DOI: 10.5061/dryad.pc866t1kt
title: Data from: Genomic variation, population history and within-archipelago adaptation between island bird populations

description: Oceanic island archipelagos provide excellent models to understand
 evolutionary processes. Colonisation events and gene flow can interact
 with selection to shape genetic variation at different spatial scales.
 Landscape-scale variation in biotic and abiotic factors may drive
 fine-scale selection within islands, while long-term evolutionary
 processes may drive divergence between distantly related populations.
 Here, we examine patterns of population history and selection between
 recently diverged populations of the Berthelot’s pipit (Anthus
 berthelotii), a passerine endemic to three North Atlantic archipelagos.
 First we use demographic trees and f3 statistics to show that genome-wide
 divergence across the species range is largely shaped by colonisation and
 bottlenecks, with evidence of very weak gene flow between
 populations. Then, using a genome scan approach, we identify signatures of
 divergent selection within-archipelagos at SNPs in genes potentially
 associated with craniofacial development and DNA repair. We did
 not detect within-archipelago selection at the same SNPs as were detected
 previously at broader spatial scales between archipelagos, but did
 identify signatures of selection at loci associated with similar
 biological functions. These findings suggest that similar ecological
 factors may repeatedly drive selection between recently separated
 populations, as well as at broad spatial scales across varied
 landscapes. 
description: Double digest restriction site-associated DNA sequencing
 (RAD-seq) and morphological data across 13 wild caught populations of the
 Berthelot's pipit across their range in the North
 Atlantic. 
description: <strong>README_datasets.txt</strong> <br>
 Describes the datasets and outlines their usage to recreate and explore
 the findings in the current publication. 
 <strong>SCRIPTS.sh</strong><br> Code used to
 undertake anlayses outlined in this paper as detailed in Table S1 of the
 current manuscript. <br> These scripts must be run <em>prior
 </em>to R scripts to produce outputs.
 <strong>R scripts to produce tables, figures and
 statistics</strong><br> FUNCTIONS, LOAD, CLEAN and DO scripts
 for population genetics/demography and selection results.<br> You
 are <em>only</em> required to run the RAD_Demography_DO.R and
 RAD_Selection_DO.R scripts. This script calls on the FUNCTIONS, LOAD,
 CLEAN scripts to produce the output figures and statistics. 
 <strong>Morphology PCA and GLLM
 models</strong><br> geno-pheno_analyses.R script produces the
 outputs relating to ADAM12 loci association analyses.
 <strong>Berthelots and All Pipits .bed
 files</strong><br> This includes the zipped .bed and
 associated .bim and .fam files for each dataset.
 <strong>Pipit sample information</strong><br>
 pipit_sample_information.csv file contains phenotypic and population
 information for each pipit sample.
 <strong>Chromosome codes</strong> <br>
 chromosome_codes.txt file contains zebra finch (Taeniopygia guttata)
 chromosome names, and their equivalent numeric codes used in the .bim
 files.