Sagebrush population genetics analysis pipeline

This repository hosts data and code for the population genetic analyses performed in Grossfurthner et al. (2023) Population structure and hybridization under contemporary and future climates in a heteroploid foundational shrub species (Artemisia tridentata). The free full text can be found here.

This project aimed to identify the distinctiveness of Artemisia tridentata subspecies as well as the detection of hybridization. To this end, we sampled five transects throughout the western United States where a subspecies overlap was predicted using subspecies-specific climate niche models. Along each transect, we sampled multiple plots representing the parental and the potential hybrid habitats. We performed reduced representation sequencing and processed the data using a ploidy-informed genotyping approach. Here, I provide the basic codes used for the analyses of the heteroploid data. Additional analyses, annotations and bug-fixes will follow soon.