DOI: 10.5061/dryad.4j0zpc8j9
title: Parallel and convergent evolution in genes underlying seasonal migration

description: 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 identify
 signals of putative selection in replicate comparisons between resident
 and migratory phenotypes within and between eastern and western clades.
 Overall, we find wide-spread support for parallel evolution at the genic
 level, particularly in genes that mediate biological
 timekeeping.  However, we find little evidence of parallelism at
 the individual SNP level, supporting the idea that there are multiple
 genetic pathways involved in the modulation of migration.
description: # 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. --- 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 the following
 software/packages: * bcftools: For manipulation and querying of VCF files.
 * vcftools: For analysis of VCF files, such as filtering or summarizing
 variant data. * Command-Line Visualization: to explore raw sequences (e.g.
 `COYE.fa`). ## data Files within this **data** repository include a
 **reference genome** used to map paired reads and a genome annotation,
 called **genotype files** from *GATK* and **genotype probability files**
 created in *ANGSD* analyses. Here, we also include the **population**
 files used to generate site allele frequencies for each population, data
 and scripts for **admixture** analyses and plots, and data used in the
 analyses of **FST outlier**, **selection scan** and phylogenetic
 reconstruction using **treemix**. * **`Reference_genome.zip`**: the Common
 Yellowthroat reference genome, and annotation data. * `COYE.fa` *
 `COYE.fa.fai` * `coye_final.all.clean.renamed.rm_matchp.sort.gff` *
 **`Genotype_files.zip`**: *
 `COYEP1-4c.merged_gatk.srs_filt.EAST.recode.vcf.gz`: called genotype file
 used in admixture analysis for eastern group. This file includes
 18,130,407 genotypes for 100 individuals. *
 `COYEP1-4c.merged_gatk.srs_filt.WEST.recode.vcf.gz`: called genotype file
 used in admixture analysis for western group. This file includes
 18,130,407 genotypes for 96 individuals. *
 **`Genotype_probability_files.zip`**: *
 `COYE.Plate1_4c.East.rm_rel.minInd50.05maf.baq.beagle.gz`: genotype
 probabilities of 100 eastern individuals from ANGSD that are used as input
 for the selection scan analysis. *
 `COYE.Plate1_4c.West.rm_rel.minInd50.05maf.baq.beagle.gz`: genotype
 probabilities of 96 eastern individuals from ANGSD that are used as input
 for the selection scan analysis. * **`Populations_angsd.zip`**: list of
 individuals per population to be compared (`bin/6.angsd_saf.sbatch`). *
 `AZ.list` : 12 individuals in the Arizona resident population. *
 `CA_n.list`: 10 individuals in the northern California resident
 population. * `FL_AL.list`: 18 individuals in the Eastern resident
 population. * `EAST_migrants.list`: 73 individuals from all migratory
 populations in the East, excluding North Carolina. * `WEST_migrants.list`:
 74 individuals from all migratory populations in the West. *
 **`Populations_admixture.zip`**: east and west datasets used in admixture
 analyses. * `popmap.east.txt`: 100 individuals from 11 localities. *
 `popmap.west.txt`: 96 individuals from 11 localities. *
 **`Admixture_plots.zip`**: * `admixture_pophelper_plots.R`: script used to
 plot admixture results. * `east`: files from the east group used for
 plotting admixture results. * `COYE.chr_number.east_cv_summary_k1_k6.txt`:
 summary of CV error values. * `.Q files`: Files that contain cluster
 assignments for each individual. * `west`: files from the west group used
 for plotting admixture results. *
 `COYE.chr_number.west_cv_summary_k1_k6.txt`: summary of CV error values. *
 `.Q files`: Files that contain cluster assignments for each individual. *
 **`FST_outlier_plots.zip`**: files and scripts used to calculate Fst
 within 50kb sliding windows, considering outlier regions that fell within
 the 99th percentile. * `AZ.West_migrants.COYE.baq.minInd4.fst.50kbwin.txt`
 *
 `AZ.West_migrants.COYE.baq.minInd4.realsfs.fst.siteA_B.out_unweighted.bed`
 * `CAn.West_migrants.COYE.baq.minInd4.fst.50kbwin.txt` *
 `CAn.West_migrants.COYE.baq.minInd4.realsfs.fst.siteA_B.out_unweighted.bed` * `FL_AL.East_migrants.COYE.baq.minInd4.fst.50kbwin.txt` * `FL_AL.East_migrants.COYE.baq.minInd4.realsfs.fst.siteA_B.out_unweighted.bed` * `MI.NB.COYE.baq.minInd4.fst.50kbwin.txt` * `MI.NB.COYE.baq.minInd4.realsfs.fst.siteA_B.out_unweighted.bed` * `WA.WY.COYE.baq.minInd4.fst.50kbwin.txt` * `WA.WY.COYE.baq.minInd4.realsfs.fst.siteA_B.out_unweighted.bed` * `99percentile.angsd.R` * **`Selection_scan.zip`**: This folder holds the scripts and results of the selection scan we used to estimate selection on positions in the east and west. The data files associated with this analysis are: east beagle files generated in angsd and the west beagle files generated in angsd. * `COYE.Plate1_4c.East.mafs.gz`: position file for selection scan of east COYE samples. * `COYE.Plate1_4c.East.sel_scan.selection.npy`: the result of the selection scan of east COYE samples. * `COYE.Plate1_4c.East.sel_scan.cov` * `COYE.Plate1_4c.West.mafs.gz`: position file for selection scan of west COYE samples. * `COYE.Plate1_4c.West.sel_scan.selection.npy`: the result of the selection scan of west COYE samples. * `COYE.Plate1_4c.West.sel_scan.cov` * `a.angsd_east_west.COYE.sh` * `b.selection_scan.COYE.sh` * `SelectionScanPCANGSD.Rmd`: This file contains the commands and packages to read Selection Scan results, such as `.npy` files (e.g. npyLoad function in RcppCNPy R package).  * `Manhattan_COYE.selection_scan.chr_order.R` * **`Treemix.zip`**: scripts and model used to convert the original vcf file into a readable file for treemix analysis using py-popgen, and the script to generate a phylogenetic reconstruction using. * `a.vcf_to_treemix.sbatch` * `b.treemix.sbatch` * `out.model` ## bin (Code/Software) Processing scripts: These bash scripts are submitted to our HPC cluster, to process raw fastq files, map to a reference COYE.fa genome, call genotypes with GATK HaplotypeCaller or generate genotype probabilities with ANGSD, and filter called genotypes. These scripts also include analysis scripts for population structure analyses (srsStuff, admixture), FST outlier analyses, selection scan analyses and treemix analyses. * **`1.trimgalore.COYE.sbatch`**: script to remove low quality fragments and trim adapters using *trimgalore*. * **`2.map.COYEP1.bwa_trim.sbatch`**: script to map paired reads to the Common Yellowthroat reference genome (`data/reference_genome/COYE.fa`) with *bwa 0.7.3a*, add read groups using *picard 2.23.2*, remove PCR duplicates and merge bam files using *samtools 1.11.0*. * **`3.coverage.sdepth.sbatch`**: script to calculate coverage using *samtools*. * **`4a.snpcalling_angsd.COYE.sbatch`**: script to get genotype probabilities using *angsd 0.935*. * **`4b.snpcalling_gatk.ALL.sbatch`**: script to get genotype calls using *GATK HaplotypeCaller*. * **`4c.mergevcf_nardfilter.COYE2.sbatch`**: This script merges all region-specifc vcf files generated in *GATK*. The script then selects SNPs, and filters based on maf and missingness. Hard filters for Variant Quality Score Recalibration (VQSR) were implemented, resulting in a final clean called genotype dataset. * **`5.allele_depth&srsStuff.Rmd`**: script to obtain allele depths using *bcftools*, identify relatedness and perform a PCA using *srsStuff*. * **`6.angsd_saf.sbatch`**: script to generate site allele frequencies for each population to be compared (`data/populations_angsd/`). * **`7.angsd_sfs.sbatch`**: script to determine global FST and identify regions potentially significant to migration strategy. * **`8a.admixture_east.sbatch`**: script used in admixture analysis for east group. * **`8b.admixture_west.sbatch`**: script used in admixture analysis for west group.