Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance

Declines in bumblebee species ranges and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumblebee (Bombus affinis) is the first federally-listed bumblebee species in North America. We conducted a range-wide population genetics study of B. affinis from across all extant conservation units to inform conservation efforts. To understand the species’ vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range wide male diploidy rate of ~15%. Our results suggest..., Please see the published manuscript for full data collection details. , , # README

\**CAUTION** Results sensitive to lat-long for users of this dataset will be slightly different than the published version due to the need to obscure coordinates of collections of an endangered species. If precise reproducibility is required, and necessary credentials/permits are held by the research team, exact coordinates can be provided upon request.

**EXPLANATION OF FILES AND DIRECTORY STRUCTURE**

This repository is intended to document the code behind the project \"Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance\". The code is all written in R.

Anyone who downloads this repository should be able to reconstruct the results of the analysis. Two steps require downloading software outside of R: COLONY and STRUCTURE. Included within these scripts are the input steps to feed into these pieces of software, and then the wrangling steps to take the output and wrangle it in R. Th...