Data from: Towards a self-updating platform for estimating rates of speciation and migration, ages, and relationships of taxa

Antonelli A, Hettling H, Condamine FL, Vos K, Nilsson RH, Sanderson MJ, Sauquet H, Scharn R, Silvestro D, Töpel M, Bacon CD, Oxelman B, Vos RA

Date Published: October 25, 2016

DOI: http://dx.doi.org/10.5061/dryad.sk81k

 

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Title zip of primate phylogeny inference
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Description Zip file containing all input, intermediate, and output files from the inference of the primate phylogeny using the SUPERSMART pipleine. See README.txt for details.
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Download supersmart-primates.zip (1.183 Gb)
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Title zip of palm phylogeny inference
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Description Zip file containing all input, intermediate, and output files from the inference of the palm phylogeny using the SUPERSMART pipleine. See README.txt for details.
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Download supersmart-palms.zip (1.275 Gb)
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Title zip of simulation study data
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Description Zip file containing all input, intermediate, and output files from the simulation study described in the manuscript. See README.txt for details.
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Download README.txt (1.601 Kb)
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Title Supplementary Figure S1
Downloaded 19 times
Description Backbone supermatrix dimensions for varying minimum marker coverage in the case of the Primates. For each value for minimum marker coverage we varied the maximum divergence for a marker to be accepted in the set from 0.05 to 0.19 in increments of 0.02, hence the scatter around each value. Higher values of maximum accepted divergence mean that more markers are included, which consequently results in more characters as well as more taxa in the supermatrix.
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Title Supplementary Figure S2
Downloaded 54 times
Description Average nodal posterior probabilities p as a function of varying minimum marker coverage and varying maximum divergence. Values are binned as p<0.8 (red), 0.8 < p < 0.95 (green), p>0.95 (blue).
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Title Supplementary Figure S3
Downloaded 27 times
Description Fully annotated primate phylogeny visualized with FigTree. Posterior support values are displayed on the internal nodes. Family names are displayed on the branches of the respective clades. Taxon names and branches are colour-coded by family. The scale bar on the bottom represents the time relative to the root node in Million years.
Download Fig_S3-Primate-tree.pdf (805.0 Kb)
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Title Supplementary Figure S4
Downloaded 14 times
Description Fully annotated palm phylogeny generated with FigTree. Posterior support values are displayed on the internal nodes. Subfamily names are displayed on the branches of the respective clades. Taxon names and branches are colour-coded by subfamily. The scale bar on the bottom represents the time relative to the root node in million years.
Download Fig_S4-Arecaceae-tree.pdf (2.019 Mb)
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Title Supplementary Figure S5
Downloaded 23 times
Description Comparison between the palm phylogeny produced by SUPERSMART (right) and that inferred in a previous study (Faurby, S., Eiserhardt, W.L., et al. 2016a, left), with crosses between phylogenies showing the placement of common species. The plot was generated using the R package ‘ape’.
Download Fig_S5-SUPERSMART-Faurby-comparison.pdf (1.058 Mb)
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Title Supplementary Figure S6
Downloaded 17 times
Description Illustration of how the relative number of dispersals (reported in Fig. 5) is calculated. First, the total branch length within a period (bold branches) is calculated (in this case 17.5 My). In order to account for the decreasing number of lineages towards the root of the tree, the relative number of dispersals is calculated by dividing the total branch length per time bin, thus computing the number of dispersal events in relation to the number of lineages available for dispersal. The green line shows a dispersal event at a node, whereas the red and yellow lines show events at branches that partially fall in another time bin.
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Title Supplementary Figure S7
Downloaded 18 times
Description Ancestral range reconstructions for palms using BioGeoBEARS, the SUPERSMART dated phylogeny, and the bioregions defined in Fig. 5.
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Title Supplementary Figure S8
Downloaded 75 times
Description Validation of the three-step phylogenetic inference process. Cladograms of the simulated tree (left) matched with the tree that was re-estimated from the synthetic dataset using SUPERSMART (right). Species present in both trees are connected by lines which are colour-coded by the subclades that the backbone tree was decomposed into. Branches in the re-estimated tree that form the backbone are coloured in red. Black lines represent genera that have less than three species. The plot was generated using the R package ‘ape’.
Download Fig_S8-Simulated-Estimated-Trees.pdf (484.4 Kb)
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Title Supplementary Figure S9
Downloaded 31 times
Description The long-term vision of SUPERSMART, including current and planned interactions with other initiatives during different analytical stages. “Global analyses”, when fully implemented, aims at providing continuously updating, dated phylogenies of all species with publicly available molecular sequences, and (in future versions) estimates of diversification and migration rates among and within a set of pre-defined GIS polygons (such as WWF’s realms and biomes). The results may be retrieved by other initiatives and will be deposited in data repositories. “User-defined analyses” are influenced by individual choices, including defined polygons (areas), taxa of interest, and fossil records. The user may also include data that are not yet published or are not public.
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Title Supplementary Table S1
Downloaded 5 times
Description Palm fossils and morphological justification for their placement in the Arecaceae phylogeny.
Download Table_S1-palm-fossil-calibrations.xlsx (126.5 Kb)
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Title Supplementary Table S2
Downloaded 6 times
Description Estimated mean crown ages in millions of years of major palm clade from SUPERSMART results as compared to previous studies.
Download Table_S2-palms-dates-comparison.xlsx (41.06 Kb)
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When using this data, please cite the original publication:

Antonelli A, Hettling H, Condamine FL, Vos K, Nilsson RH, Sanderson MJ, Sauquet H, Scharn R, Silvestro D, Töpel M, Bacon CD, Oxelman B, Vos RA (2017) Towards a self-updating platform for estimating rates of speciation and migration, ages, and relationships of taxa. Systematic Biology 66(2): 152-166. http://dx.doi.org/10.1093/sysbio/syw066

Additionally, please cite the Dryad data package:

Antonelli A, Hettling H, Condamine FL, Vos K, Nilsson RH, Sanderson MJ, Sauquet H, Scharn R, Silvestro D, Töpel M, Bacon CD, Oxelman B, Vos RA (2016) Data from: Towards a self-updating platform for estimating rates of speciation and migration, ages, and relationships of taxa. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.sk81k
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