The Black Rat (Rattus rattus) spread out of Asia to become one of the world’s worst agricultural and urban pests, and a
reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and
inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic
diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary
movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards
obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong
phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region,
southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle
Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R.
rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population
expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically
documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely
separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings
represent an important step towards deeper understanding the complex and influential relationship that has developed
between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.