Phylogeography of the black rat Rattus rattus in India and the implications for its dispersal history in Eurasia.
India is the origin to the world's most notorious invasive mammal, the black rat Rattus rattus. All previous empirical phylogeographic studies were based on very few samples originating from India-creating a paucity of data to extrapolate from. In this first specific phylogeographic study of R. rattus attempted in India, samples were obtained from 18 localities within peninsular India with a focus on the East and West coasts, regions that spread commensal R. rattus globally. The displacement loop (D-loop) and the cytochrome b (Cytb) gene were sequenced in 45 R. rattus individuals. Maximum likelihood analysis was used to assign individuals to lineages. Coalescence and Bayesian methods were employed to estimate population genetic parameters, phylogeny and divergence respectively. The phylogeography of R. rattus was elucidated by constructing median joining networks by combining newly generated D-loop and Cytb gene sequences in the current study with available sequences in the database. Our findings provide key insights into the origin, expansion and migration patterns of the black rat in India, Eurasia and in the Indian Ocean region. The study reconfirms India as the centre of origin to the global R. rattus population and identifies the Gangetic region and East coast as focal points of ancestral R. rattus populations in India. Our newly generated data provide genetic evidence in support of the origin of commensalism in R. rattus in the ancient Indus Valley region and the further spread of these commensal house rats by medieval Arab sailors in the Indian Ocean and the Mediterranean.