Population_Genetic_Structure

This pipeline and set of modules is introduced in Majoros et al. (2023) and the preprint is avaliable at https://www.biorxiv.org/content/10.1101/2023.01.23.524574v1 This repository includes R code for determining population genetic structure for various animal taxa and comparing structures across species with different biological traits. This script contains modules for reading in and filtering data, organizing data into clusters, grouping by region, running a multiple seqeunce alignment, calculating F-statisitcs and multi-allelic measures, calculating analysis of molecular variance, calaculating mismatch distributions, generating a phylogenetic tree, calculating analysis of variance, and calculating phylogenetic generalized least squares analyses. The modules can be used together or separately based on the researchers needs. The pipeline is designed to determine population genetic structure measures for a variety of taxa. My analysis was completed by running all modules as a pipeline, and can be repeated using the full script and data provided. The pipeline was tested using Diptera species from Greenland as a small example analysis, and Diptera species form Canada as an example of a larger, more complex analysis.