We suggest that the evolution of the population structure of microbial pathogens is influenced by that of modern humans. Consequently, the timing of hallmark changes in bacterial genomes within the last 100,000 yr may be attempted by comparison with relevant human migrations. Here, we used a lineage within Mycobacterium tuberculosis, a Beijing genotype, as a model and compared its phylogeography with human demography and Y chromosome-based phylogeography. We hypothesize that two key events shaped the early history of the Beijing genotype: (1) its Upper Palaeolithic origin in the Homo sapiens sapiens K-M9 cluster in Central Asia, and (2) primary Neolithic dispersal of the secondary Beijing NTFϻIS6110 lineage by Proto-Sino-Tibetan farmers within east Asia (human O-M214/M122 haplogroup). The independent introductions of the Beijing strains from east Asia to northern Eurasia and South Africa were likely historically recent, whereas their differential dissemination within these areas has been influenced by demographic and climatic factors.[Supplemental material is available online at www.genome.org.]Intriguing clues about the history of a biological species can be derived from the study of the geographical distribution of the phylogenetic/genealogical lineages, in the approach known as "phylogeography" (Avise et al. 1987). The underlying assumption of human phylogeography is that there is a correspondence between the overall distribution of haplotypes and haplogroups and past human movements. The uniparentally inherited nonrecombining haploid mtDNA and the Y chromosome loci are particularly sensitive to the influences of drift, especially founder effect. Consequently these loci are suitable for assessing the origins of contemporary population diversity and provide context for paleontological hypothesis testing (Foley 1998). The mutation rate of the maternally transmitted mitochondrial genome is ∼10 times higher than that of nuclear DNA, which provides abundance of polymorphic sites but creates difficulties in reconstructing genealogies owing to repeated and reverse mutations. By contrast, the mutation rate of the paternally inherited nonrecombining portion of the Y chromosome (NRY) is comparable to that of nuclear DNA, which means that polymorphisms are more difficult to find but genealogies are easier to reconstruct. In addition, the greater length of the NRY DNA compared with mtDNA compensates in data analysis for its lower mutation rate (Cavalli-Sforza and Feldman 2003).The rarity of back and recurrent mutations in NRY contributes to the property of displaying the strongest geographic correlation and greatest diversity among, rather than within, populations. To date, NRY binary polymorphisms have been widely used to trace the origin and migration events of modern humans (Underhill et al. 2001). Here, we propose the hypothesis that NRY-based phylogeography of H. sapiens sapiens, offers a convenient spatiotemporal framework for inferring early primary dispersals of those human pathogens that are essentially (1) devo...