Appendix

NATIVE AMERICAN

Core mutations of Native American mDNA clusters
CLUSTER	MUTATIONS
A1	223 390 319 362
A2	111 223 290 319 362
B	189 217
C	223 298 325 327
D	223 325 362
X	223 278

Calibrated origin dates and clan mother names for Native American mDNA clusters
CLUSTER	MOTHER	AGE (YRS)
A	Aiyana	15,800
B	Ina	18,700
C	Chochmingwu	19,600
D	Djigonese	16,900
X	Xenia	15,800

EUROPEAN

Calibrated origin dates, clan mother names, and frequencies for native European mDNA clusters
CLUSTER	FREQUENCY (%)	MOTHER	AGE (YRS)
U5	5.7	Ursula	47,000
HV	5.4	HV	34,000
X (I)	1.7	Xenia	26,000
U4	3.0	Ulrike	20,000
H	37.7	Helena	14,000
T	2.2	Tara	13,000
K	4.6	Katrine	12,500
T2	2.9	Tara	12,000
J	6.1	Jasmine	8,500
T1	2.2	Tara	9,000

AFRICAN

Clan mothers and ages of native African mDNA clusters
NOTATION	CLAN MOTHER	AGE (YRS)
Superclan L1
L1A	Layla	40,000
L1B	Lamia	30,000
L1C	Lalamika	60,000
L1D	Latasha	50,000
L1E	Lalla	83,000
L1F	Labana	86,000
L1K	Lakita	92,000
Superclan L2
L2A	Leisha	55,000
L2B	Lesedi	32,000
L2C	Lingaire	27,000
L2D	Lindewe	122,000
Superclan L3
L3A	Lara	60,000
L3B	Limber	21,000
L3D	Lingaire	30,000
L3E	Lila	45,000
L3F	Lungile	36,000
L3G	Lubaya	45,000

Regional distribution within Africa of the most frequent native African mDNA clusters
REGION	TOP 5 MOST FREQUENT CLUSTERS
East	L1A, L2, L3A, L3F, L3G
Southeast	L1A, L2A1a, L2A1b, L3E
South	L1A, L1D, L1K, L3B, L3E
Central	L1A, L1C, L2A1, L3E
West	L1B, L2A1, L3B, L3D
North	L1B, L2A1, L3B, L3D

FROM	TO	MUTATIONS
Superclan L1
Root	L1	16230
Root	L1D	16129, 16243
L1D	L1D1	16294
L1D	L1D2	16234
Root	L1F	16169, 16327
Root	L1A	16129, 16148, 16172, 16188G, 16278, 16320
L1A	L1A1	16168
L1A1	L1A1a	16278
L1A	L1A2	16129
Root	L1K	16172, 16209, 16214, 16291
L1K	L1K1	16166C
Root	L1E	16129, 16148, 16166
L1E	L1E1	16111, 16254, 16311
L1E	L1E2	16355, 16362
L1	L1B/C	7055R
L1	L1B	16126, 16264, 16270
L1B	L1B1	16293
L1B/C	L1C	16129, 16294, 16360
L1C	L1C1	16293
L1C1	L1C1a	16274
L1C1a	L1C1a1	16214, 16223, 16234, 16249
L1C	L1C2	16265C, 16286G
L1C	L1C3	16187, 16215
L1	L2/3	16187, 16189, 16311
Superclan L2
L2/3	L2	16390
L2	L2C	13957R
L2C	L2C1	16318
L2C	L2C2	16264
L2	L2A	13803R, 16294
L2A	L2A1	16309
L2A1	L2A1a	16286
L2A1	L2A1b	16290
L2	L2D	3693R, 16399
L2D	L2D1	16129, 16189, 16223, 16300, 16354
L2D	L2D2	16111A, 16145, 16239, 16292, 16355
L2	L2B	4157R, 16129, 16114A, 16213
L2B	L2B1	16362
Superclan L3
L2/3	L3	3592R, 16278
L3	L3F	16209, 16311
L3F	L3F1	16292
L3	L3G	16293T, 16311, 16355, 16362
L3	L3B/D	16124
L3B/D	L3B	10084R, 16278, 16362
L3B	L3B1	16124
L3B	L3B2	16311
L3B/D	L3D	8616R
L3D	L3D1	16319
L3D	L3D2	16256
L3D	L3D3	16189, 16278, 16304, 16311
L3	L3E	2349R
L3E	L3E3/4	5260R
L3E3/4	L3E4	16264
L3E3/4	L3E3	16265T
L3E	L3E2	16320
L3E	L3E2b	16172, 16189
L3E	L3E1	16327
L3E1	L3E1a	16185
L3E1	L3E1b	16325
L3A	M	10397R
L3A	N	10871R

Mutations in the African mDNA tree.

Numbers are positions of mutations in the mDNA sequence. Positions without a suffix are transitions. Suffixes A, G, C, T indicate transversions to these bases. Suffix del indicates a deletion while R is a restriction enzyme variant.

CLAN DONALD GENEALOGY

Identification of individuals on Clan Donald genealogy (see Fig.2)
CODE	NAME	DATES	BRANCH
A	Somerled	c. 1100–1164
B	Dugall, founder of Clan Dougal of Lorne	c. 1118–?
C	Donald MacRanald of the Isles	1190–1269
D	Alastair Mor MacDonald, founder of Clan Alastair	d. 1299
E	John MacDonald, Lord of the Isles	d. 1386
F	Ranald Macdonald, 1st of Clanranald and Glengarry	d. 1386
G	Donald Gallach MacDonald, 3rd of Sleat	d. 1506
H	Ranald Mor MacDonald, 7th of Keppoch	d. 1547
I	Alan MacDonald, 4th of Clanranald	1437–1481
J	Donald Gruamach MacDonald, 4th of Sleat	d. 1534
K	Ian Moidartach MacDonald, 8th of Clanranald	1502–1584
L	Sir Donald Breac Macdonald, 10th of Sleat	1605–1678
M	Ranald Alexander MacDonald, 24th of Clanranald	Living	Clanranald
N	P. M. Macdonald	Living	Glenaladale
O	J. J. Macdonald	Living	Bornish
P	Ranald MacDonell, 23rd of Glengarry	Living	Glengarry
Q	Allan Douglas MacDonald of Vallay	Living	Vallay
R	Sir Iain Godfrey MacDonald, 25th of Sleat	Living	Sleat
S	David Foster Macdonald, 17th of Castle Camus	Living	Castle Camus
T	D. B. Macdonald	Living	Sleat
U	W. F. Macdonald	Living	Achnancoichean
V	L. McDonald	Living	Bohuntin

Details of Y chromosome mutations in Clan Donald genealogy (See Fig.2)
LINK	MARKER	MUTATION
C–E	458	16–15
E–G	557	15–16
F–P	449	31–32
F–P	456	17–16
F–P	CDYa	34–35
G–T	GATAH4	12–11
H–U	448	20–21
H–U	449	30–31
H–U	GATAH4	12–11
H–V	570	18–19
H–V	390	25–24
I–O	CDYb	38–37
J–L	448	20–19
J–S	449	31–32
J–S	460	11–10
J–S	557	15–17
K–M	389a	14–13
K–M	390	25–24
K–M	449	31–32
K–M	576	17–18
K–M	CDYb	38–37
K–N	GATAH4	12–10
K–N	CDYa	34–33
K–N	449	31–30
K–N	458	15–16
L–R	607	16–15

Code letters in column 1 identify deceased (shaded) and living individuals on Fig. 2 (p. 108). Markers 1–38 are identified in row 2.

Numbers in table body are allele repeat lengths of Y chromosomes that differ from values deduced for Somerled (row A)

The location of 146 important genes, showing their order from right to left along each chromosome (Column 1), the body system involved (Column 2), the encoded protein (Column 3), and the international gene symbol (Column 4).
REF	SYSTEM	PROTEIN	SYMBOL
1.1	Digestion	Chymotrysin C	CTRC
1.2	Bones, skin, teeth, and joints	Bone morphogenetic protein 8a/b	BMP8A/B
1.3	Metabolism	Leptin receptor	LEPR
1.4	Digestion	Amylase	AMY1 and 2
1.5	Digestion	Cathepsin K and S	CTSK/S
1.6	Muscle	Tropomyosin 3	TPM3
1.7	Brain and nerves	Laminin gamma 2	LAMC2
1.8	Liver and kidney	Renin	REN
1.9	Muscle	Actin alpha 1, skeletal muscle	ACTA1
1.10	Eyes	Opsin 3	OPN3
2.1	Immunity	Immunoglobulin kappa constant	IGKC
2.2	Bones, skin, teeth, and joints	Bone morphogenetic protein 10	BMP10
2.3	Digestion	Lactase	LCT
2.4	Brain and nerves	Sodium channel 9	SCN9A
2.5	Heart and lung	Collagen type 3	COL1A3
2.6	Eyes	Crystallin gamma A	CRYGA
2.7	Pigmentation	Fibronectin	FN1
2.8	Eyes	Crystallin beta A2	CRYBA2
2.9	Liver and kidney	Collagen type 4, alpha 3/4	COL4A3/4
2.10	Metabolism	Glucagon	GCG
3.1	Eyes	Retinoic acid receptor beta	RARB
3.2	Metabolism	Parathyroid hormone 1 receptor	PTH1R
3.3	Digestion	Lactotransferrin	LTF
3.4	Metabolism	Phosphodiesterase	PDE12
3.5	Muscle	Myosin HC 15	MYH15
3.6	Eyes	Rhodopsin	RHO
4.1	Brain and nerves	Huntingtin	HTT
4.2	Bones, skin, teeth, and joints	Fibroblast growth factor 3	FGFR3
4.3	Bones, skin, teeth, and joints	Enamalin	ENAM
4.4	Bones, skin, teeth, and joints	Ameloblastin	AMBN
4.5	Immunity	Immunoglobulin J	IGJ
4.6	Liver and kidney	Alcohol dehydrogenase	ADH1A
4.7	Pigmentation	Hair color 2 (red)	HCL2
5.1	Blood	Thrombospondin 4	THBS4
5.2	Muscle	Myosin X	MYOX
5.3	Pigmentation	Solute carrier, family 45, member A2	SLC45A2
5.4	Bones, skin, teeth, and joints	Growth hormone receptor	GHR
5.5	Bones, skin, teeth, and joints	Fibroblast growth factor 10	FGF10
5.6	Bones, skin, teeth, and joints	Fibrillin 2	FBN2
5.7	Bones, skin, teeth, and joints	Lysyl oxidase	LOX
5.8	Bones, skin, teeth, and joints	Fibroblast growth factor 1	FGF1
5.9	Metabolism	Insulin dependent diabetes 10	IDDM10
6.1	Immunity	HLA region	HGC
6.2	Eyes	Opsin 5	OPN5
6.3	Muscle	Myosin VI	MYO6
6.4	Brain and nerves	Laminin alpha 2/4	LAMA2/4
6.5	Brain and nerves	Opioid receptor mu 1	OPRM1
6.6	Blood	Plasminogen	PLG
6.7	Blood	Thrombospondin 2	THBS2
7.1	Muscle	Actin beta	ACTB
7.2	Muscle	Myosin light chain 7	MYL7
7.3	Bones, skin, teeth, and joints	Elastin	ELN
7.4	Blood	Erythropoietin	EPO
7.5	Bones, skin, teeth, and joints	Collagen type 1, alpha 2	COL1A2
7.6	Brain and nerves	Acetylcholinesterase	ACHE
7.7	Eyes	Opsin 1 cone short wave	OPN1SW
7.8	Brain and nerves	Olfactory receptor 2A.25	OR2A25
8.1	Heart and lung	Surfactant protein C	SFTPC
8.2	Bones, skin, teeth, and joints	Fibroblast growth factor receptor 1	FGFR1
8.3	Blood	Plasminogen activator (tissue)	HBB
8.4	Brain and nerves	Opioid receptor kappa 1	OPRK1
8.5	Blood	Angiopoietin 1	ANGPT1
8.6	Brain and nerves	Otoconin	OC90
9.1	Immunity	Inteferon alpha	IFNA
9.2	Muscle	Tropomyosin 2	TPM2
9.3	Digestion	Beta glucosidase (bile acid)	GBA2
9.4	Bones, skin, teeth, and joints	Osteoclast stimulating factor 1	OSTF1
9.5	Bones, skin, teeth, and joints	Osteoglycin	OGN
9.6	Blood	Hemogen	HEMGN
9.7	Blood	ABO blood group	ABO
10.1	Eyes	Optineurin	OPTN
10.2	Muscle	Myosin IIIA	MYO3A
10.3	Eyes	Opsin 4	OPN4
10.4	Muscle	Actin alpha 2, smooth muscle	ACTA2
10.5	Digestion	Trypsin	TYSND1
10.6	Heart and lung	Adrenergic alpha 2A/beta receptor	ADRA2A/B1
10.7	Metabolism	Cytochrome P450, family 2C, polypeptide	CYP2C9
10.8	Heart and lung	Pancreatic lipase	PNLIP
11.1	Blood	Beta globin	HBB
11.2	Metabolism	Insulin	INS
11.3	Brain and nerves	Otogelin	OTOG
11.4	Digestion	Pepsin	PGA3
11.5	Digestion	Cathepsin C	CTSC
11.6	Pigmentation	Tyrosinase	TYR
11.7	Eyes	Crystallin alpha B	CRYAB
11.8	Immunity	Thymocyte cell surface antigen	THY1
12.1	Immunity	Alpha 2 macroglobulin	A2M
12.2	Digestion	Islet amyloid polypeptide	IAPP
12.3	Pigmentation	Keratin 1-5	KRT1-5
12.4	Bones, skin, teeth, and joints	Collagen type 2	COL2A1
12.5	Digestion	Peptidase B	PEPB
12.6	Pigmentation	KIT ligand	KITLG
12.7	Immunity	Thympoietin	TMPO
12.8	Digestion	Phopholipase A2	PLA2G1B
13.1	Brain and nerves	Olfactomedin 4	OLFM4
13.2	Brain and nerves	Olfactory receptor E	OR7E
13.3	Muscle	Myosin XVI	MYO16
13.4	Liver and kidney	Collagen type 4, alpha 1 and 2	COL4A1/2
14.1	Heart and lung	Myosin heavy chain 6 and 7, cardiac	MYH6/7
14.2	Metabolism	Estrogen receptor 2	ESR2
14.3	Bones, skin, teeth, and joints	Bone morphogenetic protein 4	BMP4
14.4	Blood	Spectrin beta	SPTB
14.5	Digestion	Chymotrypsin	CTRB1
14.6	Brain and nerves	Creatine kinase (brain)	CKB
14.7	Immunity	Immunoglobulin H alpha 1	IGHA1 et al.
15.1	Muscle	Actin alpha 1, cardiac muscle	ACTC1
15.2	Pigmentation	Oculocutaneous albinism II	OCA2
15.3	Brain and nerves	Cholinergic receptor nicotinic alpha 7	CHRNA7
15.4	Pigmentation	Solute carrier, family 24 member 5	SLC24A5
15.5	Blood	Thrombospondin 1	THBS1
15.6	Muscle	Myosin 1E	MYO1E
15.7	Pigmentation	Hair color 3 (brown)	HCL3
15.8	Bones, skin, teeth, and joints	Chondroitin sulfate proteoglycan 4	CSPG4
15.9	Bones, skin, teeth, and joints	Aggrecan	ACAN
16.1	Blood	Alpha globin	HBA1 and 2
16.2	Digestion	Myosin HC 11, smooth muscle	MYH11
16.3	Blood	Alpha hemoglobin stabilizing protein	AHSP
16.4	Muscle	Myosin light chain kinase 3	MYLK3
16.5	Blood	Haptoglobin	HP
16.6	Digestion	Chymotrypsinogen B1/2	CTRB1/2
16.7	Pigmentation	Melanocortin 2 receptor	MC2R
17.1	Muscle	Myosin, heavy chain 1, skeletal adult	MYH1-4
17.2	Eyes	Crystallin beta A1	CRYBA1
17.3	Bones, skin, teeth, and joints	Collagen type 1, alpha 1	COL1A1
17.4	Digestion	Gastrin	GAST
17.5	Heart and lung	Angiotensin 1 converting enzyme	ACE
17.6	Metabolism	Glucagon receptor	GCGR
17.7	Muscle	Actin gamma	ACTG1
18.1	Pigmentation	Melanocortin 2 receptor	MC2R
18.2	Metabolism	Insulin-dependent diabetes 6	IDDM6
18.3	Digestion	Gastrin-releasing peptide	GRP
18.4	Brain and nerves	Myelin basic protein	MBP
19.1	Metabolism	Insulin receptor	INSR
19.2	Pigmentation	Hair color (1 brown)	HCL1
19.3	Brain and nerves	Myelin-associated glycoprotein	MAG
19.4	Digestion	Gastric inhibitory polypeptide receptor	GIPR
20.1	Liver and kidney	Arginine vasopressin	AVP
20.2	Pigmentation	Agouti signaling peptide	ASIP
20.3	Metabolism	Topoisomerase 1	TOP1
20.4	Bones, skin, teeth, and joints	Bone morphogenetic protein 7	BMP7
20.5	Bones, skin, teeth, and joints	Collagen, type IX, alpha 3	COL9A3
21.1	Bones, skin, teeth, and joints	Chondrolectin	CHODL
21.2	Eyes	Crystallin alpha A	CRYAA
22.1	Immunity	Immunoglobulin lambda constant	IGKC
22.2	Eyes	Crystallin beta A4	CRYBA4
22.3	Brain and nerves	Synaptogyrin 1	SYNGR1