DOI: 10.5061/dryad.5qfttdzh4
title: Population genomics of big mice from the Faroe islands: Hybridization, colonization, and a new challenge to identifying genomic targets of selection

description: Populations that colonize islands provide unique insights into demography,
 adaptation, and the spread of invasive species. House mice on the Faroe
 Islands evolved exceptionally large bodies after colonization, generating
 interest from biologists going back to Darwin. To reconstruct the
 evolutionary history of these mice, we sequenced genomes of population
 samples from three Faroe Islands (Nolsoy, Sandoy, Mykines) and Norway as a
 mainland comparison. Mice from the Faroe Islands are inferred to be
 hybrids between the subspecies Mus musculus domesticus and M. m. musculus,
 with ancestry alternating along the genome. The mice are predominantly M.
 m. domesticus in origin, reflecting repeated backcrossing to this
 subspecies following initial hybridization. Analyses based on the site
 frequency spectrum of single nucleotide polymorphisms and the ancestral
 recombination graph indicate that mice spread to the Faroe Islands on a
 timescale consistent with dispersal by Norwegian Vikings, with
 colonization of Sandoy likely preceding colonization of Nolsoy.
 Substantial reductions in nucleotide diversity and effective population
 size associated with colonization are inferred, raising the prospect that
 mice on the Faroe Islands evolved large body size during periods of
 heightened genetic drift. Genomic scans for positive selection uncover
 windows with unusual site frequency spectra, but this pattern is mostly
 generated by clusters of singletons in individual mice. Variants showing
 evidence of selection based on the ancestral recombination graph in Nolsoy
 and Sandoy are enriched for genes with neurological functions. Our
 findings reveal a dynamic evolutionary history for the enigmatic mice from
 Faroe Island and emphasize the challenges that accompany population
 genomic inferences in island populations.
description: # Population genomics of big mice from the Faroe islands: Hybridization,
 colonization, and a new challenge to identifying genomic targets of
 selection Dataset DOI: [10.5061/dryad.5qfttdzh4](10.5061/dryad.5qfttdzh4)
 ## Description of the data and file structure There are four SNP vcf
 files, one for each of the four following population groups: 12 unrelated
 wild mice from Faroe island Sandoy; 8 unrelated wild mice from Faroe
 island Nólsoy; 7 unrelated wild mice with *domesticus (Mus musculus
 domesticus)*-major ancestry (More *domesticus *ancestry than *musculus* or
 heterogeneous ancestry) from Norway; 6 unrelated wild mice with *musculus
 (Mus musculus musculus)*-major ancestry (More *musculus* ancestry than
 *domesticus* or heterogeneous ancestry) from Norway. All Norway samples we
 sequenced are hybrids between *domesticus* and *musculus*. Tissue and DNA
 samples were provided by our collaborators. Illumina NovaSeq 150bp
 pair-end sequencing was completed by UW-Madison Genome Sequencing Center.
 The files can be viewed using Bcftools. They can also be viewed using text
 editors or options 'more' or 'less' on Linux. They can
 also be manipulated with Bcftools or Vcftools. All tools used are open
 source software. The SNP calling steps are described below and the
 commands were provided in two scripts (bwa_alignment*.*sh and
 snp*_*calling.sh). 1. Reads were mapped to reference genome mm10 using bwa
 (version 0.7.17) mem. 2. PCR and optical duplicates were marked and
 removed with Picard (version 2.24.0). 3. GATK (version 4.2.3.0) was used
 to call and filter variants for each population separately and short
 indels were removed. 4. Vcf files for all populations were merged
 together, and missing genotypes were identified for each population. 5.
 Missing genotypes were filled in using GATK –all-sites option for each
 population 6. Original genotype calls and missing genotype calls were
 merged together.  ### Files and variables #### File:
 snps\_domesticusMajor\_norway7.vcf.gz **Description:** SNPs for seven wild
 unrelated Norway mice whose genomes have majority of domesticus ancestry.
 #### File: snps\_musculusMajor\_norway6.vcf.gz **Description:** SNPs for
 six wild unrelated Norway mice whose genomes have majority of musculus
 ancestry. #### File: snps\_nolsoy8.vcf.gz **Description:** SNPs for eight
 wild unrelated mice from Faroe island Nólsoy. #### File:
 snps\_sandoy12.vcf.gz **Description:** SNPs for twelve wild unrelated mice
 from Faroe island Sandoy. ## Code/software Please see
 files bwa_alignment.sh and snp_calling.sh. The steps to call snps with
 GATK described here are standard procedure. Please see GATK best
 practices: https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows ## Access information Other publicly accessible locations of the data: * Raw sequencing reads are available from NCBI's Sequence Read Archive under the BioProject accession PRJNA1233310. Data was derived from the following sources: *