Molecular phylogeny of Rattus species and their temporal, spatial, and ecological modes of evolution

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Our analyses included more than 100 individuals in 63 recognized species from 19 genera, including all but six genera of the Rattus sensu lato. The major findings of our work include: 1) confirmation of a three way division of Rattus sensu lato into 'Maxomys',Niviventer' and 'Rattus' groups; 2) previously unsuspected association of the specialized arboreal genus Margaretamys of Sulawesi with the Niviventer group; 3) demonstration that the genus Rattus as currently defined is polyphyletic with at least three recognizable lineages: i) Rattus sensu stricto, which includes both R. norvegicus and R. rattus, along with many other species of particular interest; ii) 'Rattus' everetti of the Philippines; and iii) members of the 'Rattus' xanthurus' group together with the native 'Rattus' of Australia and New Guinea; 4) demonstration that the black rat group, Rattus rattus sensu lato contains multiple lineages, two of which are shown to be genetically and cyctologically distinct in Japan but with evidence of introgression in several areas with contrasting outcomes. From a biogeographic perspective, the most interesting findings of this study are the demonstration that members of Rattus sensu lato succeeded in colonizing the oceanic landmasses off the margins of the Sunda Shelf on multiple occasions. All major groups within Rattus sensu lato managed to reach Sulawesi, the Philippine islands and the Mentawai islands to the south of Sumatra, but only one lineage within the 'Rattus group' succeeded in going beyond these major islands to eventually colonize New Guinea and Australia in the east, and to reach the remote islands of the Ryukyu Archipelago in the north.