Quintana-Murci et 10.1073/pnas.0711467105.XXYYYYY103.

Supporting Information

Files in this Data Supplement:
SI Figure 4
SI Table 2
SI Table 3
SI Figure 5
SI Table 4
SI Table 5

SI Figure 4
Fig. 4. Simplified mtDNA phylogenetic tree showing the 33 SNPs typed to assign samples into Hgs. Those in red were typed in the entire collection; those in blue were typed hierarchically within the corresponding Hgs.

Table 2. Haplogroup frequencies for the Bantu-speaking agricultural (AGR) and Pygmy hunter-gatherer (PHG) populations

Haplogroup

AGR

Western PHG

Eastern PHG

N

%

N

%

N

%

L0a1

64

6.5

3

0.8

0

0.0

L0a2

26

2.6

7

1.8

10

25.6

L1b

63

6.4

0

0.0

0

0.0

L1c*

5

0.5

0

0.0

0

0.0

L1c1*

14

1.4

1

0.3

0

0.0

L1c1a1

113

11.5

204

53.4

0

0.0

L1c1a2

87

8.9

115

30.1

0

0.0

L1c1b

27

2.7

21

5.5

0

0.0

L1c2

28

2.8

5

1.3

0

0.0

L1c3

44

4.5

0

0.0

0

0.0

L1c4

33

3.4

13

3.4

0

0.0

L2*

3

0.3

2

0.5

0

0.0

L2a*

1

0.1

0

0.0

8

20.5

L2a1

131

13.3

0

0.0

0

0.0

L2a2

4

0.4

0

0.0

17

43.6

L2b1

13

1.3

0

0.0

0

0.0

L2b2

2

0.2

0

0.0

0

0.0

L2c2

16

1.6

0

0.0

0

0.0

L2d

12

1.2

1

0.3

0

0.0

L3*

8

0.8

0

0.0

0

0.0

L3b

30

3.1

0

0.0

0

0.0

L3d

38

3.9

2

0.5

0

0.0

L3e1*

23

2.3

2

0.5

0

0.0

L3e1a

28

2.8

0

0.0

0

0.0

L3e1b

5

0.5

0

0.0

0

0.0

L3e2*

17

1.7

0

0.0

0

0.0

L3e2b

40

4.1

0

0.0

0

0.0

L3e3

29

3.0

0

0.0

0

0.0

L3e4

7

0.7

0

0.0

0

0.0

L3f1b

56

5.7

6

1.6

0

0.0

L3h

8

0.8

0

0.0

0

0.0

L4

8

0.8

0

0.0

0

0.0

L5

0

0.0

0

0.0

4

10.3

SI Table 3

SI Figure 5
Fig. 5. Mismatch distribution of HVS-I sequences in Bantu-speaking agricultural (A) and Pygmy-hunter-gatherer (B) populations.

Table 4. Previously published African samples included in the analyses for comparison and compiled in the MURKA mitochondrial database (Zaporozhchenko, Balanovsky, Pshenichnov, and Balanovska, from the Russian Academy of Medical Sciences, Moscow, Russia)

African region

Reference

Population name

n

Central

(1)

Cameroon

104

(2)

Cameroon Bakaka

50

(2)

Cameroon Bamileke

48

(2)

Cameroon Bassa

46

(2)

Cameroon Daba

20

(2)

Cameroon Ewondo

53

(2)

Cameroon Fali

41

(2)

Cameroon Fulbe

34

(2)

Cameroon Mandara

37

(2)

Cameroon Podokwo

39

(2)

Cameroon Tali

20

(2)

Cameroon Tupuri

25

(2)

Cameroon Uldeme

28

(2)

Cameroon Western Mbenzele

57

(3)

Bubi

45

(3)

Sao Tomeans

50

(4)

Mbundu (Angola)

44

(5)

Pygmy (Africa, C.)

10

(6)

Sao-Tomeans

103

(7)

Biaka Pygmy (CAR)

17

(7)

Mbuti Pygmy (DRC),

20

(8)

Fulbe (Cameroon)

1

East

(9)

Kenya,

100

(10)

Ethiopia (Afar)

16

(10)

Ethiopia (Amhara)

120

(10)

Ethiopia (Eritrean)

8

(10)

Ethiopia (Gurage)

21

(10)

Ethiopia (Oromo)

33

(10)

Ethiopia (other)

27

(10)

Ethiopia (Tigrai)

45

(11)

Datoga

18

(11)

Hadzabe

49

(11)

Iraqw

12

(11)

Sukuma

21

(12)

Dinka (Sudan)

46

(12)

Nubians, southern Egypt & northern Sudan

68

(12)

Nubians, southern Egypt & northern Suda

14

(12)

Sudanese southern

79

(7)

Hadza (Tanzania)

17

(8)

Kikuyu (Kenya)

25

(8)

Sakuye (Kenya)

1

(8)

Somali (Ethiopia)

9

(8)

Somali (Kenya)

15

(8)

Somali (Somalia)

3

(8)

Turkana (Kenya)

37

North

(13)

Egypt

75

(14)

Souss Valley Moroccans

50

(15)

Algeria

85

(15)

Mozabites

85

FBI Laboratory

Egypt

75

(12)

Egyptians central and southern

27

(12)

Egyptians northern

49

(12)

Egyptians northern

14

(12)

Egyptians northern

4

(16)

Arabs Jerba

29

(16)

Berbers Jerba

30

Univ. Barcelona

Morocco

52

(17)

Algerians

47

(18)

Matmata

49

(17)

Moroccan Arabs

18

(17)

Moroccan Berbers

4

(17)

Saharawi

56

(18)

Sened

53

(18)

Tata

53

(17)

Tunis

47

(19)

Berbers, northern morocco

18

(19)

Mauritania

30

(19)

Moroccan Berbers

60

(19)

Moroccan non-Berbers

32

(19)

West-Saharan

25

(13)

Egypt Gurna

34

(13)

Egypt Upper

24

South

(20)

Khwe

31

(20)

Kung

43

(5)

Malawi (Africa, S.)

7

(7)

!Kung (Botswana)

25

(7)

Herero (Botswana)

27

Southeast

(21)

Bambara

19

(22)

Mozambique

109

(23)

Africa

307

(5)

Africa, S.E. (Bantu)

24

West

(24)

Cabo-Verde

292

(21)

Malinke

61

(25)

Mandenka (Senegal, E.)

119

(26)

Sierra-Leone

277

(27)

Fang (Guinea)

11

(19)

Senegalese other

50

(19)

Senegalese Serer

23

(19)

Senegalese Wolof

48

Univ. of California

Sierra Leone

109

(7)

Yoruban (Nigeria)

13

(8)

Fulbe (Benin)

1

(8)

Fulbe (Burkina Faso)

2

(8)

Fulbe (Niger)

10

(8)

Fulbe (Nigeria)

47

(8)

Hausa (Niger)

3

(8)

Hausa (Nigeria)

17

(8)

Kanuri (Niger)

1

(8)

Kanuri (Nigeria)

13

(8)

Songhai (Mali)

1

(8)

Songhai (Niger)

9

(8)

Tuareg (Mali)

1

(8)

Tuareg (Niger)

25

(8)

Yoruba (Nigeria)

21

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Table 5. Frequency and diversity measures in the various African subregions

Hg

Sub-region*

n

Frequency†, %

Coalescence age‡

Hg D (SE)

Pi (SE)

L0a1

Central

113

6.0

26,191 ± 5,556

0.900 (0.018)

2.863 (1.518)

East

62

7.9

0.894 (0.033)

3.005 (1.590)

North

17

1.5

0.949 (0.044)

2.897 (1.600)

South

3

2.3

0.667 (0.314)

2.667 (1.919)

Southeast

40

8.7

0.673 (0.074)

0.987 (0.682)

West

20

1.7

0.726 (0.092)

1.284 (0.840)

L1b

Central

116

6.2

29,366 ± 7,937

0.783 (0.033)

1.978 (1.126)

East

15

1.9

0.914 (0.056)

2.019 (1.202)

North

31

2.8

0.817 (0.067)

1.720 (1.031)

South

1

0.8

-

-

Southeast

10

2.2

0.889 (0.075)

1.422 (0.946)

West

150

13.0

0.961 (0.008)

2.665 (1.428)

L1c1a

Central

273

14.6

57,144 ± 7,937

0.746 (0.018)

3.152 (1.638)

East

0

0.0

-

-

North

0

0.0

-

-

South

0

0.0

-

-

Southeast

3

0.7

0.667 (0.314)

2.667 (1.919)

West

1

0.1

-

-

L2a1

Central

231

12.3

27,778 ± 3,968

0.939 (0.008)

3.420 (1.755)

East

90

11.5

0.902 (0.024)

3.146 (1.645)

North

51

4.5

0.903 (0.027)

2.565 (1.399)

South

3

2.3

0.000 (0.000)

0.000 (0.000)

Southeast

133

29.0

0.810 (0.022)

3.118 (1.628)

West

169

14.6

0.936 (0.011)

2.811 (1.491)

L3e1

Central

102

5.4

15,873 ± 2,381

0.931 (0.010)

2.781 (1.483)

East

9

1.1

0.778 (0.110)

2.333 (1.403)

North

12

1.1

0.576 (0.163)

2.303 (1.355)

South

8

6.0

0.000 (0.000)

0.000 (0.000)

Southeast

40

8.7

0.908 (0.024)

2.356 (1.312)

West

5

0.4

0.900 (0.161)

2.400 (1.557)

L3e2

Central

121

6.5

26,985 ± 7,143

0.868 (0.018)

2.695 (1.444)

East

3

0.4

0.000 (0.000)

0.000 (0.000)

North

8

0.7

0.786 (0.151)

2.464 (1.486)

South

5

3.8

0.000 (0.000)

0.000 (0.000)

Southeast

7

1.5

0.857 (0.137)

2.571 (1.563)

West

55

4.8

0.922 (0.025)

2.994 (1.588)

L3f1b§

Central

78

4.2

15,873 ± 2,381

0.894 (0.021)

2.333 (1.289)

East

17

2.2

0.772 (0.097)

1.500 (0.950)

North

6

0.5

0.533 (0.172)

1.067 (0.811)

South

0

0.0

-

-

Southeast

5

1.1

0.800 (0.164)

3.200 (1.979)

West

38

3.3

0.873 (0.047)

1.926 (1.119)

L1c¶

Central

496

26.5

102,383 ± 7,937

0.919 (0.008)

5.763 (2.763)

East

9

1.1

0.917 (0.073)

6.556 (3.422)

North

4

0.4

0.667 (0.204)

2.667 (1.778)

South

0

0.0

-

-

Southeast

22

4.8

0.952 (0.029)

6.632 (3.255)

West

59

5.1

0.926 (0.030)

5.744 (2.790)

L1c1¶

Central

305

16.3

73,811 ± 7,143

0.838 (0.017)

4.415 (2.185)

East

6

0.8

0.867 (0.129)

4.200 (2.425)

North

2

0.2

0.000 (0.000)

0.000 (0.000)

South

0

0.0

-

-

Southeast

13

2.8

0.936 (0.051)

5.628 (2.888)

West

45

3.9

0.875 (0.048)

5.095 (2.518)

*Region definitions follow Salas et al. (30).

†
The total number of samples were: Central (1875); East (784); North (1125); South (133); Southeast (459); West (1154).
‡
Coalescence estimates are based on complete sequences analysis as calculated in the frame of 629 complete sequences of mtDNA genomes (D.M.B., unpublished work)
§
Compared with L3f1 in the literature.
¶
These Hgs collapsed the information of all of its internal clades and do not represent a real label in the study.