Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats

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.

Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus

“…Among rodents, the species Rattus rattus (black rat, described as Lineage I in Aplin et al., 2011) is one of the most ubiquitous commensals on almost all continents (Musser & Carleton, 2005). The global lineage of R. rattus originated in south India and probably spreads westwards with the growing maritime trade, leading to the familiar name of “ship rats” (Aplin et al., 2011). In its native range of south India, R. rattus is the most commonly captured commensal (Srinivasulu & Srinivasulu, 2012).…”

Progress on research on rodents and rodent-borne zoonoses in South-east Asia

“…1). This putative species was identified previously as the diardii clade in the mitochondrial phylogeny of Robins et al (2007) and, according to Aplin et al (2011), could be a cryptic species. Pagès et al (2013) used extensive sampling, morphological data and diverse genetic markers differing in rates of evolution and parental inheritance (two mtDNA genes, one nuclear gene and eight microsatellite loci) to assess the reproductive isolation among R. tanezumi, R. sakeratensis and R3.…”

“…For example, Latinne et al (2013a) investigated the diversity and endemism of Rattini in Thai limestone karsts and confirmed the existence of the species Niviventer hinpoon in several new localities using as reference a small DNA fragment obtained from the holotype. This work illustrates the huge opportunities ancient DNA analysis may offer to taxonomists (Willerslev and Cooper 2005;Rohland and Hofreiter 2007; for rodents, see Wyatt et al 2008;Aplin et al 2011). Galan et al (2012) have developed a time-and cost-effective method suitable for barcoding thousands of samples using the 454 GS FLX platform (Roche Diagnostics Corporation, Basel, Switzerland).…”

“…R. tanezumi and R3) suggests that the Asian black rat has a complex evolutionary history (Aplin et al 2011). The presence of highly divergent mtDNA lineages within a single large species may be the result of geographical structuring during Quaternary climatic oscillations, or introgression from a species yet to be identified, either of which could account for the incongruence between mtDNA and nuclear patterns in Asian black rats.…”

“…One taxonomic change that does seem well founded is the naming of the Rattus losea-like populations from the region comprising central and northern Thailand and the Vientiane plain of Laos. According to Aplin et al (2011), these populations refer to Rattus and clusters of specimens recognised as putative species by the method of Pons et al (2006). Genetic clusters recognised as a putative species are highlighted and separated by longer black branches.…”