Abstract
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.
Highlights
The Black Rat (Rattus rattus; known as ‘House’, ‘Roof’ and ‘Ship’ Rat) is the most widely distributed of all commensal animals and the most destructive of all animal pests
Huge effort is invested in pest control and feral eradication of the species, and there is growing interest in its role in numerous zoonotic disease cycles, including the ongoing threat posed by plague (Yersinia pestis) [5] and the emerging threats posed by bunyaviruses, leptospirosis and a range of bacterial ‘‘typhus’’ syndromes in particular [6,7]
We obtained mitochondrial cytochrome b gene sequences from 165 individuals identified on morphological criteria as Black Rats, presumably representing either R. rattus or R. tanezumi
Summary
The Black Rat (Rattus rattus; known as ‘House’, ‘Roof’ and ‘Ship’ Rat) is the most widely distributed of all commensal animals and the most destructive of all animal pests. It is a remarkably adaptable species that plays multiple roles as a household pest [1], a destructive agricultural pest in cereal and vegetable crops, orchards and palm plantations [1,2], and a feral invader of natural habitats [3,4]. Huge effort is invested in pest control and feral eradication of the species, and there is growing interest in its role in numerous zoonotic disease cycles, including the ongoing threat posed by plague (Yersinia pestis) [5] and the emerging threats posed by bunyaviruses, leptospirosis and a range of bacterial ‘‘typhus’’ syndromes in particular [6,7]. More recent regional studies of Black Rat mitochondrial DNA (mtDNA) [12,13,14] identified patterns of genetic diversity that are not reconciled with this taxonomic arrangement
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