Insights into Mus musculus population structure across Eurasia revealed by whole-genome analysis

For more than 100 years, house mice (Mus musculus) have been used as a key
animal model in biomedical research. House mice are genetically diverse,
yet their genetic background at the global level has not been fully
understood. Previous studies suggested that they originated in South Asia
and diverged into three major subspecies almost simultaneously,
approximately 350,000–500,000 years ago; however, they have spread across
the world with the migration of modern humans in prehistoric and historic
times (∼10,000 years ago to present), and undergone secondary contact,
which have complicated the genetic landscape of wild house mice. In this
study, we sequenced the whole genomes of 98 wild house mice collected from
Eurasia, particularly East Asia, Southeast Asia, and South Asia. We found
that although wild house mice consist of three major genetic groups
corresponding to the three major subspecies, individuals representing
admixture between subspecies are much more ubiquitous than previously
recognized. Furthermore, several samples showed an incongruent pattern of
genealogies between mitochondrial and autosomal genomes. Using samples
likely retaining the original genetic components of subspecies with least
admixture, we estimated the pattern and timing of divergence among the
subspecies. The results are important for understanding the genetic
diversity of wild mice on a global level and the information will be
particularly useful in future biomedical and evolutionary studies using
laboratory mice established from these wild mice.