This repository contains code used in analyses and to produce figures for:
de Medeiros, B.A.S., Farrell, B.D. Evaluating insect-host interactions as a driver of species divergence in palm flower weevils. Commun Biol 3, 749 (2020). https://doi.org/10.1038/s42003-020-01482-3
Most of the R code was written as Rmarkdown files, and the html output including results and plots is also provided.
In each folder, scripts are numbered according to the order in which they were used
These folders contain parameter files and bash scripts used to assemble datasets with ipyrad.
Custom python scripts used to convert ipyrad output files to nexus and genpop formats, used in analysis for initial species delimitation
Scripts used in initial delimitation of cryptic weevil species and plot PCA results.
Analyses using ANGSD, PCAngsd and NGSdist, including:
- filter sites by Hardy-Weinberg equilibrium using population structure
- estimate genetic distances
- estimate site frequency spectra
- estimate genetic covariance
Scripts used to run and plot results for cross-validation for model selection as well as the best model in bedassle2.