Correspondence between our mtDNA lineage terminology and taxonomic usage with that employed in several recent studies, along with typical morphology, habitat use and disease associations.

1A 2n = 40 karyotype was reported by Yosida [8] from specimens referred to R. kandianus from the central highlands of Sri Lanka. MtDNA sequences reported here from the same locality are attributable to RrC LIV.
2Karyotypes of 2n = 42 reported by Yosida [8] and Badenhorst et al. [96] as R. losea were obtained from animals from Thailand. MtDNA sequences reported here from the same locality as Yosida's samples are attributable to RrC LV.
3Karyotypes of 2n = 42 reported by Yu et al. [97] for R. losea from Taiwan.
4Scansorial = able to climb and frequently doing so, but not restricted to arboreal existence.
5The degree of commensalism of each lineage.
6Probable disease associations are inferred from geographic distribution of lineages and diseases reported from ‘Rattus rattus’. Disease codes: BA: Bartonella infections; CD: Chagas Disease; LE: Leptospirosis; LM: Leishmaniasis; PL: Plague; RV: Rift Valley fever; SC: Schistosomiasis; TM: Trypanosomiasis; TY: Typhus (Rickettsial); WN: West Nile Encephalitis. See Table S3, References S1 for further details and referencing of disease associations.