Overview

This page represents an effort to aggregate all existing whole-genome sequence data from wild house mice (Mus musculus) in a single location. For now I have dubbed it, unofficially, the Wild Mouse Genomes Project, although this is not an entity recognized by any institution or funding agency. The data linked here is either available in public repositories, or submission to such repositories is in process. The underlying biological specimens have been described in published literature. Except where otherwise indicated, the maintaner of this website does not claim credit for either the sequence data or the underlying biological specimen, and users of this data are encouraged to contact the data generators with any questions regarding provenance, reanalysis or reuse.

Primary data comes from the following publications. Please cite them if using this data in pubished work.

1. Halligan DL, et al. (2013) Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents. PLoS Genetics 9: e1003995.  10.1371/journal.pgen.1003995
2. Davies RW (2015) Factors influencing genetic variation in wild mice. PhD thesis, University of Oxford.  link to Oxford University Research Archive
3. Harr B, et al. (2016) Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus. Scientific Data 3: 160075.  10.1038/sdata.2016.75
4. Pfifer-Rixey M, et al. (2018) The genomic basis of environmental adaptation in house mice. PLoS Genetics 14: e1007672.  10.1371/journal.pgen.1007672
5. Payseur BA, et al. (2021) Genomic targets of positive selection in giant mice from Gough Island. Molecular Biology and Evolution 38: 911--926.  10.1093/molbev/msaa255
6. Fujiwara K, et al. (2022) Insights into Mus musculus population structure across Eurasia revealed by whole-genome analysis. Genome Biology and Evolution 14: evac068.  10.1093/gbe/evac068
7. Morgan AP, et al. (2022) Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales. Heredity 129: 183--194.  10.1038/s41437-022-00551-z
8. Lawal RA, et al. (2022) Taxonomic assessment of two wild house mouse subspecies using whole-genome sequencing. Scientific Reports 12: 20866.  10.1038/s41598-022-25420-x

Should users of this site identify any errors or misrepresentations, please contact me via email 

Methods

Raw paired-end sequence reads were dowloaded from the European Nucleotide Archive and aligned against the most recent version of the mouse reference genome, the GRCm39/mm39 assembly. The reference sequence was obtained from UCSC, so chromosome and contig names follow their nomenclature (chr1, ... chrM). Because the pseudoautosomal region (PAR) is the only region of the genome represented as diploid rather than haploid in the reference, one copy was masked (sequence forced to N) to avoid read-depth artefacts between sexes. Reads were aligned with bwa mem with default parameters, and putative optical/technical duplicates marked with samblaster in a streaming fashion. When applicable, alignments from multiple lanes per individual were merged with Picard. The resulting alignments were indexed with samtools in the usual fashion.

Sample sex and preliminary taxonomic assignment in the table below are based on a combination of information provided in the original publications and preliminary SNV calls in coding regions.

Full pipeline to be available on Github soon.

Alignments are available in *.bam format via Amazon Web Services in the public S3 bucket wild-mouse-genomes. No guarantee is made as to how long these files will be available as there is no funding stream to cover storage costs.

Samples

The table below lists samples currently available as part of the Wild Mouse Genomes Project. Sample IDs are those assigned by the original authors. Taxon assignments should be considered preliminary at best -- many of these individuals are inter-subspecies hybrids but are labelled with their "modal" ancestry. Location metadata is taken from the original publications. Countries are denoted by ISO 3166 2-letter code. "Region" and "site" are meant to indicate increasingly precise geographic place names. "Locale" is a 3-letter code, assinged by the author of this page, as a convenience for data aggregation. NB: None of the geographic labels here necessarily correspond to a "population" in the ecological or genetic sense.

"Accessions" link to the European Nucleotide Archive, which also mirrors the NCBI Short Read Archive (USA) and DDBJ (Japan). "BAM" and "index" link to the full alignment and index files, respectively, in AWS S3. MD5 checksums can be found here. For batch downloads, a text file of URLs to BAM files is here.

Acknowledgements

The community of researchers interested in the genetics of wild mice is indebted to the many people who collected mice, prepared specimens for sequencing, and generated sequence data. I am grateful to Bret Payseur, Michael Nachman, Megan Phifer-Rixey, Betina Harr, Jeremy Searle, Diethard Tautz, Francois Bonhomme, Robbie Davies, Richard Mott, Beth Dumont, Fernando Pardo-Manuel de Villena and many others who have helped me to navigate the literature and keep track of available datasets. This project would not be possible without the support of the Research Computing service at the University of North Carolina at Chapel Hill.