DOI: 10.5061/dryad.s1rn8pkgh
title: Data from: Genetic structure and demographic history of house mice in Western Europe inferred using whole genome sequences

description: The movement of human populations has greatly influenced the distributions
 of human commensals. Patterns of genetic variation in contemporary
 populations can shed light on their demographic history, including
 long-range migration events and changes in effective population size. The
 western house mouse, Mus musculus domesticus, is a human commensal and an
 outstanding model organism for studying a wide variety of traits and
 diseases. However, we have few genomic resources for wild mice and only a
 rudimentary understanding of the demographic history of house mice in
 Europe. Here, we sequenced 59 whole-genomes of mice collected from
 England, Scotland, Wales, Guernsey, northern France, Italy, Portugal, and
 Spain. We combined this dataset with 24 previously published sequences
 from southern France, Germany, and Iran, and compared patterns of
 population structure and inferred demographic parameters for house mice in
 Western Europe to patterns seen in humans. Principal component and
 phylogenetic analyses identified three genetic clusters in Western
 European mice. Admixture and f-branch statistics identified historical
 gene flow between these genetic clusters. Demographic analyses suggest a
 shared history of population bottlenecks prior to 20,000 years ago.
 Estimated divergence times between populations of house mice from Western
 Europe ranged from 1,500 to 5,500 years ago, in general agreement with the
 zooarchaeological record. These results correspond well with key aspects
 of contemporary human population structure and the history of migration in
 Western Europe, highlighting the commensal relationship of this important
 genetic model.
description: # Data from: **Genetic structure and demographic history of house mice in
 Western Europe inferred using whole genome sequences**
  https://doi.org/10.5061/dryad.s1rn8pkgh *
 **ALL_Europe_unfiltered_merged_noAlloption.vcf.gz** Unfiltered vcf of 59
 wild-caught house mice from England, Scotland, Wales, Guernsey, northern
 France, Italy, Portugal, and Spain collected and deposited as prepared
 specimens in the University of Michigan, Museum of Zoology, and 24
 wild-caught mice from southern France, Germany, and Iran from a previous
 publication (Harr et al. 2016). Sequences were aligned to the mouse
 reference genome (GRCm38/mm10, RefSeq: GCF_000001635.20). See Tables S1
 and S2 of the associated manuscript for sample information, including
 sample locations and alignment statistics. **Sharing/Access information**
 The raw fastq files used to generate this data is accessible from: * NCBI
 SRA BioProject ID PRJNA1050608 -
 **ALL_Europe_83samples_filtered_merged_autosomes.recode.vcf.gz** Filtered
 vcf of 83 wild-caught house mouse samples combining autosomal SNPs from 59
 whole-genomes of mice collected from England, Scotland, Wales, Guernsey,
 northern France, Italy, Portugal, and Spain with autosomal SNPs from 24
 previously published sequences from southern France, Germany, and Iran
 (Harr et al. 2016). Information on all sequences can be found in Materials
 and Methods of associated manuscript. Specific sample collection and
 alignment information on 59 newly sequenced whole-genomes can be found in
 Tables S1 and S2, and similar details can be found on 24 previously
 published sequences in Harr et al. 2016.