DOI: 10.5061/dryad.25131
title: Data from: When can clades be potentially resolved with morphology?

description: Morphology-based phylogenetic analyses are the only option for
 reconstructing relationships among extinct lineages, but often find
 support for conflicting hypotheses of relationships. The resulting lack of
 phylogenetic resolution is generally explained in terms of data quality
 and methodological issues, such as character selection. A previous
 suggestion is that sampling ancestral morphotaxa or sampling multiple taxa
 descended from a long-lived, unchanging lineage can also yield clades
 which have no opportunity to share synapomorphies. This lack of character
 information leads to a lack of ‘intrinsic’ resolution, an issue that
 cannot be solved with additional morphological data. It is unclear how
 often we should expect clades to be intrinsically resolvable in realistic
 circumstances, as intrinsic resolution must increase as taxonomic sampling
 decreases. Using branching simulations, I quantify intrinsic resolution
 across several models of morphological differentiation and taxonomic
 sampling. Intrinsically unresolvable clades are found to be relatively
 frequent in simulations of both extinct and living taxa under realistic
 sampling scenarios, implying that intrinsic resolution is an issue for
 morphology-based analyses of phylogeny. Simulations which vary the rates
 of sampling and differentiation were tested for their agreement to
 observed distributions of durations from well-sampled fossil records and
 also having high intrinsic resolution. This combination only occurs in
 those datasets when differentiation and sampling rates are both
 unrealistically high relative to branching and extinction rates. Thus, the
 poor phylogenetic resolution occasionally observed in morphological
 phylogenetics may result from a lack of intrinsic resolvability within
 groups.
description: tree_constant_07-15-12R file for running the 'clade-constant' simulations as described in the paper.ntaxa_constant_07-01-12R script for the 'size-constant' simulations described in the paper.100extant_07-28-12R script file for simulations of extant only taxa.ratesVsResolved_anag_08-18-12R script for simulations with varying sampling and differentiation rates under a pure-anagenesis model.propDur_r0.01_09-15-12R script simulating clades under various models of differentiation and estimating the proportion of taxa with an observable, sampled duration.modeComparison_propDur_workspace_09-16-12An R workspace file containing all simulation data needed for plotting the figures where multiple models of differentiation are compared (Fig. 3-6, 8). Can be read into R with function load().ratesVresolved_08-16-12An R workspace file containing all simulation data needed for plotting the results of the simulations comparing sampling and differentiation rates (i.e. Fig. 7). Can be read into R with function load().plotting_scriptR plotting script for all supplemental figures and figures 3-6 of the main text.plotting_anag_results_08-23-12R file for plotting Figure 7 of the main text, which is the analysis comparing rates of sampling and differentiation.plot_propDur - 09-16-12R script for plotting figure 8 from the main text.