_GBSSI_cluster1183_10pclean.fasta
63.90 KB
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mortimer_etal_2021_ITS_cluster1259_10pclean.fasta
616.02 KB
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mortimer_etal_2021_matK_cluster1252.10pclean.fasta
1.29 MB
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mortimer_etal_2021_PHYA_cluster1218_10pclean.fasta
177.37 KB
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mortimer_etal_2021_PHYB_cluster1226_10pclean.fasta
188.07 KB
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mortimer_etal_2021_psbA_cluster1212_10pclean.fasta
86.64 KB
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mortimer_etal_2021_rbcL_cluster1268_10pclean.fasta
592.84 KB
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mortimer_etal_2021_rpl32_cluster1284_10pclean.fasta
18.54 KB
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mortimer_etal_2021_rps16_cluster1224_10pclean.fasta
253.86 KB
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mortimer_etal_2021_rps2_cluster1245_10pclean.fasta
150.73 KB
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mortimer_etal_2021_trnL_cluster1253_10pclean.fasta
975.23 KB
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Schneider_Calibrated_1k_dated.nexus.trees
18.80 MB
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Schneider_Calibrated_1k_target_summary_medianHts.tre
719.62 KB
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Schneider_Calibrated_point_estimation_1K_dated.nexus.tre
37.66 KB
Abstract
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.
Methods
pyphlawd mined genbank accessions.
Usage notes
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 |