Authors: Thilina De Silva, Marlon E. Cobos, Sumudu W. Fernando, Claudia Nuñez-Penichet, Utku Perkas, A. Townsend Peterson
Corresponding Author: Thilina De Silva
Address: Department of Ecology & Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, Kansas 66045, USA.
Email: nethmin999@gmail.com
This repository serves to store the code and data for reproducing analyses performed in this project.
The folder Scripts contains three files:
- Complete_process.R contains the code to reporduce analysis and figures done in R.
- Functions.R contains R functions used in the previous script.
- To_run_BayesTraits_analyses.txt is a basic step by step guide to perform analysis in BayesTraits.
The folder Characters contains two files:
- all_characters.csv contains the state of the ecological characters for all species considered in our study (based on a existing phylogeny, see below).
- all_characters_117.csv the state of the ecological characters for an extended group of species considered for an analysis in our study (based on a phylogeny extended based on unresolved tips, see below).
The folder Trees contains three files:
- raxml108.tre is a phylogeny of 108 species of weaverbirds constructed based on Maximum likelihood.
- BEASTMCC.tre is a phylogeny of 108 species of weaverbirds constructed as a Bayesian maximum clade credibility tree.
- 117_beast_Rmodified.tre is a the Bayesian phylogeny modified to consider other species (as unresolved tips), not included in the previous phylogenies.