Content-Type: multipart/related; start=; boundary=----------dGVE3730075ApgTdKhBR0S Content-Location: http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2234190&blobname=pnas_0711467105_index.html Subject: =?utf-8?Q?Maternal=20traces=20of=20deep=20common=20ancestry=20and=20asymmetric=20gene=20flow=20between=20Pygmy=20hunter-gatherers=20and=20Bantu-speaking=20farmers=20--=20Quintana-Murci=20et=20al.=20105=20(5):=201596=20Data=20Supplement=20-=20HTML=20Page=20-=20index.htslp=20--=20Proceedings=20of=20the=20National=20Academy=20of=20Sciences?= MIME-Version: 1.0 ------------dGVE3730075ApgTdKhBR0S Content-Disposition: inline; filename=pnas_0711467105_index.html Content-Type: text/html; name=pnas_0711467105_index.html Content-Id: Content-Location: http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2234190&blobname=pnas_0711467105_index.html Content-Transfer-Encoding: Quoted-Printable Maternal traces of deep common ancestry and asymmetr= ic gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers -= - Quintana-Murci et al. 105 (5): 1596 Data Supplement - HTML Page - inde= x.htslp -- Proceedings of the National Academy of Sciences

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

Suppor= ting 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. Simpli= fied mtDNA phylogenetic tree showing the 33 SNPs typed to assign samples= into Hgs. Those in red were typed in the entire collection; those in bl= ue were typed hierarchically within the corresponding Hgs.





Table 2. Haplogroup frequencies for t= he Bantu-speaking agricultural (AGR) and Pygmy hunter-gatherer (PHG) pop= ulations

3

= =

0

=

L2a2

=

0

= =

L3e1a

=

6

=

0

=

0

Haplogroup

AGR

We= stern PHG

Eastern PHG

N

= %

N

%

N

%

L0a1

64

6.5

0.8

0

0.0

L0a2

26

2.6

7

1.8

1= 0

25.6

L1b

<= p align=3D"CENTER">63

6.4

0

0.0

0

0.0

L1c*

<= /td>

5

0.5

<= p align=3D"CENTER">0

0.0

0

0.0

L1c1*

14

1.4

1

0.3

0

0.0

L1c1a1

113

11.5

204

<= /td>

53.4

0

0.0

L1c1a2

87

8.9

115

30.1

<= /td>

0

0.0

L1c1b

27

2.7

21

5.5

0

0.0

=

L1c2<= /p>

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

L2a*

1

0.1

0

0.0

8

20.5

L2a1

<= /td>

131

13.3

0

0.0

0

0.0

4

0.= 4

0

0.0

17

43.6

L2b1

13

1.3

0.0

0

0.0

L2b2

2

0.2

0

0.0

0<= /p>

0.0

L2c2

<= p align=3D"CENTER">16

1.6

0

0.0

0

0.0

L2d

12

1.2

<= p align=3D"CENTER">1

0.3

0

0.0

L3*

8

0.8

0

0.0

<= p align=3D"CENTER">0

0.0

L3b

30

3.1

0

0.0

0=

0.0

L3d

<= p align=3D"CENTER">38

3.9

2

0.5

0

0.0

L3e1*

=

23

2.3

2

0.5

0

0.0

28

2= .8

0

0.0

0

0.0

L3e1b

5

0.5

0

<= /td>

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<= /p>

29

3.0

0

0.0

0

0.0

L3e4

7

= 0.7

0

0.0

0

0.0

L3f1b

56

5.7

1.6

0

0.0

L3h

8

0.8

0

0.0

0.0

L4

8

0.8

0

0.0

0

0.0

L5

0.0

0

0.0

4

10.3


=


SI Table 3



SI Figure 5

Fig. 5. Mismatc= h distribution of HVS-I sequences in Bantu-speaking agricultural (A) and Pygmy-hunter-gatherer (B) populations.




Table 4. Previously published African samp= les included in the analyses for comparison and compiled in the MURKA mi= tochondrial database (Zaporozhchenko, Balanovsky, Pshenichnov, and Balan= ovska, from the Russian Academy of Medical Sciences, Moscow, Russia)=

<= td height=3D"21" valign=3D"MIDDLE" width=3D"21%">

(1)=

<= td height=3D"21" valign=3D"MIDDLE" width=3D"10%">

50<= /p>

Camer= oon Bassa

<= /tr>

 

Camer= oon Tupuri

 

Biaka= Pygmy (CAR)

20

 

 

<= tr><= td height=3D"21" valign=3D"MIDDLE" width=3D"21%">

(11= )

= = <= tr><= td height=3D"21" valign=3D"MIDDLE" width=3D"21%">

(15= )

<= td height=3D"21" valign=3D"MIDDLE" width=3D"18%">

 

(18)<= /p>

(19)=

= = <= td height=3D"21" valign=3D"MIDDLE" width=3D"18%">

 

<= td height=3D"21" valign=3D"MIDDLE" width=3D"10%">

7

<= /tr>

307

Cabo= -Verde

<= td height=3D"21" valign=3D"MIDDLE" width=3D"18%">

 

 

 

<= tr><= td height=3D"21" valign=3D"MIDDLE" width=3D"21%">

(8)=

<= td height=3D"21" valign=3D"MIDDLE" width=3D"18%">

 

17

= =

Yorub= a (Nigeria)

African r= egion

Reference

Population name

n

Central

Cameroon

104

 

(2)

Cameroon Bakaka

&n= bsp;

(2)

<= p align=3D"CENTER">Cameroon Bamileke

48

 

(2)

46

 

(2)

Cameroon Daba

20

 

<= /td>

(2)

Cameroon Ewondo

53

 

(2)

Cameroon Fali

41

 

<= p align=3D"CENTER">(2)

Cameroon Fulbe

34

(2)

<= /td>

Cameroon Mandara

37

 

(2)

Cameroon Podokwo

= 39

 

(2)

Cameroon Tali

20

 

(2)

25

 

(2)

Cameroon Uldeme

28

 

(2)

Cameroon Western Mbenzele

57

 

(3)

B= ubi

45

 

(3)

Sao Tomeans

50

(4)

<= /td>

Mbundu (Angola)

44

 

(5)

Pygmy (Africa, C.)

10

<= p> 

(6)

Sao-Tomeans

103

 

(7)

<= p align=3D"CENTER">17

 

(7)

Mbuti Pygmy (DRC),

&nb= sp;

(8)

<= p align=3D"CENTER">Fulbe (Cameroon)

1

East

(9)

Kenya,

<= /td>

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

<= p> 

(10)

Ethiopia (Tigrai)

45

(11)

=

Datoga

18

 

(11)

Hadzabe

49

 

Iraqw

=

12

 

(11)

Sukuma

21

 

(1= 2)

Dinka (Sudan)

46

 

(12)

Nubians, southern = Egypt & northern Sudan

68

 

(12)

Nubians, southe= rn Egypt & northern Suda

14

 

(12)

Sudanese sou= thern

79

 

(7)

Hadza (Tanzania)

17

 

(= 8)

Kikuyu (Kenya)

25

 

(8)

Sakuye (Kenya)

<= /td>

1

<= p> 

(8)

Somali (Ethiopia)

9

 

(8)

= Somali (Kenya)

15

 

(8)

Somali (Somalia)

3

<= /td>

 =

(8)

Turkana (Kenya)

37

North

(13)

Egypt

=

75

 

(14)

Souss Valley Moroccans

50

 

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

2= 9

=  

(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

 

Tata

53

 

(17)

Tunis

47

 

Berbers, northern morocco

18

 

(19)

Mauritan= ia

30

 

(19)

Moroccan Berbers

60

 

(1= 9)

Moroccan non-Berbers

32

 

(19)

West-Sahara= n

25

 

(13)

Egypt Gurna

34

(13)

Egypt Upper

24

South

(20)

Khwe

31

 

(= 20)

Kung

=

43

 

(5)

Malawi (Africa, S.)

&nb= sp;

(7)

<= p align=3D"CENTER">!Kung (Botswana)

25

 

(7)

Herero= (Botswana)

27

Southeast

(21)

Bambara

19

 

<= /td>

(22)

Mozambique

109

 

(23)

Africa

&nb= sp;

(5)

<= p align=3D"CENTER">Africa, S.E. (Bantu)

24

West

(24)

292

 

(21)

Malinke

61

(25)

Mandenka (Senegal, E.)

119

 

(26)

Sierra-Leone

277

 

<= p align=3D"CENTER">(27)

Fang (Guinea)

11

(19)

=

Senegalese other

50

 

(19)

Senegalese Serer

23

<= p> 

(19)

Senegalese Wolof

48

Univ. of = California

Sierra Leone

109

 

(7)

Yoruban (Ni= geria)

13

 

(8)

Fulbe (Benin)

1

 

Fulbe (Burkina Faso)

2

 

(8)

Fulbe (Niger)

10

 

<= p align=3D"CENTER">(8)

Fulbe (Nigeria)

47

(8)

=

Hausa (Niger)

3

 

(8)

Hausa (Nigeria)

&nb= sp;

(8)

<= p align=3D"CENTER">Kanuri (Niger)

1

 

(8)

Kanuri (N= igeria)

13

 

(8)

Songhai (Mali)

1

 

(8= )

Songhai (Niger)

9

 

(8)

Tuareg (Mali)

1

 

(8)

Tuareg (Niger)

25

 

(8)

21

1. Černý V, H&= aacute;jek M, Cmejla R, Bruzek J, Brdicka R (2004) mtDNA sequences of Ch= adic-speaking populations from northern Cameroon suggest their affinitie= s with eastern Africa. Ann Hum Biol 31:554-569.

2. Coia V, = et al. (2005) Brief communication: mtDNA variation in North Camer= oon: Lack of Asian lineages and implications for back migration from Asi= a to sub-Saharan Africa. Am J Phys Anthropol 128:678-681.

3= . Mateu E, et al. (1997) A tale of two islands: Population histor= y and mitochondrial DNA sequence variation of Bioko and São Tom&e= acute;, Gulf of Guinea. Ann Hum Genet 61:507-518.

4. Plaza = S, et al. (2004) Insights into the western Bantu dispersal: mtDNA= lineage analysis in Angola. Hum Genet 115:439-447.

5. Sood= yall H, Vigilant L, Hill AV, Stoneking M, Jenkins T (1996) mtDNA control= -region sequence variation suggests multiple independent origins of an &= quot;Asian-specific" 9-bp deletion in sub-Saharan Africans. Am J= Hum Genet 58:595-608.

6. Trovoada MJ, et al. (2004) Pa= ttern of mtDNA variation in three populations from São Tomé= ; e Principe. Ann Hum Genet 68:40-54.

7. Vigilant L, Stonek= ing M, Harpending H, Hawkes K, Wilson AC (1991) African populations and = the evolution of human mitochondrial DNA Science 253:1503-1507.

8. Watson E, et al. (1996) mtDNA sequence diversity in Afric= a. Am J Hum Genet 59:437-444.

9. Brandstätter A, et= al. (2004) Mitochondrial DNA control region sequences from Nairobi = (Kenya): Inferring phylogenetic parameters for the establishment of a fo= rensic database. Int J Legal Med 118:294-306.

10. Kivisild = T, et al. (2004) Ethiopian mitochondrial DNA heritage: Tracking g= ene flow across and around the gate of tears. Am J Hum Genet 75:7= 52-770.

11. Knight A, et al. (2003) African Y chromosome an= d mtDNA divergence provides insight into the history of click languages.= Curr Biol 13:464-473.

12. Krings M, et al. (1999) m= tDNA analysis of Nile River Valley populations: A genetic corridor or a = barrier to migration? Am J Hum Genet 64:1166-1176.

13. Stev= anovitch A, et al. (2004) Mitochondrial DNA Sequence Diversity in= a Sedentary Population from Egypt. Ann Hum Genet 68:23-39.

14. Brakez Z, et al. (2001) Human mitochondrial DNA sequence var= iation in the Moroccan population of the Souss area. Ann Hum Biol= 28:295-307.

15. Corte-Real HB, et al. (1996) Genetic diver= sity in the Iberian Peninsula determined from mitochondrial sequence ana= lysis. Ann Hum Genet 60:331-350.

16. Loueslati BY, et al= . (2006) Islands inside an island: reproductive isolates on Jerba is= land. Am J Hum Biol 18:149-153.

17. Plaza S, et al. = (2003) Joining the pillars of Hercules: mtDNA sequences show multidirect= ional gene flow in the western Mediterranean. Ann Hum Genet 67:31= 2-328.

18. Fadhlaoui-Zid K, et al. (2004) Mitochondrial DNA= heterogeneity in Tunisian Berbers. Ann Hum Genet 68:222-233.

=

19. Rando JC, et al. (1998) Mitochondrial DNA analysis of nort= hwest African populations reveals genetic exchanges with European, near-= eastern, and sub-Saharan populations. Ann Hum Genet 62:531-550.

20. Chen YS, et al. (2000) mtDNA variation in the South Afri= can Kung and Khwe-and their genetic relationships to other African popul= ations. Am J Hum Genet 66:1362-1383.

21. Ely B, Wilson JL, = Jackson F, Jackson BA (2006) African-American mitochondrial DNAs often m= atch mtDNAs found in multiple African ethnic groups. BMC Biol 4:3= 4.

22. Pereira L, et al. (2001) Prehistoric and historic tr= aces in the mtDNA of Mozambique: insights into the Bantu expansions and = the slave trade. Ann Hum Genet 65:439-458.

23. Salas A, = et al. (2002) The making of the African mtDNA landscape. Am J Hum= Genet 71:1082-1111.

24. Brehm A, Pereira L, Bandelt H-J, Prat= a MJ, Amorim A (2002) Mitochondrial portrait of the Cabo Verde archipela= go: The Senegambian outpost of Atlantic slave trade. Ann Hum Genet 66:49-60.

25. Graven L, et al. (1995) Evolutionary correl= ation between control region sequence and restriction polymorphisms in t= he mitochondrial genome of a large Senegalese Mandenka sample. Mol Bi= ol Evol 12:334-345.

26. Jackson BA, et al. (2005) Mitoc= hondrial DNA genetic diversity among four ethnic groups in Sierra Leone.= Am J Phys Anthropol 128:156-163.

27. Pinto F, Gonzalez AM,= Hernandez M, Larruga JM, Cabrera VM (1996) Genetic relationship between= the Canary Islanders and their African and Spanish ancestors inferred f= rom mitochondrial DNA sequences. Ann Hum Genet 60:321-330.




Table 5. Frequency and diversi= ty measures in the various African subregions

n

<= /tr>

South= east

West<= /p>

<= td height=3D"20" valign=3D"MIDDLE" width=3D"10%">

L1b

2.019= (1.202)

 

West<= /p>

= =

-

L2a1

=

2.56= 5 (1.399)

= <= td height=3D"20" valign=3D"MIDDLE" width=3D"14%">

2.8= 11 (1.491)

=

6.0<= /p>

0.4<= /p>

<= /tr>

South= east

West<= /p>

<= td height=3D"20" valign=3D"MIDDLE" width=3D"10%">

L3f1b§

<= td height=3D"20" valign=3D"MIDDLE" width=3D"20%">

0.8= 94 (0.021)

0.772= (0.097)

 

<= td height=3D"20" valign=3D"MIDDLE" width=3D"15%">

0.4=

0.0

<= td height=3D"20" valign=3D"MIDDLE" width=3D"14%">

5.7= 44 (2.790)

North=

<= td height=3D"20" valign=3D"MIDDLE" width=3D"10%">

 

<= td height=3D"20" valign=3D"MIDDLE" width=3D"20%">

0.9= 36 (0.051)

0.875= (0.048)

Hg

Sub-region*

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)

 

<= /td>

North

17

1.5

 

0.949 (0.044)

2.897 (1.600)

 

S= outh

3

2.3

 

0.667 (0.314)

2.667 (1.919)

 

40

8.7

 

0.673 (0.074)

0.987 (0.682)

 

20

1.7

 

=

0.726 (0.092)

1.284 (0.840)

Central

116

6.2

29,366 ± 7,937

0.783 (0.033)

1= .978 (1.126)

 

East

15

1.9

 

0.914 (0.056)

 

=

North

31

2.8

 

0.817 (0.067)

1.720 = (1.031)

 

<= p align=3D"CENTER">South

1

0.8

 

-

-

Southeas= t

10

2.2

 

0.889 (0.075)

1.422 (0.946)

 

150

13.0

 

0.961 (0.008)

2.665 (1.428)

L1c1a

Centra= l

273

14.6

57,144 ± 7,937

0.746 (0.018)

<= /td>

3.152 (1.638)

 

East

0

0.0

 

-

-

 

No= rth

0

0.0

 

-

-

 

South

0

0.0

 

-

 

Southeast

3

0.7

 

0.667 (0.314)

2.667 = (1.919)

 

<= p align=3D"CENTER">West

1

0.1

 

-

-

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)

 

South

3

2.3

 

0.000 (0.000)

0.000 = (0.000)

 

<= p align=3D"CENTER">Southeast

133

29.0

 

0.810 (0.022)

3.= 118 (1.628)

 

West

169

14.6

 

0.936 (0.011)

L3e1

=

Central

102

5.4

15,873 ± 2,3= 81

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

 

<= /td>

0.000 (0.000)

0.000 (0.000)

 

Southeast

40

8= .7

 

0.908 (0.024)

2.356 (1.312)

 

West

5

 

<= /td>

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)

 

<= /td>

North

8

0.7

 

0.786 (0.151)

2.464 (1.486)

 

S= outh

5

3.8

 

0.000 (0.000)

0.000 (0.000)

 

7

1.5

 

0.857 (0.137)

2.571 (1.563)

 

55

4.8

 

=

0.922 (0.025)

2.994 (1.588)

Central

78

4.2

15,873 ± 2,381

2.333 (1.289)

 

East

17

2.2

 

1.500 (0.950)

 

North

6

0.5

0.533 (0.= 172)

1.067 (0.811)

 

South

0

0.0

 

-

-

 <= /p>

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= ¶

<= p align=3D"CENTER">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

 

=

0.667 (0.204)

2.667 (1.778)

 

South

0

 

-

-

 

Southeast

22

4.8

 

0.952 (0.029)

= 6.632 (3.255)

 

West

59

5.1

 

0.926 (0.030)

L1c1

Central

305

16.3

7= 3,811 ± 7,143

0.838 (0.017)

4.415 (2.185)

 

E= ast

6

0.8

 

0.867 (0.129)

4.200 (2.425)

 

2

0.2

 

=

0.000 (0.000)

0.000 (0.000)

South

0

0.0

 

-

-

 

Southeast

13

2.8

 

5.628 (2.888)

 

West

45

3.9

 

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 w= ork)

§

Compared with L3f1 in the literature. =

These Hgs collapsed the information of all of its int= ernal clades and do not represent a real label in the study. ------------dGVE3730075ApgTdKhBR0S--