instability_multicore.py

This script will calculate I^s scores, as described in (Hinchliff, C. E. and E. H. Roalson. 2012. Using supermatrices for phylogenetic inquiry: an example using the sedges. Systematic Biology). It requires a set of trees sharing a common set of tips, to be input as a newick file (though any format readable by dendropy should be trivial to use, just change the format in the appropriate line). It outputs a comma-delimited table containing the raw instability scores (the numerator from the right side of the equation in the referenced paper), as well as the scaled I^s scores. Taxa that move more have higher scores

phase_2_contree_all_genes_stable_tips

phase_2_contree_all_genes_stable_tip

Correlation of branch support (ICA) with locus sampling depth (number of loci with decisive taxon sampling).

<p>Original data points correspond to individual internal branches in the ML topology, and are shown in gray. Large colored dots represent mean ICA values for all branches with the corresponding number of loci with decisive sampling, and error bars extend to plus or minus the standard deviation of the data from each mean. Two regression lines are plotted, one for the entire dataset (labeled “all ”; , , , ) and one for only those branches with greater than five but fewer than 25 loci with decisive sampling (labeled “”; , , , ).</p

Generic phylogeny of plants with branches colored according to ICA support values.

<p>Branches with strong positive values (high support) are light blue, while branches with low positive values (low support) are gray, and branches with negative values (which imply relatively strong conflicting signal in the data) are colored yellow to red. Most branches deep in the tree are moderately well supported, whereas most strongly supported branches occur within smaller clades, and most branches that appear to be in conflict with the signal from the alignment occur near the tips of the tree. Terminal branches (i.e. tips) were pruned from the tree for display purposes, as they do not have meaningful support values. A large version of this figure with legible tip names is presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098986#pone.0098986.s006" target="_blank">File S3</a>.</p

phase_3_contree_has_ndhf_or_rbcl_no_bad_taxa

phase_3_contree_has_ndhf_or_rbcl_no_bad_tax

cyp_states

Latitudinal range data for all currently recognized species of Cyperaceae from Govaerts et al. (2007), World Checklist of Cyperaceae. Range data are encoded as tropical (state 1) or extratropical (state 0), and represent the position of the latitudinal midpoint of each species range, as estimated based on the geographic distribution data encoded within the World Checklist of Cyperaceae referenced above

Taxonomic sampling depth and overlap for chloroplast loci in GenBank.

<p>Data shown are representation of genera in GenBank release 185 for all chloroplast loci sampled for this study, superimposed on a genome map of the <i>Coffea arabica</i> genome. Overall generic sampling depth across the chloroplast is quite low. Dark blue bar plots on the outside of the ring show the number of genera represented by at least one exemplar sequence for each locus, out of total genera, while light blue bars show , and illustrate relative sampling proportions among loci when absolute proportions are small. Ribbon plots in the center of the figure identify pairs of loci, and indicate the proportion of genera that are represented by exemplar sequences for both loci in the pair. Dark ribbons label locus pairs that are co-represented for many genera; light ribbons label pairs that are co-represented for few. Locus colors correspond to gene groupings by function, and tick marks show linear distance in kilobases. The most well sampled locus in our entire alignment was <i>trnT–trnL–trnF</i>, with 55% of genera represented. Mitochondrial and nuclear loci are not shown in the figure, but the most well-sampled nuclear markers were ITS (53%) and ETS (8%; similar to <i>rps4</i> in the figure), and for the mitochondrion <i>atpA</i> (7%), <i>rps3</i> (5%), <i>matR</i> (5%), and <i>atp1</i> (5%); all other nuclear and mitochondrial markers were sampled for fewer than 4% of genera. Exact counts of genera represented for all markers sampled in this study are available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098986#pone.0098986.s003" target="_blank">Table S3</a>.</p

Genetic sampling depth for branches in the ML generic topology of Figs. 1, 5, and 6.

<p>Data shown are the proportion of branches for which each number of loci have decisive taxon sampling. Black bars are actual proportions, and grey bars are square roots of each proportion, which illustrate relative differences when proportions are very small. The dark grey line is the cumulative proportion of branches, which indicates the proportion of branches in the tree for which the number of loci with decisive taxon sampling is less than or equal to the indicated value. Exact values used to create this figure are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098986#pone.0098986.s002" target="_blank">Table S2</a>.</p

generic_tree_dated

A configuration file for treePL used to generate the "generic.ultrametric.tre" file

phase4_sc_rf.phy

Nucleotide data for Cyperaceae species from various markers, collected from GenBank using the software tool "phlawd". This alignment corresponds to the maximally filtered alignment: scaffolded and having had rogues removed--labeled SC/RF in our manuscript