Data from: A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)

Stein RW, Brown JW, Mooers AØ

Date Published: July 7, 2015

DOI: http://dx.doi.org/10.5061/dryad.p2pn8

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title BEAST xml file for taxon set with molecular data
Downloaded 56 times
Description This .xml file includes the alignments and specifications used in the analysis of the molecular data matrix. Additionally, this file includes the code that helped to resolve the convergence problems (low ESS values) stemming from a sparse molecular data matrix.
Download Stein et al. 2015 - BEAST xml file for ta...ta.xml (3.774 Mb)
Download README.pdf (91.84 Kb)
Details View File Details
Title Stein et al. 2015 - BEAST xml file for simulation of the calibrated tree prior on the MCC tree from analysis of the taxon set with molecular data
Downloaded 12 times
Description This .xml file includes the specifications used to simulate the calibrate tree prior on the fully constrain maximum clade credibility trees generated from three replicate analyses of the molecular data matrix using: Stein et al. 2015 - BEAST xml file for taxon set with molecular data.xml
Download Stein et al. 2015 - BEAST xml file for si...ta.xml (393.9 Kb)
Details View File Details
Title Stein et al 2015 - BEAST xml file for taxon-complete analyses
Downloaded 53 times
Description This xml file includes the alignments, specifications and additional taxonomic constraints used in the taxon-complete analyses. Additionally, this file includes the code that helped to resolve the convergence problems (low ESS values) stemming from a sparse molecular data matrix. The approach was developed by Dr. Joseph W. Brown and involves the following: 1. Create a new compoundParameter to update mean clock rates as a set see lines: 19329 - 19339 2. Comment out the upDownOperators for each mean clock rate see lines: 20378 - 20483 3. Create a new upDownOperator for the new compound parameter see lines: 20495 - 20504 Searching for “compoundParameterSetUp” (omitting the “”) within the .xml file will locate each of the edits associated with setting up the new compoundParameter for mean clock rates.
Download Stein et al 2015 - BEAST xml file for tax...es.xml (4.817 Mb)
Download README.pdf (91.84 Kb)
Details View File Details
Title Stein et al. 2015 Fig. 1 in nexus file format
Downloaded 13 times
Description Phylogenetic hypothesis resulting from analysis of the molecular data matrix in the nexus file format.
Download Stein et al. 2015 Fig. 1.nex (9.171 Kb)
Details View File Details
Title Stein et al. 2015 Fig. 1 in newick file format
Downloaded 14 times
Description Phylogenetic hypothesis resulting from analysis of the molecular data matrix in the newick file format.
Download Stein et al. 2015 Fig. 1.tre (9.126 Kb)
Details View File Details

When using this data, please cite the original publication:

Stein RW, Brown JW, Mooers AØ (2015) A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves). Molecular Phylogenetics and Evolution 92: 155-164. http://dx.doi.org/10.1016/j.ympev.2015.06.005

Additionally, please cite the Dryad data package:

Stein RW, Brown JW, Mooers AØ (2015) Data from: A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.p2pn8
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: