On the basis of patterns of allele frequency variation in nuclear genes (Din et al., in press) it has been proposed that the house mouse M. musculus originated in the northern Indian subcontinent, from where it radiated in several directions to form the well-described peripheral subspecies (M. m. domesticus, M. m. ~~lusculu.s and M. MZ. custuneus). Here we use a mitochondrial DNA (mtDNA) phylogeny to test this hypothesis and to analyse the historical and demographic events that have accompanied this differentiation. This marker also provides a powerful means to check for genetic continuity between the central and peripheral populations. We studied restriction site polymorphism of samples from India and the Middle East as well as samples from the rest of Eurasia and northern Africa. M. m. domesticus and M. m. muscdus are both monophyletic for mtDNA and belong to the subspecies-specific mtDNA lineages that have been described previously. Average nucleotide diversity is low in M. 112. mu,r~ulu.s (0,2L5%). It is not only higher in M. m. domesticus (0.7-0.9%) but the distribution of pairwise divergence is wider, and the rate of evolution in this branch appears to be higher than in M. m. mus~u/us. The nucleotide diversity found in M. m. castaneus (0.4%) is due to the existence of two rather divergent linages with little intralineage variation. These two lineages are part of a diversified bush of the phylogenetic tree that also comprises several previously undescribed branches and includes all samples from the northern Indian subcontinent and Iran. The degree of diversity found in each of the samples from this region is high (1.2Z2.4%) although they come from small geographic areas. This agrees well with the idea that the origin of the radiation was in the northern Indian subcontinent. However, as neither haplotypcs on the M. MI. r1on~c.vtia1.v nor on the M. 171. ~~~cr.sc~ulus branches were found in this region, there appear to be important phylogeographic discontinuities between this central region and these periphcrial subspecies. On the basis of the present results and the nuclear data (Din et al., in press), we propose that M. n~u.cc~u1zr.s originated in the north of the Indian subcontinent. Our calibration of the evolutionary rate of mtDNA in mice suggests that the mouse settlement in this region could be as old as 900 000 years. Possibly from there, a first radiation could have reached the Middle East and the Caspian Sea, where the M. 1~. ~lot~~~stic~~~.s and M. tw. t~~u.s~~du.s lineages, respectively, would have started to difrcrentiate a few hundred thousand years ago, and from where they could have coloniscd the peripheral part of their ranges only recently. M. MI. c~ostmcus appears from its mtDNA to be a recent offshoot of the northern Indian population. This multiple and gradual radiation ultimately led to recent peripheral secondary contacts, such as the well-known European hybrid zone.

Although quite a lot is known about the genetic structure of the polytypic species Mus musculus at the periphery of its range, the centre of origin and dispersion of the species remains unknown. To investigate the amount of genetic subdivision that occurs in the central parts of its range, we analysed the genetic variation in four new samples of mice coming from Iran, Pakistan, northern and southern India using 3.5 autosomal protein loci and restriction fragment length polymorphisms of three genes of the Vg gene complex of the immune system. The variation was then compared with that found in the subspecies occupying the peripheral regions of the species range. The two samples from the northern part of the Indian subcontinent were shown to be more heterozygous than the samples from any of the other regions. They also contain the majority of the alleles that exist in the differentiated subspecies at the periphery of the species range. A neighbour-joining analysis on Nei's genetic distances and a factorial analysis of correspondences on the allelic composition of each sample both place the Pakistani and Indian populations in a phylogenetically and genetically central position compared to the peripheral subspecies. These results suggest that the populations in this geographically central area have retained most of the ancestral polymorphisms, which in turn indicates that the Indian subcontinent is probably the cradle of the species. The nature of the genetic relationships between the various populations throughout the species range and the possibility that they form an incipient ring species are also discussed. Our results are in agreement with the classical model of geographic differentiation where genetic divergence in allopatry is considered to be the prime cause of subspecies formation that may eventually lead to partial reproductive isolation on secondary contact.

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