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Table 1 Summary of the cytochrome b gene sequences generated in this study for the three invasive Rattus species occurring in South Africa and the reference sequences used for genetic analyses

From: Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in south Africa

Rattus tanezumi(south Africa)
Haplotype Sampling Locality N Genbank AN (Museum AN) Reference
RT01 Giyani (Nkomo-B), LP 7 DQ439816- DQ439822 This study
RT01 Tshilimbani, LP 19 HQ157805 This study
RT01 Tholakele, Paulpietersburg, KZN 2 DQ439823, DQ439826 This study
RT01 Mvuzini, Vryheid, KZN 3 DQ439824-5, DQ439827 This study
RT01 Ophuzane, Paulpietersburg, KZN 6 DQ439829, DQ439845-8 This study
RT01 Hammanskraal, GP 12 DQ439828 This study
RT01 Rietondale, Pretoria, GP 1 DQ444864 This study
RT01 Moreleta Park, Pretoria, GP 1 FJ842262 This study
RT01 Tembisa, GP 3 HQ157804 This study
RT01 Roodeplaat, GP 13 HQ157807 This study
RT01 Richmond, KZN 1 FJ842263 (DM8685) This study
RT01 Shongweni, Durban, KZN 2 DQ439849-50 (DM8401, DM8402) This study
RT01 Swaziland (Mcaphozini Area) 6 FJ842264 (DM8892, DM8896-8900) This study
RT02 Tembisa, GP 1 FJ842265 This study
2 14 localities 77   
Rattus tanezumi (elsewhere)
Haplotype Country (Locality) N Genbank AN (Museum AN) Reference
RT03 Japan, Vietnam 3 AB355899-900, AB211040 [29, 30]
RT04 Japan (Amami Island) 1 EU273712 [9]
RT05 Japan 1 AB211041 [29]
RT06 Vietnam 1 AB355901 [30]
RT07 China 1 AB096841 [28]
5 3 countries 7   
Rattus rattus (South Africa)
Haplotype Sampling Locality N Genbank AN (Museum AN) Reference
RR01 Giyani (Nkomo-B), LP 9 DQ439830, DQ439851-8 This study
RR01 Sekhukhune (Bloublommetjieskloof), LP 2 DQ439831-2 This study
RR01 Tshilimbani, LP 4 HQ157802 This study
RR01 Tembisa, GP 1 HQ157801 This study
RR03 Hammanskraal, GP 4 DQ439834-5 This study
RR03 Moreleta Park, Pretoria, GP 1 FJ842266 This study
RR03 Tembisa, GP 2 HQ157800 This study
RR03 Verena, MP 1 HQ157803 This study
RR04 Renosterkop, LP 1 HQ157806 This study
RR04 Hammanskraal, GP 1 DQ439833 This study
RR04 Hillcrest, Pretoria, GP 1 FJ842267 This study
RR04 Umkomaas, KZN 5 DQ439836-8 (DM8403-7) This study
RR05 Hammanskraal, GP 1 FJ842268 This study
RR06 Cape Town, WCP 2 GQ891608 [4]
RR10 Melmoth, KZN 1 [HQ157808] (DM8820) This study
RR11 Ladysmith, KZN 1 [HQ157809] (DM8907) This study
7 13 localities 37   
Rattus rattus (elsewhere)
Haplotype Country (Locality) N Genbank AN Reference
RR01 Tanzania 1 H217365 [8]
RR02 Indonesia 1 AB033702 [27]
RR06 New Zealand (Titirangi) 1 EU273707 [9]
RR07 Japan 2 AB211039 [AB211042] [29]
RR08 India 1 H217367 [8]
RR09 Oman 1 H217366 [8]
6 6 countries 7   
Rattus norvegicus (South Africa)
Haplotype Sampling Locality N Genbank AN (Museum AN) Reference
RN01 Sydenham, Durban, KZN 2 FJ842270 (DM7744, DM7745) This study
RN01 Durban CBD, KZN 3 FJ842271 (DM7783, DM7804-5) This study
RN01 Montclair Park, Durban, KZN 2 DQ439842-3 (DM7788, DM7789) This study
RN01 Cato Crest IS, Durban, KZN 2 FJ842272 (DM7802, DM7803) This study
RN01 Cato Manor Rd, Durban, KZN 1 DQ439844 (DM7820) This study
RN01 Tembisa, GP 1 FJ842269 This study
RN01 O.R. Tambo International Airport, GP 1 FJ842273 This study
RN01 Johannesburg Zoological Gardens 8 HQ157799 This study
RN02 Cato Crest IS, Durban, KZN 2 FJ842274 (DM7790, DM7791) This study
RN03 Durban Harbour, KZN 2 DQ439840-1 (DM7706, DM7711) This study
RN04 Warwick Ave, Durban, KZN 1 DQ439839 (DM7645) This study
RN12 O.R. Tambo International Airport, GP 9 FJ842275 This study
RN12 Tembisa, GP 3 FJ842276 This study
5 10 localities 37   
Rattus norvegicus (elsewhere)
Haplotype Sampling Locality of wild caught animals/(Lab Strain) N Genbank AN Reference
RN01 (BN/SsNHsdMCW) 1 AY172581 [46]
RN01 China*, Sweden 2 [GU592972*], FJ919765 [11]
RN09 (GH/OmrMcwi), [GH/Swe] 2 DQ673911, [DQ673913] [2]
RN10 Milwaukee, USA 1 DQ673916 [2]
RN05 Indonesia 1 FJ842279 This study
RN07 Vietnam 1 FJ842278 This study
RN08 Vietnam 2 AB355902, [AB355903] [30]
RN11 Copenhagen, Denmark 1 AJ428514 [47]
RN06 Vietnam 1 FJ842277 This study
RN13 Tokyo, Japan 1 DQ673917 [2]
RN13 (T2DN/Mcwi) 1 DQ673915 [2]
RN14 (Sprague-Dawley) 1 AB033713 [48]
RN15 (Wistar) 1 X14848 [49]
11 7 countries 16   
  1. AN: Accession Number; LP: Limpopo Province; GP: Gauteng Province; KZN: KwaZulu-Natal Province; MP: Mpumalanga Province; WCP: Western Cape Province; CBD: Central Business District; IS: Informal Settlement; DM: Durban Natural Science Museum; []: Sequences that were not used for phylogenetic inference; * Unpublished record.