Data from: Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants

Wicke S, Müller KF, dePamphilis CW, Quandt D, Bellot S, Schneeweiss GM

Date Published: July 27, 2016

DOI: http://dx.doi.org/10.5061/dryad.t2m75

 

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Title Dataset S1
Downloaded 14 times
Description Annotation details and presence/absence list of plastid genes
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Title Dataset_S2
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Description Results of the relative rate tests (dN)
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Title Dataset_S3
Downloaded 16 times
Description Results of relative rate tests (dS)
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Title Dataset_S4
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Description Results from functional complex-wise tests for relaxation of selection strength and lifestyle effects
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Title Dataset_S5
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Description Reconstruction of the ancestral states of all plastid genes and functional complexes
Download Dataset_S5.xlsx (61.05 Kb)
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Title Dataset_S6
Downloaded 15 times
Description Results of phylogenetic principal component analysis
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Title Dataset_S7
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Description Phylogenetic principal regression using MCMC-GLMM
Download Dataset_S7.xlsx (18.09 Kb)
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Title Dataset_S8
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Description Indel frequency as length variation per gene per species relative to the average length of the respective intact gene
Download Dataset_S8.xlsx (26.39 Kb)
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Title Dataset_S9
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Description Model-ranked results of Monte Carlo Markov chain coupled generalized linear mixed models with cumulative BIC weights
Download Dataset_S9.xlsx (22.41 Kb)
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Title Dataset_S10
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Description Model-ranked results of Monte Carlo Markov chain coupled generalized linear mixed model statistics of models with a cumulative BIC-weight of at least 0.8
Download Dataset_S10.xlsx (26.79 Kb)
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Title HBL/Perl/R scripts
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Description Example scripts (HyPhy batch language, perl) for analysing evolutionary rates and indels; R scripts for producing heatmaps from relative rate data and reconstructing the indel history over a given phylogeny after indel-coding with SeqState; includes five example data and tree files.
Download scripts_for_rates_and_indel_analysis.zip (61.87 Kb)
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When using this data, please cite the original publication:

Wicke S, Müller KF, dePamphilis CW, Quandt D, Bellot S, Schneeweiss GM (2016) Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants. Proceedings of the National Academy of Sciences of the United States of America 113(32): 9045–9050. http://dx.doi.org/10.1073/pnas.1607576113

Additionally, please cite the Dryad data package:

Wicke S, Müller KF, dePamphilis CW, Quandt D, Bellot S, Schneeweiss GM (2016) Data from: Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.t2m75
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