Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird

Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations. Across island systems, contemporary patterns of genetic diversity reflect complex population demography, including colonisation events, bottlenecks, gene flow and genetic drift. Here, we investigate whether island founder events have prolonged effects on genome-wide diversity and runs of homozygosity (ROH) distributions, using whole genome resequencing from six populations across three archipelagos of Berthelot’s pipit (Anthus berthelotii) – a passerine which has undergone island speciation relatively recently. Pairwise sequential Markovian coalescent (PSMC) analyses estimated divergence from its sister species approximately two million years ago. Results indicate that all Berthelot’s pipit populations had shared ancestry until approximately 50,000 years ago, when the Madeiran archipelago populations were founded, while the Selvagens were colonised within the last 8,000 years. We ide..., Whole genome data from six populations of Berthelot's pipit across the three archipelagos of their range in the North Atlantic. Resequencing data was generated by mapping Illumina HiSeq reads to a reference genome and calling variants using GATK HaplotypeCaller., README_datasets.txt Describes the datasets and outlines their usage to recreate and explore the findings in the current manuscript.
All Pipits, Berthelots and Tawny VCF files These are the three datasets in variant call format as referred to in the manuscript.
Individual level .fastq filesThese files are used to generate the input files required to run the PSMC analyses, on an individual-by-individual basis. Example files are given for EH_161
Chromosome codes Genome_chromosome_codes.txt file contains Zebra finch (Taeniopygia guttata) chromosome names and their equivalent numeric codes used in the VCF files.
SCRIPTS.sh Code used to undertake analyses outlined in this paper. These scripts must be run prior to R script to produce associated outputs.
R scripts to produce tables, figures and statistics ROH_analyses.R details R scripts and produces output figures and statistics detailed in the manuscript.
Creating VCF datasets
The first steps are detailed in example_gVCF.sh, which contains t...