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Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among house mouse subspecies

François Bonhomme1*, Eric Rivals2, Annie Orth1, Gemma R Grant3, Alec J Jeffreys3 and Philippe RJ Bois34

Author Affiliations

1 Biologie Intégrative, ISEM CNRS Université de Montpellier 2 UMR 5554, Montpellier 34095, France

2 LIRMM, CNRS Université de Montpellier 2 UMR 5506, rue Ada, Montpellier 34392 Cedex 5, France

3 Department of Genetics, University of Leicester, Leicester LE1 7RH, UK

4 The Scripps Research Institute, Department of Cancer Biology, Genome Plasticity Laboratory, Parkside Drive, Jupiter, Florida 33458, USA

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Genome Biology 2007, 8:R80  doi:10.1186/gb-2007-8-5-r80

Published: 14 May 2007



Four hypervariable minisatellite loci were scored on a panel of 116 individuals of various geographical origins representing a large part of the diversity present in house mouse subspecies. Internal structures of alleles were determined by minisatellite variant repeat mapping PCR to produce maps of intermingled patterns of variant repeats along the repeat array. To reconstruct the genealogy of these arrays of variable length, the specifically designed software MS_Align was used to estimate molecular divergences, graphically represented as neighbor-joining trees.


Given the high haplotypic diversity detected (mean He = 0.962), these minisatellite trees proved to be highly informative for tracing past and present genetic exchanges. Examples of identical or nearly identical alleles were found across subspecies and in geographically very distant locations, together with poor lineage sorting among subspecies except for the X-chromosome locus MMS30 in Mus mus musculus. Given the high mutation rate of mouse minisatellite loci, this picture cannot be interpreted only with simple splitting events followed by retention of polymorphism, but implies recurrent gene flow between already differentiated entities.


This strongly suggests that, at least for the chromosomal regions under scrutiny, wild house mouse subspecies constitute a set of interrelated gene pools still connected through long range gene flow or genetic exchanges occurring in the various contact zones existing nowadays or that have existed in the past. Identifying genomic regions that do not follow this pattern will be a challenging task for pinpointing genes important for speciation.