Cytochrome b gene tree inferred using full-length sequence data (1140 bp) and depicting the genetic relatedness of the three Rattus species haplotypes in South Africa. Taxon names comprise the Genbank accession number, followed by the country of origin (for South African samples this is preceded by a province code: LP = Limpopo Province, MP = Mpumalanga Province, GP = Gauteng Province, KZN = KwaZulu-Natal), haplotype and the number of individuals characterised. Nodal support values are given in percentages and are indicated ME/ML/BPP next to the relevant nodes. -- indicates nodes that were either not recovered or that had support values < 50 for ME and < 70 for ML and BPP. Haplotypes are colour-coded as follows to indicate the region and source of the data: Yellow = Southern Africa (This study), Blue = Outside Africa (This study), Green = Africa (Genbank), Grey = Outside Africa (Genbank), Purple = Laboratory strain (Genbank). Terminal nodes connecting different haplotypes and having ≥99 percent support from all three methods of inference are denoted by a black-filled circle. Country codes given in brackets behind a taxon name, indicate shared presence of a particular haplotype identified from the partial 1043 bp dataset (additional file 3, Figure S3) and are abbreviated: COM = Comores, MOZ = Mozambique, GUA = Guadeloupe, MAD = Madagascar, RSA = Republic of South Africa and SEN = Senegal.