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. 

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. 

README_datasets.txt 
Describes the datasets and outlines their usage to recreate and explore the findings in the current publication. 

SCRIPTS.sh
Code used to undertake anlayses outlined in this paper as detailed in Table S1 of the current manuscript. 
These scripts must be run prior to R scripts to produce outputs.

R scripts to produce tables, figures and statistics
FUNCTIONS, LOAD, CLEAN and DO scripts for population genetics/demography and selection results.
You are only 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. 

Morphology PCA and GLLM models
geno-pheno_analyses.R script produces the outputs relating to ADAM12 loci association analyses.

Berthelots and All Pipits .bed files
This includes the zipped .bed and associated .bim and .fam files for each dataset.

Pipit sample information
pipit_sample_information.csv file contains phenotypic and population information for each pipit sample.

Chromosome codes 
chromosome_codes.txt file contains zebra finch (Taeniopygia guttata) chromosome names, and their equivalent numeric codes used in the .bim files.