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Table 1 Summary of COI sequence variability and genetic diversity measures of 22 R. appendiculatus populations

From: Analyses of mitochondrial genes reveal two sympatric but genetically divergent lineages of Rhipicephalus appendiculatus in Kenya

Populationª

Sample size

No. of haplotypes

Haplotype diversity (SD)

Nucleotide diversity ± (SD)

Mean number of nucleotide differences (SD)

Fu’s F S (P-value)

Tajima’s D (P-value)

Sum of squared deviation (SSD) (P-value)

Harpending’s Raggedness Index (RI)

GenBank Accession numbers

Field (Cattle only)

 Kilifi (KF)

20

2

0.100 (0.088)

0.0002 (0.0002)

0.100 (0.1775)

-0.879 (0.080)

−1.164 (0.123)

0.000 (0.288)

0.650 (0.810)

KX276888–89

 Makuyu (MK)

25

9

0.817 (0.055)

0.005 (0.001)

2.820 (1.539)

-1.340 (0.264)

−1.015 (0.175)

0.029 (0.140)

0.080 (0.228)

KX276901–09

 Kitale (KT)

29

10

0.865 (0.037)

0.010 (0.006)

5.584 (2.760)

0.747 (0.678)

0.999 (0.860)

0.039 (0.489)

0.030 (0.747)

KX276890–99

 Busia (BU)

18

7

0.784 (0.085)

0.011 (0.006)

6.183 (3.0824)

2.062 (0.8440)

0.463 (0.715)

0.089 (0.210)

0.099 (0.421)

KX276868–74

 Rusinga (RU)

21

5

0.700 (0.073)

0.004 (0.002)

2.010 (1.178)

0.781 (0.690)

−1.749 (0.026)

0.128 (0.180)

0.096 (0.280)

KX276934–38

 Ruma (RUM2)

5

4

0.900 (0.161)

0.0145 (0.004)

8.100 (4.534)

1.261 (0.657)

1.497 (0.932)

0.120 (0.131)

0.130 (0.839)

KX276930–33

 Average

20

20

0.833 (0.0238)

0.0127 (0.007)

7.089 (3. 352)

0.423 (0.611)

1.477 (0.934)

0.072 (0.030)

0.0479 (0.060)

 

Field (Cattle – Wildlife only)

 Field Ol Pejeta (FP)

23

10

0.830 (0.067)

0.005 (0.0017)

2.988 (1.620)

-2.258 (0.109)

−1.536 (0.048)

0.004 (0.792)

0.015 (0.983)

KX276875–84

 Bomet (BO)

23

6

0.719 (0.074)

0.010 (0.0024)

5.518 (2.7532)

3.628 (0.936)

0.479 (0.7160)

0.100 (0.168)

0.227 (0.090)

KX276862–67

 Average

23

14

0.792 (0.056)

0.008 (0.0043)

4.315 (2.175)

-1.578 (0.322)

−0.576 (0.297)

0.025 (0.370)

0.039 (0.650)

 

Field (Wildlife only)

 Nairobi National Park (NB)

21

6

0.729 (0.065)

0.00450 (0.002)

2.5095 (1.408)

0.468 (0.640)

−1.600 (0.038)

0.0246 (0.279)

0.079 (0.521)

KX276924–29

 Maasai Mara (MA)

22

6

0.788 (0.050)

0.01022 (0.002)

5.7013 (2.839)

3.618 (0.925)

1.086 (0.889)

0.0691 (0.304)

0.0761 (0.556)

KX276910–15

 Average

22

7

0.801 (0.031)

0.091 (0.005)

5.102 (2.518)

4.639 (0.957)

1.294 (0.924)

0.439 (0.470)

0.034 (0.820)

 

Laboratory stocks

 Lab Ol Pejeta (LP)

14

1

0 (0)

0 (0)

0 (0)

0

0.000 (1.000)

0.0000

0.00 (0.000)

KX276900

 Kiambu High-line (KH)

12

2

0.485 (0.106)

0.0104 (0.0023)

5.8182 (2.993)

9.2418 (0.998)

1.9499 (0.984)

0.4701 (0.0000)

0.7355 (0.924)

KX276885–86

 Kiambu unselected line (KU)

10

1

0 (0)

0 (0)

0 (0)

0

0.000 (1.000)

0.0000

0.000 (0.000)

KX276887

 Muguga infected (MF)b

12

3

0.545 (0.144)

0.0116 (0.003)

6.4849 (3.300)

6.887 (0.995)

1.701 (0.978)

0.4418 (0.000)

0.449 (0.957)

KX276916–18

 Muguga unselected (MU)c

12

4

0.682 (0.102)

0.0092 (0.003)

5.1364 (2.677)

3.752 (0.953)

0.1463 (0.570)

0.1545 (0.103)

0.3693 (0.700)

KX276919–22

 Muguga low-line (ML)d

11

1

0 (0)

0 (0)

0 (0)

0

0.000 (1.000)

0.0000

0.000 (0.000)

KX276923

 Uganda (UG)

12

1

0 (0)

0 (0)

0 (0)

0

0.000 (1.000)

0.0000

0.000 (0.000)

KX276941

 South Africa Natal province (SAN)

5

1

0 (0)

0 (0)

0 (0)

0

0.000 (1.000)

0.0000

0.000 (0.000)

KX276940

 South Africa Lab stock (SAL)

5

1

0 (0)

0 (0)

0 (0)

0

0.000 (1.000)

0.0000

0.000 (0.000)

KX276939

 Zambia Sothern province (ZS)

8

1

0 (0)

0 (0)

0 (0)

0

0.000 (1.000)

0.0000

0.000 (0.000)

KX276943

 Zambia Eastern province (ZE)

12

1

0 (0)

0 (0)

0 (0)

0

0.000 (1.000)

0.0000

0.000 (0.000)

KX276942

 Zimbabwe West Mashonaland (ZM)

12

1

0 (0)

0 (0)

0 (0)

0

0.000 (1.000)

0.0000

0.000 (0.000)

KX276944

 Average (Lab stocks)

10

5

0.634 (0.023)

0.012 (0.006)

6. 445 (3.022)

15.042 (0.994)

3.198 (0.996)

0.190 (0.040)

0.297 (0.130)

 

Haplogroups

 Haplogroup A

193

20

0.664 (0.035)

0.003 (0.002)

1.569 (0.939)

-10.348 (0.00)

−1.650 (0.017)

0.0126 (0.550)

0.050 (0.740)

 

 Haplogroup B

139

8

0.514 (0.046)

0.001 (0.001)

0.651 (0.507)

-3.462 (0.057)

−1.087 (0.125)

0.0028 (0.170)

0.102 (0.210)

 

 Overall

332

28

0.802 (0.014)

0.012 (0.006)

6.865 (3.239)

−0.122 (0.549)

1.244 (0.914)

0.076 (0.090)

0.061 (0.070)

 
  1. The number of individual sequences analysed (sample size), number of haplotyes and their corresponding GenBank Accession numbers for each population are listed. Tajima’s D was negative and statistically significant in RU, FP and NB but positive and not significant for all the other tick populations except the nine laboratory stocks that did not show diversity. KH had the highest Fu’s FS (9.2418). SSD was statistically significant in KH, MF, RE and RZ
  2. ªPopulation: Source population or origin of the tick stock. Tick populations were grouped on the basis of the source of the sequences as field ticks (collected from areas grazed by cattle), Field (Cattle – Wildlife only) collected from areas co-grazed by cattle and wildlife, laboratory stocks maintained at ILRI Tick Unit and wildlife only ticks (collected from areas grazed by wildlife)
  3. bMuguga infected (MF): T. parva-infected ticks derived from the original unselected Muguga stock (MU)
  4. cThis is the laboratory stock used in Kenya for T. parva transmission studies. It was originally collected from the Central Highlands of Kenya in the 1950s and has subsequently been maintained at the East African Veterinary Research Organisation (EAVRO) (now Kenya Agricultural Research Institute (KARI)) and ILRI [27]
  5. dMuguga low-line (ML): This selected stock was derived from a family line of Muguga that had low susceptibility to T. parva infection [24]
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