Ken P. AplinHitoshi SuzukiAlejandro A. ChinenR. Terry ChesserJosé ten HaveStephen C. DonnellanJeremy AustinAngela FrostJean Paul GonzalezVincent HerbreteauFrancois CatzeflisJulien SoubrierYin Ping FangJudith RobinsElizabeth Matisoo-SmithAmanda D.S. BastosIbnu MaryantoMartua H. SinagaChristiane DenysRonald A. van Den BusscheChris ConroyKevin RoweAlan CooperCommonwealth Scientific and Industrial Research OrganizationHokkaido UniversitySmithsonian InstitutionOffice of the Gene Technology RegulatorUniversity of AdelaideMahidol UniversityInstitut des Sciences de l'Evolution UMR 5554National Chiayi UniversityUniversity of AucklandOtago School of Medical SciencesUniversiteit van PretoriaLembaga Ilmu Pengetahuan IndonesiaMuseum National d'Histoire NaturelleOklahoma State University - StillwaterUniversity of California, Berkeley2018-05-032018-05-032011-11-02PLoS ONE. Vol.6, No.11 (2011)193262032-s2.0-80355129314https://repository.li.mahidol.ac.th/handle/123456789/11245The 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. © 2011 Aplin et al.Mahidol UniversityAgricultural and Biological SciencesBiochemistry, Genetics and Molecular BiologyArticleSCOPUS10.1371/journal.pone.0026357