Species Delimitation

Scripts and Datasets for Phylogenomics of spiny rats - Genus Proechimys

Used in Dalapicolla et al. 2024. Phylogenomics and species delimitation of an abundant and little-studied Amazonian forest spiny rat. DOI: https://doi.org/10.1016/j.ympev.2023.107992

Dataset to this article can be found online at: https://doi.org/10.6084/m9.figshare.24786918

How to cite:

Dalapicolla et al., 2024. Phylogenomics and species delimitation of an abundant and little-studied Amazonian forest spiny rat. Molecular Phylogenetics and Evolution. DOI: https://doi.org/10.1016/j.ympev.2023.107992

Folders

01. ipyrad: Paramaters used for SNPs filtering;

02. RScripts: R Scritps for editing inputs for analyses:

• A. Splitting a phylip alignment into two datasets;
• B. Estimate bootstraps below 50% in Paup/SVDQuartets;
• C. Preparing outputs from ipyrad to BP&P and iBP&P inputs;
• D. Preparing morphometric data to iBP&P inputs - with auxiliary functions: normalidade.R, contar_NA.R and outliers.R;
• E. Repeatability for Morphometric Data.