1 Figure S1: Uniparental Lineages Found in Madagascar

Home , African Pygmies, Haplogroup L3 (mtDNA)

Figure S1: Uniparental lineages found in Madagascar

A) mtDNA lineages

Mitochondrial,African,lineages,(n=1023), Mitochondrial,Asian,lineages,(n=1208), Haplogroup) n) Haplogroup) n) Haplogroup) n) L0a, 3, L3a+709, 11, B4a1a1b, 510, L0a1+16293, 3, L3a1, 1, E1a1, 1, L0a14, 1, L3a1b, 2, E1a1a, 156, L0a1a2, 2, L3b1a+16124, 1, F3b1b, 120, L0a1b1a, 2, L3b1a11, 2, F4b, 17, L0a1b1a1, 32, L3b1a1a, 157, M20, 2, L0a1e, 1, L3b1a3, 5, M32c, 118, L0a2, 8, L3b1a8, 15, M7c1c3, 279, L0a2a1a, 4, L3b2, 2, Q1, 5,

L0a2a1a2, 1, L3d1a, 3, Mitochondrial,Unknown,lineages,(n=178), L0a2a1b, 5, L3d1a1a, 47, Haplogroup) n) L0a2a2a, 79, L3d1a1a1, 39, M23, 178, L0a2d, 1, L3d3a1, 2, L0d1c, 1, L3d3b, 2, L0f, 4, L3e1, 4, L1b1a, 1, L3e1a1a, 20, L1b2a, 5, L3e1a3a, 60, Q1# L1# L1c1, 2, L3e1b2, 7, <1%#0%# 2%# M20# L1c1d, 8, L3e1d1, 14, M23# L0# <1%#0%# L1c2a1a, 8, L3e1e, 1, 7%# 6%# L1c2a2, 1, L3e1e1, 4, L2# L1c2a3a, 1, L3e1f1, 1, M7c1c3# L1c2b1ab, 1, L3e2b, 9, 11%# 12%# L1c2b1b, 1, L3e2b+152, 9, L1c2b2, 1, L3e2b1a2, 3, M32c# L1c3a, 11, L3e2b3, 1, 5%# L1c3a1a, 1, L3e3a, 57, L1c3a1b, 1, L3e3b, 2, F# L1c3b1a, 3, L3e3b1, 36, 6%# L1c3c, 15, L3e3b2, 2, L3# L2a1+143, 1, L3f, 2, E1a# 23%# L2a1a, 10, L3f1b1a1, 1, 6%# L2a1a2, 53, L3f1b4a, 3, L2a1a2a1a, 2, L3f1b4a1, 11, L2a1a3c, 2, L3h1a2, 1, B4a1a1b# L2a1b1a, 156, L3k1, 6, 21%# L2a1c, 1, L3x1a2, 1, L4# L2a1f, 7, L4b1a, 6, 1%# L2a1f3, 1, L4b2a1, 8, L2a1g, 2,,, ,, L2a1h, 2,,, ,, L2a5, 6,,, ,, L2b1a3, 9,,, ,, L2b2a, 3,,, ,, L2c2b1b, 2,,, ,, L2d1a, 1,,, ,,

1 B) Y chromosome lineages

Y"African"lineages"(n=1100)" Haplogroup) Marker) n) A1b1a1" M14" 3" B2A" M150" 92" B2B" M112" 52" E1b1a1" rs9785941" 76" E1b1a1a1d1c" M154" 6" E1b1a1a1c1a1" rs16980586" 317" E1b1a1a1d1" rs16980502" 272" P# L# G# A2# E1b1a1a1d1a" rs16980406" 112" T# <1%#0%# <1%#0%#1%# <1%#0%# E1b1a1a1d1a1" rs16980589" 18" 1%# E1b1b1" M35" 7" C# J# 0%# R# B2# E1b1b1a1" M78" 38" <1%$ 3%# E1b1b1b2a1" M34" 1" 3%# 9%# E2b1" rs2032620" 106" E2b# O1# Y"Asian"lineages"(n=322)" 7%# E1b1b# 13%# Haplogroup) Marker) n) 3%# C" rs35284970" 3" O1a1a" rs13447354" 1" O1a2" rs2032632" 201" O1b1a1a" rs2032650" 117" O2# Y"Eurasian"lineages"(n=132)" 8%# Haplogroup) Marker) n) G" rs2032636" 1" G2a*E"P15" P15" 7" J1" rs9341313" 2" J1a2b" rs34043621" 2" J2a" M410" 11" E1b1a# J2a1b" rs2032628" 8" 52%# J2b*" rs3903" 10" J2b2" rs8179022" 16" L" rs3911" 1" L1a1" M76" 6" P*" M207" 5" R*" rs2032658" 4" R1a1a" rs3908" 35" R1b" rs9786194" 6" R1b1a1a2" rs9786153" 8" T1a" rs2032672" 10"

2 C) M23 Network root M

root M 417 533 2706 8188 8360 9438 9545 10142 10295 11569 11899 12618 15025 16263

D) mtDNA haplotype diversity

3 E.1) Phylogenetic tree for L0 and L1 haplogroups

L0a2c L1c3b2 L0a2b L0a2b1

L0a2b1 L1c3b2 5 L0a2d

1 1 L0a2a1b

L1c3a1b L1c3b1b 2 4

1 L0a2a1b L0a2a1a1 L1b3 L1c3b1 L0a2a1

L1b2 1 L0a2a1a2

1 L0a2a1a1 L1c3b1a

L1c3a1a 1 2

L1b3 1 2 1 L1b2 L1c3a1a

L1b2a

L1c3b1b 1 L1b2a

4 1 1 L1c3a 1 1 L0a2a2a3

9 L1c3a1b 50 1

L1c3a 1 L1c2a2 1 1

1 1 L1c3c L0a2a2a1

1 15 1 L1c2a3a 1

L1c2a3 1 8 L1c2a1a 6 2 1 1 1 1 5 L0a2a2 1 3 rSRS 1 L0a3 1 L0a3

1 L0a1a 1 L1c1d 1 6 L0a1e L0a4

1 L1c1d1

1 1 L0a1a3

L1c1d1 L0a1c1 L1c1a

L0a1cL0a1c1 L1c1b1 L1c1b

L0a1dL0a1a_200

L1c1b1

L0d1c L0a1d

L0d1c3 L0a1a2L0a1a L0d1c3 1

L0d1c1a1a1 L0d1c1a1a1

L0d1c1 L0a1a2

1 L0d1c1a L0d1c1a1a2

L0a1a1 2

L0d1c1a2

L0d1c2a

L0d1c1a2 L0a2d L0a1b1

L0d1c1a1b L0a1b1

L0d1c2 1

L0d1c1a1

L0d1c1a L0d1c2a1 1

L0d1c2 1 6 1 2 L0a1b2a L0a1a1 14 L0a1b1a 1 2 L0a1b1a1

L0a1b2 L0a1b2a L0a1b1a 4 2

2 L0f2a1

L0f2a1

L0f1

L0f2b 2

L0f2a

H sample population country publication L0a2a2a EU092787 Oman Oman Behar et al. 2008 JQ705109 NA NA Behar et al. 2012 L0a1b1a EU935434 el-Hayez Egypt Kujanova et al. NA19703 Southwest Usa USA HAPMAP L1c3a EU092703 Mozambique Mozambique Behar et al. 2008 JX303824 Zambia Zambia Barbieri et al. 2012 L1c3c EU273493 Makina Gabon Quintana-Murci et al. 2008 L1c1b NA19917 African ancestry USA HAPMAP in southwest EU273499 Mitsogo Gabon Quintana-Murci et al. 2008 L1c2a1a AF346992 Kikuyu Kenya Ingman et al. 2000 JX303855 Zambia Zambia Barbieri et al 2012

4 E.2) Phylogenetic tree for L2 haplogroups

L2b2a rSRS

4 L2a5

L2b2a 2 L2d1a

L2d1a

6 L2b2

L2a5 L2a1k 2 L2a1c6

L2a1c2a L2a1c2 L2a1c2a

L2a1c2

L2d1 L2a1c

8 L2b1a3

L2a1f1 L2d 2 L2b1a2 L2a1c6

L2a1f2 L2a1f2 L2b1a L2a1k L2a1b3 4

10 L2a1c5 L2a1c1a2

L2d_16129 L2a1l2a1

L2b1 L2a1m L2a1c1a2

L2b1 L2a1l2

L2b1a4

L2b1b L2a1b3

L2b1a2 L2a1l2a L2a1m1a

L2a1i1 L2b1b

L2a1m1a L2c2a L2a1c1 L2a1i L2a1c1a1

L2a1d1

L2a1d1 L2a1_16189 (16192)

L2c2b1b L2a1c L2c2a1

L2c2b1a

L2c2b1b L2a1f

L2a1d2 L2a1d2 4 L2a1f3 L2a1j

L2c2b1a L2a1f

L2a1p 14 2 L2a1l3 L2a1l3

L2a1p L2a1b2

L2a1c4a1 L2a1b2

L2a1c4a1 L2a1o L2a1o

L2a1c4a L2a1c4

L2a1c4a L2a1l1a2 L2a1e

L2a1l1a L2a1l1a2 L2a1e1 L2a1l1 L2a1l1a1

L2a1e1 L2a1n L2a1l1b

L2a1c3b2 L2a1c3b2

L2a1c3b1 L2a1l1b

L2a1c3b1 L2a1c3b L2a1b1a2 L2a1c_16129

2 L2a1c3a

L2a1q

L2a1q 2 2

L2a1g 2 L2a1c3a 22

2 24

L2a1c3a1 4 L2a1c3a1 2 276 22

L2a1h 2 22 2

L2a1h 4 L2a1f1a 88

2 L2a1f1a L2a1a3a L2a1a272

L2a1a1

L2a1a3a L2a1a2a L2a1a2c L2a1a3b 4 L2a1a3b

L2a1a3c L2a1a2 22 2 L2a1a2a1

L2a1a1 2242 4 626 L2a1a3c L2a1a2a1

L2a1a2a1a

L2a1a2c 2 4

L2a1a2a1a

L2a1a2b L2a1a2b

H sample population country publication L2a1b1a EU092690 Chopi Mozambique Behar et al. 2008 JX303858 Zambia Zambia Barbieri et al. 2012 L2a1a2 JN214449 Umbria (Centre) Italy Cerezo et al. 2011 DQ304968 African American United states Just et al. 2008 L2a1f DQ304959 African American United states Just et al. 2008 NA19125 Yoruba in ibadan Nigeria hapmap L2b1a3 JX303882 Zambia Zambia Barbieri et al. 2012 DQ304978 African American United states Just et al. 2008

5 E.3) Phylogenetic tree for L3d and L3e haplogroups

25 1 1 1

L3d1a1a1 10 1

1 rSRS

L3d1a1a 2 L3d1a1a 1 L3e1g 1 3 L3e1g 2 1 L3e1f 2

1 L3e1b2

L3d1a2 L3d1a2 L3e1b1 L3e1d L3e1 1 L3e1a3b

4 L3e1b2 1 33 L3e1f2 L3e1b1 L3d1a1b 1 L3e1a2 L3e1a2

L3e1

L3e1c

L3d3a

3L3d1a 3 3 L3d3a1b 50 L3d3a1 L3e1 L3e1a3a 1 L3e1f1a 1 1

2 1

L3d3b

L3d3b 2 L3e4

4 L3e1e2

L3e2a1b3

L3e1e11 L3e1e L3e2a1b3 L3e2a1b1 L3e2a1b2

L3e2a1b2 L3e1a1a

L3e2a1b 2

L3e2a1b

L3e2a1a 1

L3e2a2 L3e1a1a

L3e2a2 L3e2a 2

L3e2b4

L3e2a3

L3e2a 12 1

L3e2b4 2

L3e2b3

1 L3e2b6

L3e2b3 L3e1d1aL3e1d1

L3e2b1a2

L3e2b6

L3e2b8 3 2

L3e2b1 3 L3e2b2 2

1 1 L3e1d1

12 L3e2b7

L3e2b_152

L3e2b8 L3e2b2

1 L3e2b L3e2b5 L3e2b7 L3e2b5

L3e2b 1 L3e2b1a 1

L3e2b1a1 1 2 1 42 1 L3e3a L3e3a 6 1 1 16 L3e3b L3e3b3

L3e3b L3e3b1 1 1 L3e3b2 2

L3e3b1 1 1

L3e3b3 9 7 2

H sample population country publication L3e1a3a KC533488 Limpopo South Africa van der Walt et al 2012 HM771173 Fang (bantu) Gabon Batini et al 2011 L3e3a JN655812 Somalia Somalia Soares et al. 2012 DQ305012 African American United states Just et al. 2008 L3e3b1 HM771231 Nzebi (bantu) Gabon Batini et al 2011 DQ305013 African American United states Just et al. 2008 L3d1a1a1 KC533458 Gauteng South Africa van der Walt et al 2012 EU092932 Brahui Pakistan Behar et al. 2008 L3d1a1a JN655800 Somalia Somalia Soares et al. 2012 AF347014 Yoruba West africa Ingman et al 2000 L3e1a1a EU092749 S. Arabia S. Arabia Behar et al. 2008 KC533483 Gauteng South Africa van der Walt et al 2012

6 E.4) Phylogenetic tree for Remaining of L3 and L4 haplogroups

rSRS 2

L3x1a1 2 L3b2a

L3k L3k1 L3b2 L3b2a

L4b1a

L3x1b L4b1

L3x1a2 1

L3b2b

L3k1 10 L3x1a2 L4b1a 1

L3b3 1 L3x1a1 122 14 L3b2b 1

8 1 L3x1b 1

L3b3 1

L3a1a L4b2a1 2

L3a_709 L3b1a1a1

L4b2a1 2

L3a1a 1 1 L3a1b 9 3 1 1

L3a1b 1 1

2 L3b1a1

L3a2

L3a2a

L3h1a1 L3b1a3

L3a2a L3b1a11 L3h1a1 L3b1a9

L3b1a9 L3h1a2b L3b1a

L3b1a6 L3h1a2b L3b1a2 L3b1a_152 1 L3b1a10 L3b1a8

L3b1a2

L3f1b_16292 L3h1a2a1

L3h1a2a1 L3b1a9a

L3f1b_16292_150 2 L3b1a9a

19L3b1a10 L3b1a_@16124 L3f1b1a

L3f1b1a L3h1a2a L3f1b1a1

L3f2a1a

L3f1b1

L3f1b4b

1L3f1b5 L3b1a4

L3f1b5 L3b1a5a

L3f1b4b L3b1b1 L3b1a4 L3f1b3 1 1 L3b1a8 L3b1a5 L3f

L3f2a1a L3f1b2a L3b1a5a L3b1a7a L3b1a5 L3f2b

2 L3f1b3 L3b1b

1 L3b1a7a L3f1b2 2 L3f2a1

L3f1b4a1

8 L3b1a7 L3f1a1

3L3f1b4a1

L3f1a1

L3f3 L3f1b4a

L3f1a L3f3 L3f3a

L3f3b L3f2b

L3f3b

H sample population country publication L3b1a1a EU597490.1 Bantu_N.E. Kenya Hartmann, A. et al. DQ304995.1 African American United-States Just et al .2008 L3b1a EU092726 Cassanga G. Bissau Behar et al. 2008 L3a_709 JN655803 Somalian Somalia Soares et al .2012 (L3a2) NA19438 Luhya in webuye Kenya HAPMAP L4b2a1 EU092942 Ethiopian Ethiopia Behar et al. 2008 DQ341065 Ethiopian Ethiopia Torroni et al. 2005 L3f1b4a1 EU092912 Kenyan Kenya Behar et al. 2008 EU092791 Oman Oman Behar et al. 2008 L3k1 JN655789 Chad Chad Soares et al. 2012 JQ705310 NA NA Behar et al. 2012

7 E.5) Phylogenetic tree for M haplogroups (Q, M20, M32, M23, M7c1c3)

rSRS

1 1 1 M20 1 M20 2 2 Q1c 2 147 Q1 2 Q1a Q3a 11 Q1b 1 1 Q1b 1 Q2a 6 1 M29a4 Q2a 1 1 4 Q1a 2 1 M29a 1 1 Q1 Q3b 5 1 Q3a 1 2 2

2 1 M23 M23 6 1

1 89 1

M75 1

1 M23 1 M75

1 M 1

M1a1

M7a_16324 M

M32 M32

M7b1a1 M M18a

M7b1a1

M7c1b M7c1a 1 M7c1c2 1 2 M7c1c3e2

1 1 3M7c1c3 1 1 2 1 1 M7c1c3e 71 M7c1c3b 1 1 M7c1c3g 2 M7c1c3b 1 1 1 11 1 1M7c1c3f 11 11 1 161 1M7c1c

1 M7c1c3d 11

1 M7c1c2 1 M7c1c1

1 M7c1c3a1 2 21 M7c1c3a1 1 M7c1c1 M7c1c3a 1

M7c1c3c

H sample population country publication Q1 DQ372885 Samoa Samoa Pierson et al. 2006 AY289090 Papua (Highland) New Guinean Ingman and Gyllensten 2003

M20 AP012349 Bidayuh Borneo Jinam,T.A et al. 2012 JX289112 Arakanese Myanmar Summerer,M. et al. 2014 M32a AY950296 Andaman Andaman Thangaraj,K et al. 2005 DQ149512 Jarawa Andaman Rao,V.R. 2007 Unpublished M7c1c3 JX987452 NA Indonesia Trejaut,J.A. et al.2012 HM596650 Sumatra Sumatra Gunnarsdottir E.D. et al. 2011 M75 HM030540 Qinghai China Kong,Q.P. et al. 2010 (closest to HM030524 Qinghai China Kong,Q.P. et al. 2010 M23)

8 E.6) Phylogenetic tree for N haplogroups (B4, F3 and F4)

rSRS

F4b

F4a2 F4a2 1 1 1

F4b

14 B4a1a1a F4a1b B4a1a1a1 B4a1a1a1a1 B4a1a1a1b

1 B4a1a1a2a

B4a1a1a1a1 2 F3b1a

1 B4a1a1d F4a1b 1 2 B4a1a1a2a B4a1a1d1 1 B4a1a1cB4a1a1f1 1 B4a1a1 2 1 1 11 6 1 1 1 1 4 1 1 1 1 2 1

3 2

93F3b1b 2 B4a

F3b1b 1

1 F3a_207

1 B4a1a F3a 1 1

B4a1a 1

F3a1 1 F3a1 F3b_152 1

B4a1a1b F3b 1 1 1 440 33 1 2 11 22 321 11213211111

H sample population country publication F3b1b KC994125.1 Kankanaey Philippines Delfin F et al. 2014 JF739538 Batak Negritos from Philippines Scholes,C. et al. 2011 Palawan F4b AY289095 Taiwan Aborigine Taiwan Ingman et al. 2003 NA18592 Han - Bejing China HAPMAP B4a1a1 JX900371 Choiseul Solomon Duggan,A.T et al . 2013 Islands HQ873499 Ujung Pandang Indonesia Soares,P. et al. 2011 B4a1a1a HQ873525 Banks and Torres Vanuatu Soares,P. et al. 2011 B4a1a1d Isabel Solomon Isl. Duggan,A.T et al . 2013 B4a1a1e JX900634 Ranongga Solomon Isl. Duggan,A.T et al . 2013 B4a1a1f JX900410 Guadalcanal Solomon Isl. Duggan,A.T et al . 2013

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