DOI: 10.5061/dryad.ksn02v75k
title: Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird

description: 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
 identify extensive long ROH (&gt;1 Mb) in genomes in the most recently
 colonised populations of Madeira and Selvagens which have experienced
 sequential island founder events and population crashes. Population
 expansion within the last 100 years may have eroded long ROH in the
 Madeiran archipelago, resulting in a prevalence of short ROH (&lt;1
 Mb). Extensive long and short ROH in the Selvagens reflects strong recent
 inbreeding, small contemporary effective population size and past
 bottleneck effects, with as much as 37.7% of the autosomes comprised of
 ROH &gt;250 kb in length. These findings highlight the importance of
 demographic history, as well as selection and genetic drift, in shaping
 contemporary patterns of genomic diversity across diverging
 populations. 
description: 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.
description: <strong>README_datasets.txt </strong><br>Describes the datasets and outlines their usage to recreate and explore the findings in the current manuscript. <strong>All Pipits, Berthelots and Tawny VCF files </strong><br>These are the three datasets in variant call format as referred to in the manuscript. <strong>Individual level .fastq files</strong><br>These 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 <strong>Chromosome codes </strong><br><em>Genome_chromosome_codes.txt</em> file contains Zebra finch (<em>Taeniopygia guttata</em>) chromosome names and their equivalent numeric codes used in the VCF files. <strong>SCRIPTS.sh </strong><br>Code used to undertake analyses outlined in this paper. <br>These scripts must be run prior to R script to produce associated outputs. <strong>R scripts to produce tables, figures and statistics </strong><br>ROH_analyses.R details R scripts and produces output figures and statistics detailed in the manuscript. <strong>Creating VCF datasets</strong> The first steps are detailed in <em>example_gVCF.sh</em>, which contains the pipeline used to generate the GATK haplotype called gVCF file on an individual-by-individual basis (for further details see <em>gvcf pipeline description.txt</em>).  Second individual gVCF files are converted to joint genotype called VCF datasets, and contig locations are mapped to Zebra finch chromosomes using SatsumaSynteny. This pipeline is detailed in <em>gvcf</em> to <em>vcf.txt</em>. Third, <em>Satsuma_output_vcf.R</em> is used on the output files from SatsumaSynteny to assign contigs to chromosomes, and determine their order, location and orientation.  Finally, the three VCF datasets detailed in this manuscript are created and filtered; Tawny is created directly from gVCF to VCF, Berthelot’s by joint calling all 11 Berthelot’s gVCF files and All pipits by joint calling all Berthelot’s induvial and the Tawny sample gVCFs.