Parallel and convergent evolution in genes underlying seasonal migration

Seasonal migration has fascinated scientists and natural historians for centuries.  While the genetic basis of migration has been widely studied across different taxa, there is little consensus regarding which genomic regions play a role in the ability to migrate and whether they are similar across species.  Here, we examine the genetic basis of intraspecific variation within and between distinct migratory phenotypes in a songbird. We focus on the Common Yellowthroat (Geothlypis trichas) as a model system because the polyphyletic origin of eastern and western clades across North America provides a strong framework for understanding the extent to which there has been parallel or convergent evolution in the genes associated with migratory behavior.  First, we investigate genome-wide population genetic structure in the Common Yellowthroat in 196 individuals collected from 22 locations across breeding range. Then, to identify candidate genes involved in seasonal migration, we..., , , # Parallel and convergent evolution in genes underlying seasonal migration: Repository

## Luz E. Zamudio-Beltrán, Christen M. Bossu, Alfredo A. Bueno-Hernández, Peter O. Dunn, Nick D. Sly, Christine Rayne, Eric C. Anderson, Blanca E. Hernández-Baños, Kristen C. Ruegg.

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This repository includes the scripts and data used in the analyses performed in Zamudio-Beltrán et. al. 2024. This also contains the scripts and files to visualize results in plots.

This study includes low coverage whole genome sequencing data from 202 individuals of the Common Yellowthroat warbler (*Geothlypis trichas*). Raw reads were processed following a pipeline adapted from the *GATK Best Practices Guide* (Van der Auwera et al., 2013).

## Description of the data and file structure

Files within this repository are organized in two main directories: **data** and **bin**.

## Usage notes

Files within this repository may contain genomic variant data, including SNPs and annotations. We recommend the usage of th...,