Data from: Molecular dating, evolutionary rates, and the age of the grasses

 

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Title genomes
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Description Data set of nuclear genes used for dating analyses
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Title genomes_beast_1
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Description This file contains the consensus tree inferred on nuclear markers by BEAST with the topology fixed. External calibration only was used. Each time unit corresponds to 20 million years.
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Title genomes_beast_2
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Description This file contains the consensus tree inferred on nuclear markers by BEAST with the topology fixed. External calibration plus phytoliths were used. Each time unit corresponds to 20 million years.
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Title plastid28
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Description Data set of plastid markers for 28 species used for dating analyses.
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Title plastid245
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Description Data set of plastid markers for 245 species used for dating analyses.
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Title plastid245_beast_1
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Description This file contains the consensus tree inferred on plastid markers by BEAST with the topology fixed. External calibration only was used. Each time unit corresponds to 20 million years.
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Title plastid245_beast_2
Downloaded 39 times
Description This file contains the consensus tree inferred on plastid markers by BEAST with the topology fixed. External calibration plus phytoliths were used. Each time unit corresponds to 20 million years.
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Title FigureS1
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Description Supplementary Figure 1: Comparison of concatenated and partitioned analyses. Ages are plotted in million years ago for a) plastid markers and b) nuclear markers. Analyses were performed with BEAST and the dataset was partitioned by codon position. Black lines indicate 1:1 relationships.
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Title FigureS2
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Description Supplementary Figure 2: Comparison of prior and posterior distribution of nodes for the plastid phylogeny under calibration #1. For each calibration point, the calibration density is indicated by the black line, the marginal prior distribution by the blue bars and the posterior distribution by the red bars.
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Title FigureS3
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Description Supplementary Figure 3: Comparison of prior and posterior distribution of nodes for the plastid phylogeny under calibration #2. For each calibration point, the calibration density is indicated by the black line, the marginal prior distribution by the blue bars and the posterior distribution by the red bars.
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Title FigureS4
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Description Supplementary Figure 4: Comparison of prior and posterior distribution of nodes for the nuclear phylogeny under calibration #1. For each calibration point, the calibration density is indicated by the black line, the marginal prior distribution by the blue bars and the posterior distribution by the red bars.
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Title FigureS5
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Description Supplementary Figure 5: Comparison of prior and posterior distribution of nodes for the nuclear phylogeny under calibration #2. For each calibration point, the calibration density is indicated by the black line, the marginal prior distribution by the blue bars and the posterior distribution by the red bars.
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Title FigureS6
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Description Supplementary Figure 6: Comparison of evolutionary rates. Boxplots of inferred evolutionary rates (in expected mutations per site per billion years) are shown for plastid markers (top row) and nuclear markers (bottom row) under calibration #1. Rates are sorted by phylogenetic groups: basal angiosperms (“basal”), eudicots, monocots without graminids, graminids without BEP-PACMAD and BEP-PACMAD. The results obtained with four different methods are shown: BEAST, PB_ug = uncorrelated gamma method implemented in PHYLOBAYES, PB_ln = log-normal autocorrelated method implemented in PHYLOBAYES, MD = MULTIDIVTIME.
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Title FigureS7
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Description Supplementary Figure 7: Age for the BEP-PACMAD crown estimated by MULTIDIVTIME under different priors. The age for the node (in million years ago) is indicated as a function of the prior for the mean of the Brownian motion constant mean. Results are aggregated for different values of the other priors. Analyses with a value of 0.01 for the Brownian motion constant standard deviation are in black.
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Title FigureS8
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Description Supplementary Figure 8: Detailed comparison of methods and datasets. For calibration #1, the age estimates (in million years ago) are represented for nodes that were shared between phylogenetic trees of plastid and nuclear markers. The ages are represented independently when produced by BEAST and MULTIDIVTIME. Black circles are ages based on the whole plastid dataset, red squares are ages based on plastid markers for 28 species only, black triangles are aged based on the whole nuclear dataset, and red bars indicate the interval between the 1st and 3rd quartiles of 100 replicates of the nuclear dataset decreased to the size of the plastid dataset. Taxonomic groups are indicated on the bottom. The last point corresponds to the crown of BEP, and the horizontal bar indicates the minimal age for the clade that would be congruent with the 67 Ma phytolith fossil (Prasad et al. 2011). Numbers can be used to identify the corresponding nodes in Supplementary Figure 9.
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Title FigureS9
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Description Supplementary Figure 9: Node identity. Nodes represented in Figure 2 and Supplementary Figure 8 are indicated on the phylogenetic tree showing the expected relationships among nuclear genes without branch lengths. Taxonomic groups represented in the tips are delimited on the right.
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When using this data, please cite the original publication:

Christin P, Spriggs E, Osborne CP, Stromberg CAE, Salamin N, Edwards EJ (2013) Molecular dating, evolutionary rates, and the age of the grasses. Systematic Biology 63(2): 153-165. http://dx.doi.org/10.1093/sysbio/syt072

Additionally, please cite the Dryad data package:

Christin P, Spriggs E, Osborne CP, Stromberg CAE, Salamin N, Edwards EJ (2013) Data from: Molecular dating, evolutionary rates, and the age of the grasses. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.t5v58
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