This repository contains R scripts used for figures and analysis in O'Donnell et al. (2022) Molecular and morphological analyses support recognition of Prostanthera volucris (Lamiaceae), a new species from the Central Tablelands of New South Wales
MAP - This script produces a species distribution map with cartographic features, seen as Fig. 1 in O'Donnell et al. (2022)
DART - This script outlines the processing and analysis pipeline that was used on genomic SNP data delivered by DArTseq. This includes:
- Data import and filtering
- Identification and removal of potential clones
- PCA ordination
- Compute a distance matrix and export for Neighbour-Network analysis in SplitsTree
- Calculate species and population level statistics
- SNMF clustering analysis
- SNMF plotting (bar plot and map with pie charts)
- Create data subset for coalescent analysis
- Export SNP matrix to SVDQuartets
- Import and plot resultant phylogeny