We evaluated the house mouse (Mus musculus species complex) and its la
boratory descendents as models for three aspects of systematic biology
: hybrid zone biology, chromosomal evolution and speciation, and tests
for methods of phylogenetic reconstruction. The taxonomy and genetic
relationships of the species in the complex are summarized. The compar
ative phylogenetic method was used to illucidate biogeographical, ecol
ogical, and chromosomal events in the group. Hybridization in house mi
ce was evaluated with respect to the emerging discipline of hybrid zon
e biology. Inter- and intraspecific contact zones are described and co
mpared. Zone-specific electrophoretic alleles, new metacentric chromos
omes, and increased levels of parasitism are explained as consequences
of genome disruption. The interspecific zone is widest in the area of
most recent contact between species. Variation in the widths of indiv
idual clines is discussed. Chromosomal evolution is proceeding along a
lternative paths in different commensal lineages of house mice. A kary
otypic revolution occurred within the species M. domesticus that led t
o the reproductive isolation between two local populations. The recenc
y of this karyotypic revolution permits a study of how Robertsonian po
pulations evolve and an evaluation of whether the stasipatric model of
speciation is a good explanation for this case. The genealogical hist
ory of the inbred strains of mice is well known, and this information
has been used to test how faithfully different kinds of data and diffe
rent kinds of analytical techniques recreate the known phylogeny. Mole
cular data recapture the correct phylogeny better than do morphologica
l data, and the commonly used analytical methods are all equally robus
t in producing this phylogeny.