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

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


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.

Bastos et al. BMC Genetics 2011 12:26   doi:10.1186/1471-2156-12-26

Open Data