The genome of the laboratory mouse is thought to be a mosaic of regions with distinct subspecific origins. We have developed a high-resolution map of the origin of the laboratory mouse by generating 25,400 phylogenetic trees at 100-kb intervals spanning the genome. On average, 92% of the genome is of Mus musculus domesticus origin, and the distribution of diversity is markedly nonrandom among the chromosomes. There are large regions of extremely low diversity, which represent blind spots for studies of natural variation and complex traits, and hot spots of diversity. In contrast with the mosaic model, we found that most of the genome has intermediate levels of variation of intrasubspecific origin. Finally, mouse strains derived from the wild that are supposed to represent different mouse subspecies show substantial intersubspecific introgression, which has strong implications for evolutionary studies that assume these are pure representatives of a given subspecies.
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We thank S. Ahmed for technical assistance; K. Paigen, K. Broman and B. Payseur for helpful comments during the preparation of the manuscript; J. Felsenstein for advice and L. Wu for assistance with the phylogenetic tree computations and A. Smith for developing a genome browser format for displaying phylogenetic trees. CIM/Pas was provided by F. Bonhomme (University Mont Pellier II). This work was supported by the US National Institute of General Medical Sciences as part of the Center of Excellence in Systems Biology (1P50 GM076468).
The authors declare no competing financial interests.
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Yang, H., Bell, T., Churchill, G. et al. On the subspecific origin of the laboratory mouse. Nat Genet 39, 1100–1107 (2007). https://doi.org/10.1038/ng2087
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