Table 5.
Rhipicephalus appendiculatus cox1 haplotypes and their distribution among agro-ecological zones of the Great lakes region and other sub-Saharan African countries
| Haplotyped | Haplotypes from GenBank: Country (original haplotype name and GenBank number) | Present study | Haplogroup |
|---|---|---|---|
| CH1a | Kenya (H2: KU725891, H4: KU725893, H6: KU725895)e, Rwanda (H3:DQ901360)f Zambia-east (H4: KX276942e, H5: DQ859266g, H3:DQ901361f, H2: DQ859265g) | Burundi (AEZ1, AEZ3), DRC (AEZ1, AEZ2, AEZ3), Tanzania (TZ18, TZ10, TZ08, TZ20), Rwanda (AEZ2) | A |
| CH3 | – | Burundi AEZ1 | A |
| CH4 | Rwanda (H6: DQ901362)f | Burundi AEZ1, Rwanda (AEZ2) | A |
| CH6b | Kenya (H5: KU725894)e | Burundi (AEZ1, AEZ3), DRC (AEZ1, AEZ2) | A |
| CH7c | Kenya (H1: KU725890)e, South Africa (H1: KX276939e, H1: KX276940e, H1: DQ901356f), Zambia-east (H1: DQ859261)g, Zambia-south (H1:KX276943e, H1: DQ859262)g, Zimbabwe (AF132833h, KC503257i, H1: KX276944e), Grande Comore (H1)j | Burundi AEZ1, DRC (AEZ1, AEZ2, AEZ3), Rwanda (AEZ2) | B |
| CH9 | – | Burundi AEZ3 | A |
| CH10 | – | Burundi AEZ1 | A |
| CH11d | Kenya (H3: KU725892)e, Rwanda (H3: DQ901363)f, Grande Comore (H3)j | DRC (AEZ1, AEZ2, AEZ3), Rwanda (AEZ2) | A |
| CH12 | Kenya (H11: KU725900)e | DRC (AEZ2, AEZ3) | A |
| CH14 | – | DRC AEZ3 | A |
| CH16 | – | DRC AEZ1 | A |
| CH18 | – | DRC AEZ2 | A |
| CH20 | – | DRC AEZ2 | B |
| CH23 | Uganda (H8: KX276941, KU725897)e | – | B |
| CH24 | Kenya (H14: KU725903)e | – | B |
| CH25 | Kenya (H27: KU725916)e | – | B |
| CH26 | Grande Comore (H2: DQ901357)f,j, Kenya (H7: KU725896, H13: KU725902)e | – | B |
| CH27 | Kenya (H16: KU725905)e | – | B |
| CH28 | Kenya (H21: KU725910e, H9: DQ901359f, H9: DQ901358f) | – | B |
| CH29 | Kenya (H28: KU725917)e | – | B |
| CH30 | Kenya (H9: KU725898)e | – | A |
| CH31 | Kenya (H17: KU725906e | – | A |
| CH32 | Kenya (H24: KU725913)e | – | A |
| CH33 | – | Tanzania (TZ13) | A |
| CH34 | Kenya (H22: KU725911)e | – | A |
| CH35 | Kenya (H23: KU725912)e | – | A |
| CH36 | Kenya (H10: KU725899)e | – | A |
| CH37 | Kenya (H15:KU725904)e | – | A |
| CH38 | Kenya (H20: KU725909)e | – | A |
| CH39 | Kenya (H19: KU725908)e | – | A |
| CH40 | Kenya (H26: KU725915)e | – | A |
| CH41 | Kenya (H25: KU725914e | – | A |
| CH42 | Kenya (H18: KU725907)e | – | A |
| CH43 | Kenya (H12: KU725901)e | – | A |
| CH44 | Zambia-east (H3: DQ859263)g | – | A |
| CH45 | Zambia-east (H4: DQ859264)g | – | A |
aCH1: variants CH1, CH2, CH5, CH15, CH17 and CH21 (Additional file 3: Table S3)
bCH6: variants CH6, CH8 and CH22 (Additional file 3: Table S3)
cCH7: variants CH7 and CH13; d CH11: CH11 and CH19 (Additional file 3: Table S3)
dHaplotypes underlined are exclusive to the Great Lakes region. Similar data for 12S rRNA are detailed in Additional file 7: Table S6