Project Whalehead

Introduction

Project Whalehead (arbitrarily named for the shoebill genus) is a GitHub repository for a project comparing phylogenetic outputs of Bayesian and parsimony analysis of morphological character matrices using stratigraphic congruence metrics. The authors are April Wright and Graeme Lloyd and this repository also serves as supplementary information for the final published version.

tl;dr of the paper:

The aim of a Bayesian analysis is not a single point estimate of a solution. Rather, it is to examine solutions and outcomes that are plausible given the model and the data. This is particularly important in phylogenetics, where we are estimating lineage divergences that occurred tens or hundreds of millions of years ago. We do this from scarce, and likely biased data, using models that may or may not adequately capture reality. To responsibly present a solution under these conditions must mean incorporating uncertainty in that solution. It is prudent to avoid using a single point estimate summary of a posterior sample

What is here?

A talk from #SBE2020 by April Wright describing the paper can be seen here

Below is a summary of the contents:

  • Data (Folder containing the data used)
    • Ages (Tip age text files generated for each data set primarily using calls to the Paleobiology Database API)
    • Boxplots (Boxplots showing the distribution of stratigraphic congruence metrics for Bayesian and parsimony trees calculated in the strap R package for each data set)
    • Combined trees (The combined Bayesian and parsimony trees in NEXUS format)
    • kMeans_MIG (k-means clusters based on MIG scores)
    • kMeansTreespace (kmeans clusters based on Robinson-Foulds score)
    • MIGDifferences (Bivariate plots showing distance in MDS space verus difference in MIG for just the first 2 MDS axes and for all MDS axes)
    • MPTs (The most parsimonious trees generated from TNT searches for each data set in Newick format)
    • NEXUS (The original morphological character matrix in NEXUS format as taken from graemetlloyd.com)
    • RevBayesOutput (The raw RevBayes output for each data set; NB: Missing from GitHub as too large to upload, but called in scripts)
    • StratCongruenceResults (The stratigraphic congruence results output from the strap R package for each data set)
    • TreeSpacePlots (Treespace visualisations using modified RWTY R package code for each data set)
    • ViolinPlots (Violin plots showing the distribution of stratigraphic congruence metrics for Bayesian and parsimony trees calculated in the strap R package for each data set)
    • XML (XML files for each data set containing metadata used to generate pseudo-independent data sets and reconcile OTU names with Paleobiology Database taxa)
  • Figures (Final and draft versions of manuscript figures)
  • R (R package folder for replicating study)
  • man (R package folder for replicating study)
  • rb_scripts (RevBayes scripts used in Bayesian analysis)
  • vignettes (Vignettes for replicating analysis)
  • DESCRIPTION (R package file for replicating study)
  • NAMESPACE (R package file for replicating study)
  • README.md (This file)
  • TableS1.md (Supplementary Table 1 summarising full results for each data set)
  • refs.bib (BibTex file containing references cited)