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BMC Evolutionary Biology

BioMed Central

Open Access

Research article

Eurasian and African mitochondrial DNA influences in the Saudi
Arabian population
Khaled K Abu-Amero*1, Ana M González2, Jose M Larruga2,
Thomas M Bosley3 and Vicente M Cabrera2
Address: 1Mitochondrial Research Laboratory, Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia,
2Department of Genetics, Faculty of Biology, University of La Laguna, Tenerife, Canary Islands, Spain and 3Neurology Division, Cooper University
Hospital, Camden, NJ, USA
Email: Khaled K Abu-Amero* - kamero@kfshrc.edu.sa; Ana M González - Gonzalez@ull.es; Jose M Larruga - Larruga@ull.es;
Thomas M Bosley - tmbosley@cooper.com; Vicente M Cabrera - vcabrera@ull.es
* Corresponding author

Published: 1 March 2007
BMC Evolutionary Biology 2007, 7:32

doi:10.1186/1471-2148-7-32

Received: 25 September 2006
Accepted: 1 March 2007

This article is available from: http://www.biomedcentral.com/1471-2148/7/32
© 2007 Abu-Amero et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract
Background: Genetic studies of the Arabian Peninsula are scarce even though the region was the
center of ancient trade routes and empires and may have been the southern corridor for the
earliest human migration from Africa to Asia. A total of 120 mtDNA Saudi Arab lineages were
analyzed for HVSI/II sequences and for haplogroup confirmatory coding diagnostic positions. A
phylogeny of the most abundant haplogroup (preHV)1 (R0a) was constructed based on 13 whole
mtDNA genomes.
Results: The Saudi Arabian group showed greatest similarity to other Arabian Peninsula
populations (Bedouin from the Negev desert and Yemeni) and to Levantine populations. Nearly all
the main western Asia haplogroups were detected in the Saudi sample, including the rare U9 clade.
Saudi Arabs had only a minority sub-Saharan Africa component (7%), similar to the specific NorthAfrican contribution (5%). In addition, a small Indian influence (3%) was also detected.
Conclusion: The majority of the Saudi-Arab mitochondrial DNA lineages (85%) have a western
Asia provenance. Although the still large confidence intervals, the coalescence and phylogeography
of (preHV)1 haplogroup (accounting for 18 % of Saudi Arabian lineages) matches a Neolithic
expansion in Saudi Arabia.

Background
This study represents mtDNA data regarding the population of Saudi Arabia. Geographically, desert is the most
prominent feature of the Arabian Peninsula, which comprises the modern countries of Saudi Arabia, Yemen,
Oman, the United Arab Emirates, Qatar, Bahrain, and
Kuwait. Saudi Arabia occupies eighty percent of the Arabian Peninsula and is divided into five major regions –
Central, Northern, Southern, Eastern and Western. From

the western coastal region (At-Tihamah), the land rises
from sea level to a peninsula-long mountain range (jabal
al-Hijaz) beyond which are plateaus to the east. The
southwestern 'Asir region has mountains as high as 3,000
metres (9,840 ft) and is known for having the most hospitable climate in the country. The east is primarily rocky
or sandy lowland continuing to the shores of the Arabian
Gulf. Although vast arid tracts dominate, stretches of
coastline along the Arabian Gulf and the Red Sea and sevPage 1 of 15
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BMC Evolutionary Biology 2007, 7:32

eral major oases in the central and eastern regions have
provided water necessary for human habitation. The
coastal areas have been trading centers for centuries with
resultant population diversity. In addition, for 1400 years
the Haj has brought millions of Muslims annually to the
region between Mecca and Jeddah, some of whom have
stayed for generations. Traditionally, the central (arid)
region of the country has had more population stability.
More than 95% of the population now is settled in population centers that are mainly located along the eastern
and western coasts and near interior oases such as Hofuf,
Buraydah, and Riyadh.
The Arabian Peninsula is a region through which numerous migrations between Africa and Asia took place since
ancient times. Anthropological [1,2], archaeological [3],
and genetic [4,5] evidence has given support to the
hypothesis that modern humans may have dispersed out
of Africa, following a southern route through the Arabian
Peninsula before they pursued a Levantine route [6].
According to this scenario, the Arabian Peninsula may
have been the first step in the colonization of southern
and eastern Asia. Middle Palaeolithic artefacts discovered
in southwestern areas of the Arabian peninsula are similar
to ones recovered in Africa, providing support for the suggestion that the Red Sea coasts may have been important
in this southern expansion [7]. The presence of obsidian
lithics on the African and Arabian sides of the Red Sea
attests to Neolithic contacts as well. Archaeological evidence supports late Neolithic Levantine colonization of
the Arabian Peninsula with successive population expansions and contractions depending on climatic conditions
[8].
The strategic position of the Arabian Peninsula made it a
crucial area for trade, cultural exchange, and warfare after
the emergence of Old World Western civilizations. Mesopotamian states invaded the Arabian Peninsula from the
north since prehistoric times [9], Ionic and Roman-Byzantine classic cultures took control of strategic trade routes
in Arabia, and the Sassinid Persians dominated southern
Arabia around 575 AD. Influences from the African side
were also present as Pharanoiac Egypt and the Sudanese
Meroitic and Abyssinian Askumite kingdoms extended
their borders well inside Arabia [10]. Arabian Nabatean
and Sabean cultures exerted their influence in turn on the
Levant and Ethiopia, although to a lesser degree. Events
changed dramatically with the rise of Islam in Arabia during the 7th century AD. In a short span of time, Arabs built
a military and cultural empire that extended from Pakistan in the east to the Iberian Peninsula in the west. Even
more complete Arabization occurred later in North Africa
with the Bedouin Hilalian invasion in the 11th century
AD.

http://www.biomedcentral.com/1471-2148/7/32

The impact of these migrations on the Arab gene pool
remains unclear because genetic information about the
region has been scarce. Arab populations (Bedouin,
Saudi, and Yemenite) are distinct from other Near East
populations and from India and Central Asia in an analysis based on classical markers, suggesting the possibility of
an ancient expansion from East Africa [11]. Early studies
could not discriminate remote from recent contacts, but
non-recombining uniparental markers have allowed
more refined phylogeographic analysis at both continental [12,13] and regional [14,15] levels.
The rapid mutation rate of mitochondrial DNA (mtDNA)
and Y-chromosome microsatellites permits estimates of
lineage expansion age and of the most probable geographic origin of these expansions [16,17]. Only two studies regarding the Arabian Peninsula have been based on
mtDNA. Lineage classification of a small sample of 29
Bedouins [18] revealed that 25 (86%) had a Eurasian origin, two (7%) belonged to the sub-Saharan Africa L0 and
L2 haplogroups, and two were left undetermined. A study
of 115 Yemeni mtDNAs showed that Eurasian-specific
and African-specific lineages existed in almost equal proportion in that southern Arabian Peninsula sample [19].
In a sample of 120 Saudi Arabs, we sequenced the noncoding HVSI/II mtDNA regions and further characterized
haplogroup diagnostic coding region positions by restriction fragment length polymorphism (RFLP) or by partial
sequencing in order to estimate the genetic structure of the
Arabian Peninsula and to search for archaic N and/or M
lineages such as those found in India, Australia, and
Southern-east Asia that trace a rapid human expansion
outside Africa. The comparison of this sample to 2,204
classified sequences from the Near East and 728 from East
Africa allowed us to estimate the relative gene flow
between these areas and the Arabian Peninsula. We also
provide a detailed mtDNA phylogeny of haplogroup
(preHV)1, the most frequent and diverse haplogroup in
the Arabian Peninsula. The analysis of this haplogroup,
recently renamed R0a [20], is based on complete
sequences and a global phylogeographic analysis based
on 255 HVSI sequences.

Results
The total number of different haplotypes in our sample of
120 Saudi Arabs were 107 (K = 89%) when HVSI and II
variation and RFLP were taken into account [see Additional file 1]; however, the K value dropped to 64% when
only partial HVSI variation was used in comparison with
other populations (see Table 1). Some lineages had to be
included into imprecise groups such as H/HV/R for haplotype and haplogroup frequency comparison, although
all Saudi haplotypes were completely sorted into their
respective clades and sub-clades [see Additional file 1].

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BMC Evolutionary Biology 2007, 7:32

The bulk of individuals (86%) belonged to the Eurasian
macrohaplogroup N and its main R branch (75%), while
the Sub-Saharan Africa macrohaplogroup L (7%) and the
Asian macrohaplogroup M (7%) accounted for a smaller
proportion of haplotypes.
Sub-Saharan African macrohaplogroup L lineages
Five of the eight Saudi Arabian L lineages belonged to different L3 sub-clusters. Although L3d is a widespread African clade, the single Saudi representative (Individual 49;
[see Additional file 1]) had exact duplicates only in Yemen
and Ethiopia [19]. L3f was the most frequent L3 cluster in
Yemen and Ethiopia, and the sole Saudi L3f sequence
(457) matched an Ethiopian sequence [19]. Sequence 429
was peculiar because it belonged to the recently defined
East Africa haplogroup L3i [19] yet lacked the 16223 transition and included the 16318T transversion. The remaining two L3 sequences (221, 430) had L3h designation.
One of them (221) harboured 16192–16218 transitions
and presented the 16129-16223-16256A-16311-16362
HVSI motif that was first reported in West Africa [21]. The
other (430) belonged to the subset of L3h sequences
found in Ethiopia [19] and in Tanzania [22] that had the
combined 16179–16274 HVSI motif. This haplogroup
was present in moderate frequency in Ethiopians and
Yemenis [19] but no matches existed between them and
the Saudi population. The three remaining Saudi L haplotypes fell into the L2 macrohaplogroup. One of the
sequences (433) belonged to the western L2c clade and
had matches in West Africa Guineans [21] and in Mozambique [23]. The last two L2 Saudi sequences (225, 452)
fell into the widespread L2a cluster [24] and had matches
in East Africa and Yemen.

In general the sub-Saharan Africa maternal gene flow to
Saudi Arabia was moderate (7%) and fell into the range
found for other Arab populations in the Near East [25]. A
small portion of this sub-Saharan Africa genetic input
could be due to contacts with Yemeni communities from
southern Arabia, but the most characteristic Yemeni L6
clade [19] was not present in the Saudi sample.
Macrohaplogroup M
Five of the eight M Saudi Arab lineages clustered into the
M1 African haplogroup [26]. Three of them had the
16359 transition that was diagnostic of the M1a East African cluster, and the remaining one belonged to the rare
but widespread M1b1 cluster characterized in the HVSI
region by 16185 transition and the 16190d deletion that
had been identified in the northwest Africa, Jordan, and
the Iberian Peninsula [27]. The other three M sequences
belonged to Indian clades. One had the basic motif
(16126, 16223) of the M3 haplogroup [28]. A second had
the 15928 and 16304 transitions that defined haplogroup
M25 [29], although this sequence [see Additional file 1]

http://www.biomedcentral.com/1471-2148/7/32

did not match any of the definite or putative M25
sequences found in India [29-31] or Pakistan [26].
The last M sequence (16111A, 16223) has been found
with the central motif in Bhoksa from Uttar Pradesh [32]
and with the central motif and the 16129 transition in two
derivatives in Yerava from South India [33]. Because these
lineages were pooled as undetermined M*, we completely
sequenced our sample (Ar201) and compared it to 91
complete Indian M sequences [34-36] to know its phylogenetic position. Our Ar201 sequence shared only transition 3010 with the basal mutations that defined
haplogroup M34 [35] so that the most parsimonious tree
clustered it with this haplogroup (Figure 1). However, we
think that Ar201 may be representative of a new Indian
branch of macrohaplogroup M because 3010 is a highly
recurrent mutation that has independently appeared in
the tips (M40) and sub-cluster roots (D4) of other M haplogroups. The M contributions to the Saudi Arab gene
pool represented gene flow from East and North Africa
(4%) and India (3%) but not from Central Asia.
Macrohaplogroup N
All the main western Eurasian branches of N (R, N1a,
N1b, N1c, I, W, X) were present in Saudi Arabia, with the
least common ones (N1a, N1b, N1c, I, W, X) having an
infrequent presence in Saudi Arabs (Table 1). N1a was the
only one of these haplogroups that seemed to have a consistent presence across the Arabian Peninsula because it
was also moderately frequent (6.9%) and diverse (h =
0.89) in Yemeni [19]. N1a frequency dropped to 4% in
Saudi Arabs, where it harboured only two different haplotypes. The most abundant one, with the 16147A-1617216218-16223-16248-16261-16274-16355 HVSI motif
and the 41-73-199-204 HVSII motif, had not been
observed in the Near East or in East Africa, and the second
(16147G-16172-16223-16248-16355) was only shared
with Ethiopians.

Saudi Arabs had the main European and western Asian
haplogroups (H, J, T, K, U) included in R, the main branch
of N, albeit in different frequencies. Haplogroup H was
the most frequent cluster in European (45%) and Near
East (25%) populations [16] but only accounted for 13%
of Saudi lineages, comparable to the frequency in
Bedouin and Yemeni. H frequencies significantly diminished with latitude from Turkey to Yemen through the
Levant (r = 0.953; two-tail p < 0.01).
Haplogroups K (6%) and T (7%) had similar frequencies
in Saudi Arabs to those found in Europe and the Near East
[16]. However, the subgroup composition of haplogroup
U clearly differed from Europe in Saudi Arabia and in
other Near Eastern regions. The most prevalent haplogroup in Europe (U5) was represented in Saudi Arabs by

Page 3 of 15
(page number not for citation purposes)

Kur

Irn

Irq

Syr

Pal

Drz

Jor

Bed

Ara

Yem

Egy

Sud

Eth

Ken

494

212

712

116

119

118

45

145

29

120

214

126

159

344

99

Refs2

3,4,7,12,14,15,16

5,14,1516

6,13,14,15,16,20

1,16

18,19,20

18,20

16

20

16

20

9,16,18

10,17

10,20

9,18

2

CRS

0.14

0.11

0.08

0.07

0.06

0.07

0.02

0.10

-

0.03

0.03

0.06

0.01

-

-

H/HV/R

0.09

0.04

0.05

0.07

0.09

0.12

0.02

0.05

0.07

0.02

0.04

0.04

0.04

0.02

-

H/HV/R

0.13

0.09

0.07

0.16

0.11

0.12

0.07

0.16

-

0.08

0.03

0.05

-

-

-

V

0.01

-

0.01

-

0.03

-

-

-

-

-

-

0.01

0.02

-

-

H/HV

0.01

0.01

0.01

0.03

0.02

-

0.02

0.01

-

-

-

-

-

-

-

HV

0.01

-

0.03

0.04

0.01

-

-

0.01

-

-

0.01

-

-

-

-

HV1

0.02

0.02

0.01

-

0.02

0.01

0.09

0.02

-

-

0.01

-

0.01

0.03

-

HV2

-

-

0.02

0.01

-

-

-

0.01

-

-

0.01

-

-

-

-

HV/R

0.01

-

0.01

-

-

-

-

-

-

-

-

-

-

-

-

(preHV)1

0.01

-

0.01

0.04

0.03

0.03

0.04

0.03

0.14

0.18

0.09

0.02

0.04

0.10

0.01

R

-

0.01

0.01

-

-

-

-

-

-

-

-

-

-

-

-

R2

-

0.01

0.01

0.01

0.03

-

-

0.01

-

-

0.01

-

-

-

-

R5

-

-

0.01

0.01

-

-

-

-

-

-

-

-

-

-

-

B

-

0.01

0.01

0.01

-

-

-

-

0.03

-

-

-

-

-

-

F

-

-

-

-

-

0.01

-

-

-

-

-

-

-

-

-

0.03

-

0.04

0.04

0.05

0.03

0.04

0.02

-

0.06

0.03

0.03

0.01

0.01

0.01

J1

0.02

0.02

0.04

0.03

0.01

0.02

-

0.01

0.03

0.03

0.04

-

-

-

-

J1a

-

0.01

-

-

0.01

0.01

0.02

0.01

-

-

-

-

-

-

-

J1b

0.01

0.02

0.03

0.04

0.01

0.02

-

0.01

0.14

0.12

0.04

0.02

-

-

-

J1b1

0.01

-

-

-

-

-

-

-

-

-

-

-

-

-

-

J1d

0.02

0.03

0.02

0.02

0.01

0.03

-

-

0.03

0.02

0.01

0.02

0.01

0.01

-

T

0.04

0.08

0.04

0.03

0.04

0.04

-

0.01

-

0.01

-

0.02

0.01

0.01

-

T1

0.03

0.02

0.03

0.04

0.03

0.03

0.04

0.01

0.03

0.01

0.01

0.07

0.01

0.02

-

T2

-

-

0.01

0.01

0.03

0.02

-

0.03

-

-

-

0.02

-

0.01

-

T3

BMC Evolutionary Biology 2007, 7:32

J

0.01

0.01

0.01

-

0.01

0.02

-

0.02

-

0.03

-

0.02

-

0.01

-

T4

-

-

-

-

-

0.01

-

-

-

-

-

0.02

-

-

-

T5

-

-

-

-

0.01

0.01

-

-

0.03

0.02

-

0.01

-

-

-

U

0.02

-

-

0.02

-

-

-

0.01

-

-

0.01

-

-

-

-

U1

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

U1a

0.04

0.01

0.02

0.01

0.03

0.01

0.07

0.01

0.07

0.01

0.01

0.01

-

-

-

U1b

0.01

-

-

-

0.03

-

-

0.02

-

0.01

-

-

-

-

-

U2b

-

-

-

-

-

-

-

-

-

-

0.01

-

-

-

-

U2d

-

-

-

-

-

0.01

-

0.01

-

-

-

-

-

0.01

-

U2e

0.01

0.02

0.01

0.02

0.01

0.01

-

0.01

-

0.01

-

-

-

-

-

U3

0.05

0.03

0.03

0.06

0.07

0.01

-

0.16

0.03

0.03

0.01

0.02

0.01

0.01

-

U4

0.01

-

0.01

0.02

0.03

0.02

-

0.01

-

-

-

0.02

-

-

-

U5

-

-

-

-

-

-

-

-

-

-

-

0.01

-

-

U5a1

0.01

0.02

0.01

-

0.01

-

-

0.01

-

-

-

-

-

-

-

U5a1a

0.01

0.01

0.02

0.01

0.01

0.01

-

-

-

0.01

0.01

-

-

-

-

Page 4 of 15

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Table 1: Haplogroup and macrohaplogroup frequencies in the Near East and eastern-African populations1, gene diversity (H) with standard error (± s.e.) and percentage of number of
haplotypes per sample size (K)

0.01

-

-

-

-

-

-

-

-

-

-

0.01

-

-

U6a

-

-

-

0.01

-

0.01

-

-

-

0.01

-

-

-

-

-

U6a1

-

-

-

-

0.03

-

-

-

-

-

-

0.01

-

0.03

0.01

U6b

-

-

-

-

-

-

-

-

0.07

-

-

-

-

-

-

U7

0.01

0.06

0.07

0.03

0.03

0.03

-

-

-

-

-

0.01

-

-

-

U8b

0.01

0.01

0.01

-

-

-

-

0.01

-

0.01

-

-

-

-

-

U9

-

-

-

-

-

-

-

-

-

0.03

-

-

-

-

-

K

0.05

0.11

0.06

0.05

0.06

0.08

0.20

0.03

-

0.06

0.05

0.02

0.01

0.01

-

A

0.01

-

-

-

0.01

-

-

-

0.03

-

-

-

-

-

-

N2a

-

-

0.01

-

-

-

-

0.01

-

-

-

-

-

-

-

N9

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

Y1

-

-

-

-

-

-

-

-

-

-

-

0.01

-

-

-

N1a

-

-

-

-

-

-

-

-

-

N1b

0.01

0.01

0.02

0.02

0.02

0.01

0.02

0.01

N1c

-

0.01

-

-

-

0.02

0.02

-

W

0.02

0.04

0.02

-

0.03

0.02

-

0.01

-

X

0.03

0.01

0.02

0.02

0.01

0.04

0.27

0.01

0.03

I

0.01

0.01

0.01

-

-

-

0.02

0.02

-

N

-

-

0.01

-

-

-

-

0.01

-

I/M/L

0.01

0.02

0.02

-

-

-

-

-

N/L/M

0.03

-

0.02

-

-

0.02

-

0.01

-

-

0.04

0.04

0.02

-

0.02

0.03

0.03

-

0.05

-

-

-

-

0.02

-

-

-

-

-

0.01

-

0.01

0.01

0.01

0.01

0.02

0.02

0.02

0.01

0.01

-

0.01

-

0.02

-

0.01

-

-

-

-

-

-

-

-

-

-

0.02

-

0.01

-

0.03

-

0.01

0.02

0.08

0.01

0.03

-

-

0.01

0.01

-

-

-

-

-

0.02

0.02

0.02

-

-

-

M1

-

-

-

-

-

-

-

0.01

0.03

0.01

-

0.05

0.03

0.08

0.02

M1a

-

-

-

-

-

0.02

0.02

0.01

0.03

0.03

0.01

0.05

0.04

0.07

0.02

M3

-

-

0.01

-

-

-

-

-

0.03

0.01

0.02

-

-

-

-

Z

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

C

0.01

0.02

0.01

-

-

-

-

-

-

-

-

-

-

-

-

G

-

-

0.01

-

-

-

-

-

-

-

-

-

-

-

-

M/D

BMC Evolutionary Biology 2007, 7:32

M

0.02

-

0.01

-

-

-

-

-

-

-

-

0.02

0.01

-

-

D

0.01

-

-

-

-

-

-

-

-

-

-

-

-

-

-

L*

-

-

-

-

-

0.01

-

0.01

-

-

-

0.01

-

-

0.03

L3b

-

-

-

-

-

0.01

-

0.03

-

-

0.01

0.01

0.02

-

0.06

L3d

-

-

-

-

-

0.03

-

0.01

-

0.01

0.04

-

0.01

0.03

-

L3e1

-

-

-

-

-

0.01

-

-

-

-

-

0.01

-

-

0.05

L3e2

-

-

-

-

0.01

0.01

-

-

-

-

-

-

-

-

0.02

L3e3

-

-

-

-

-

0.02

-

-

-

-

0.02

-

-

-

0.03

L3e4

-

-

-

-

0.01

-

-

-

-

-

-

-

0.01

-

-

L3e5

-

-

-

-

-

-

-

-

-

-

0.01

-

-

-

-

L3f

-

-

-

-

0.01

-

-

-

-

0.01

-

-

0.04

0.02

0.05

L3f1

-

-

-

0.02

-

-

-

0.01

-

-

0.02

-

0.03

0.03

0.03

L3h

-

-

-

-

-

0.01

-

-

-

0.02

-

-

0.03

0.01

0.04

L3i

-

-

-

-

-

-

-

-

-

0.01

0.01

-

-

0.01

-

Page 5 of 15

U5b

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Table 1: Haplogroup and macrohaplogroup frequencies in the Near East and eastern-African populations1, gene diversity (H) with standard error (± s.e.) and percentage of number of
haplotypes per sample size (K) (Continued)

-

-

-

-

-

-

-

-

-

-

0.02

0.05

-

-

-

-

-

-

-

-

-

0.01

-

-

-

-

-

0.03

0.01

L3x1

-

-

-

-

-

-

-

-

-

-

-

-

-

0.03

0.01

L3x2

-

-

-

-

-

-

-

0.01

-

-

-

0.02

-

0.01

-

L4a

-

-

-

-

-

-

-

-

-

-

0.01

-

-

0.01

-

L4a1

-

-

-

-

-

-

-

-

-

-

-

-

0.01

0.04

0.02

L4g

-

-

-

-

0.01

0.01

-

-

-

-

-

0.01

0.03

0.03

0.14

L2a/L2c

-

-

-

-

-

-

-

0.01

-

-

0.01

0.02

0.08

0.01

0.03

L2a1

-

-

-

0.04

0.02

0.03

-

0.01

-

-

0.01

0.02

0.07

0.05

0.03

L2a1a

-

-

-

-

-

0.01

-

-

-

0.01

0.03

-

-

-

-

L2a1b3

-

-

-

-

-

0.01

-

-

0.03

-

-

0.01

0.01

0.03

0.02

L2a2

-

-

-

-

-

-

-

-

-

0.01

-

0.01

0.03

0.02

-

L2a3

-

-

-

-

-

-

-

-

-

-

-

-

0.04

-

-

L2b

-

-

-

-

-

-

-

-

-

-

-

0.01

0.01

0.02

-

L2c2

-

-

-

-

-

-

-

0.01

-

0.01

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

0.01

-

0.01

-

0.01

L6

-

-

-

-

-

-

-

-

-

-

0.07

-

-

0.01

-

L5a1

-

-

-

-

-

-

-

-

-

-

-

0.02

0.01

0.01

0.01

L5a2

-

-

-

-

-

-

-

-

-

-

-

0.02

0.03

0.01

0.01

L5b

-

-

-

-

-

-

-

-

-

-

-

-

-

0.01

-

L1b

-

-

-

-

-

-

-

-

-

-

-

0.01

0.01

-

0.01

L1b1

-

-

-

-

0.01

-

-

0.01

-

-

-

-

0.03

0.03

0.01

L1c

-

-

-

0.02

-

-

-

-

-

-

0.01

-

0.01

-

0.02

L1e

-

-

-

-

-

-

-

-

-

-

-

-

-

-

0.01

L0a

-

-

-

-

-

-

-

-

-

-

-

-

0.01

0.01

0.02

L0a1

-

-

-

-

0.01

0.01

-

0.01

0.03

-

0.02

0.05

0.09

0.04

0.05

L0a1a

-

-

-

-

-

-

-

0.01

-

-

-

0.01

0.01

-

0.03

L0a2

-

-

-

0.01

-

-

-

-

-

-

0.04

-

0.01

0.01

0.05

L0f

-

-

-

-

-

-

-

-

-

-

-

-

0.01

-

0.08

L0k

-

-

-

-

-

-

-

-

L

0.01

0.01

-

0.09

0.07

0.14

-

0.12

M

0.04

0.04

0.05

0.01

-

0.02

0.02

0.03

0.10

0.07

0.06

0.13

0.08

0.15

0.04

N

0.09

0.11

0.11

0.03

0.06

0.08

0.33

0.07

0.10

0.12

0.07

0.11

0.01

0.05

0.01
0.03

-

-

0.01

-

-

-

-

0.07

0.07

0.37

0.22

0.65

0.51

0.89

R

0.82

0.82

0.80

0.87

0.87

0.74

0.64

0.77

0.69

0.75

0.49

0.48

0.18

0.27

others

0.03

0.02

0.04

-

-

0.02

-

0.01

0.03

-

0.01

0.05

0.08

0.01

0.03

H

0.979

0.984

0.990

0.992

0.995

0.995

0.946

0.978

0.995

0.986

0.989

0.993

0.989

0.993

0.995

± s.e.

0.004

0.004

0.002

0.004

0.003

0.003

0.019

0.006

0.011

0.004

0.002

0.003

0.003

0.001

0.002

81

56

67

80

53

64

93

67

56

86

83

80

60

65

63

K (%)

1 Population abbreviations: Tuk Turkey, Kur Kurds, Irn Iran, Irq Iraq,
2 Data source references are detailed in [see Additional file ].

2

Syr Syria, Pal Palestine, Drz Druze, Jor Jordanian, Bed Bedouin, Ara Saudi Arabs, Yem Yemen, Egy Egypt, Sud Sudan, Eth Ethiopia, Ken Kenia.

Page 6 of 15

-

L3w

L2d

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L3i/N2a

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Table 1: Haplogroup and macrohaplogroup frequencies in the Near East and eastern-African populations1, gene diversity (H) with standard error (± s.e.) and percentage of number of
haplotypes per sample size (K) (Continued)

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representative lineages in Saudi Arabs except for U4, U7,
which were also absent from Bedouin of the Negev desert,
and Yemeni samples (Table 1).
The rare haplogroup U9 was present in our sample with a
frequency of 3% (Table 1). This haplogroup was first
defined by RFLP-6383 HaeIII and observed only in South
Pakistan [26]. It was later proven to be a sister branch of
haplogroup U4 [37] on the basis of two complete U9
sequences (one Ethiopian and one Pakistani), both of
which shared the 499–5999 motif. In addition to 6386,
transitions at 3531, 3834, and 14094 defined the basal
motif of U9. The Ethiopian sequence was considered representative of sub-cluster U9a and the Pakistani sequence
as representative of sub-cluster U9b. The three Saudi U9
sequences belonged to U9a because all of them shared the
HVSI 16051–16278 motif with the Ethiopian sequence
while none of them shared any HVSI or HVSII mutations
with the U9b Pakistani sequence ([see Additional file 1];
[37]). These three U9a sequences may be different occurrences of an old implantation of this haplogroup in the
Arabian Peninsula.
A feature that differentiated Near Eastern populations
from European and West Asian populations was the high
frequency of haplogroups J and (preHV)1 [16,38], and
this was also true for Saudi Arabia. J haplotypes represented 25% of the Saudi sample, and its main contributor
was the J1b cluster (12%). Saudi and Bedouin samples
showed an identical trend in this respect and were different from Yemenis, whose J1b frequency (4%) was similar
to other Near Eastern samples (Table 1). The J1b frequency in the Arabian Peninsula was significantly higher
than in the rest of the Near East, even when Yemenis were
included (p < 0.0001). However, J1b in Arabia displayed
a low level of haplotypic diversity in spite of its relative
abundance (h = 0.57). Unlike the derived J1b1 lineage,
J1b was scarce in North Africa [39] and practically absent
in Europe [39] except for Italy [40].

Figure 1
sequence
Phylogenetic position of the haplogroup M Arab 201
Phylogenetic position of the haplogroup M Arab 201
sequence. All mutation differences are listed with respect
to the revised Cambridge Reference Sequence (rCRS) [66].
This sequence has accession number DQ904234 in GenBank.

Haplogroup (preHV)1 was even more frequent than J1b
in Saudi Arabs (18%). The frequency of this sequence in
Saudi Arabs was not significantly different from that
observed in Yemeni Jews (20.4%) and Bedouins of the
Negev desert (14%), but it dropped to 3.4% in Yemenis
[19] (Table 1). Like J1b, the (preHV)1 frequency in the
Arabian Peninsula was significantly higher than in the rest
of the Near East (p < 0.001).

only one U5a1a derived lineage [see Additional file 1].
Likewise, the North-African U6 haplogroup [15] is represented by only one lineage (1%). Several minority European U sub-clades (U1, U2e, U3, U4, and U7) may have
had their origins in the Near East [16]. All of them had

Phylogeny of haplogroup (preHV)1 based on complete
mtDNA sequences
The relative abundance and diversity of (preHV)1 in the
Saudi sample permitted more detailed phylogenetic and
phylogeographical analyses of this haplogroup. The phylogenetic tree based on 13 complete mtDNA (preHV)1

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BMC Evolutionary Biology 2007, 7:32

sequences (Figure 2) confirmed that the basic motif of this
group harboured the 2442, 3847, 13188, 16126 and
16362 transitions [41]. In addition, the transition at 64
was a basic diagnostic mutation for this haplogroup.
Three main branches sprouted from this trunk. (preHV)1a
was characterized by a transition at 827, while (preHV)1b
was defined by the 57i-2355-15674 motif. The 15674
transition was already documented as a defining mutation
of a group of (preHV)1 sequences comprising one Druze,
one Eritrean, four Ethiopian Jews, and two Yemeni Jews
[42]. (preHV)1c was a potential third branch that can be
diagnosed by the 9531 transition because this mutation
was shared by the EU258 sequence (Figure 2) and a partial
sequence from a Moroccan Jew [42]. The Saudi Arab
sequences 20, 448, and 505 (Figure 2) constitute a
(preHV)1a1 sub-branch within (preHV)1a, defined by
transitions 8292, 11761 and 16355. We excluded 58 and
146 as diagnostic positions because 146 was a highly
mutable site and because the 58 change was recurrent
within (preHV)1 (Figure 2). A (preHV)1b1 sub-cluster
was defined by sequences IP969 and Ert41 that shared the
8701 transition. We estimated a radiation age of 18,959 ±
8,478 years for the entire (preHV)1 haplogroup. The
(preHV)1a branch, with an age of 9,248 ± 7,604 years, is
somewhat younger than the (preHV)1b branch (13,205 ±
7,193).
Phylogeography of haplogroup (preHV)1
Figure 3 shows the reduced median network obtained
from 255 (preHV)1 haplotypes found in a global search
comprising nearly 40,000 HVSI sequences. The basic central motif (16126–16362) was the most abundant and
widespread, being present in all of northern Africa and in
Eurasia from India to the Iberian Peninsula. However,
Saudi Arabs were represented by only a single haplotype.
The next most abundant clade, defined by 16355 and
encompassing the majority of (preHV)1a1 sequences
(Figure 2), was overwhelmingly composed of Near East
and North African haplotypes with some European outsiders. Saudi Arabs again occupied more peripheral than
central positions. The third most abundant clade was
characterized by the 16304 transition and probably constituted a sub-cluster of the (preHV)1b branch represented in the genomic tree by the Ar439 sequence (Figure
2). The Arabian Peninsula was the major contributor to
this clade.

In addition, several minority clusters provided valuable
information. For instance, the one defined by 16309 was
formed exclusively by East African sequences. The one
identified by 16126 loss or by 16301 was centrally composed of Pakistani and Iranian sequences and had a derivative Yemeni sequence which pointed to some maternal
gene flow to Yemen from those areas. The same could be
said of the 16172 branch, although the gene flow was

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from Ethiopia to Saudi Arabia in this case. Ethiopia
seemed to have been a secondary center of (preHV)1
expansions to the Near East, Arabian Peninsula, and
northwest Africa, as could be deduced from branches
defined by 16114 and the motif 16168–16266. Given the
peripheral position of Saudi haplotypes, Saudi Arabia
seemed to have acted more as receiver than a focus of
(preHV)1 expansions with the exception of the 16304
clade. Radiation ages for the whole (preHV)1 haplogroup
based on HVSI sequences were 18,993 ± 6,999 years;
9,624 ± 2,994 years for the 16355 ((preHV)1a1) subclade, and more recent for the 16304 subclade.
Population comparisons
We first performed AMOVA using haplogroup and haplotypic frequencies in order to assess the degree of homogeneity within and between the different geographic areas.
As customary, the bulk of the variation was found within
populations (99.32% for haplotypes and 97.71% for haplogroups). Variance distribution for haplogroups was
greater among groups than among populations (1.34%
vs. 0.95%), while variance distribution for haplotypes was
less among groups than among populations (0.24% vs.
0.44%). Differences were highly significant in all cases (p
< 0.001).

Pair-wise FST distances based on haplotype frequencies
[see Additional file 3] showed that comparatively high
heterogeneity within areas was due to the Druze sample
that was significantly different from all the other populations, mainly because of a high frequency of haplotypes
(27%) belonging to the minority haplogroup X and to K
(20%). The Druze sample was a clear outlier in a graphic
representation based on FST distances (Figure 4a), separating from the remaining populations along the first dimension. Founder effects or sample bias were the most likely
causes of this deviation, as only two X1 and X2 haplotypes
[43] accounted for the X percentage. In addition, Druze
had the lowest diversity indices of all studied populations
(Table 1). The second dimension of this haplotype analysis included the Arabian samples with those of east Africa,
while Egyptians were aligned in the cluster of Near East
populations.
A somewhat different picture appeared after PC analysis
based on haplogroup frequencies (Figure 4b). In this
graph, the Druze were not outliers, most probably due to
the fact that its variation is not correlated with that in
other populations and therefore not reflected by the two
first components. The first component separated all the
Near East populations from a cluster including Egyptians
and other east African groups. The majority of L haplogroups, pulling positively, and haplogroup H, pulling
negatively, were predominantly responsible for this split.
The second component divided the Near East cluster into

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Figure 2
Haplogroup (preHV)1 phylogeny based on thirteen complete or nearly complete sequences
Haplogroup (preHV)1 phylogeny based on thirteen complete or nearly complete sequences. The Iberian Peninsula (IP969) and the seven Saudi Arab (Ar) sequences are from this study. Five additional sequences were taken from the literature as detailed in Methods. Numbers along links refer to nucleotide positions with i indicating insertions, d indicating
deletions, underlining indicating recurrent mutations in the (preHV)1 haplogroup. From the star all individuals present the following mutations with respect to rCRS: 263, 750, 1438, 2706, 4769, 7028, 8860, 14766, 15326. All mutation differences are
detailed with respect to the revised Cambridge Reference sequence (rCRS) [66]. Our eight sequences were given GenBank
accession numbers [GenBank: DQ904235], [GenBank: DQ904236], [GenBank: DQ904237], [GenBank: DQ904238], [GenBank: DQ904239], [GenBank: DQ904240], [GenBank: DQ904241] and [GenBank: DQ904242] for sequences # Ar20, Ar440,
Ar505, Ar439, Ar448, Ar194, Ar222 and IP969 respectively.

three groups. The first comprised northeastern populations characterized by higher frequencies of H haplogroups and absence of L haplogroups. The second
combined the Levantine population with Egypt, and the
three Arabian Peninsula samples were left in a third
group. The major determinants of the Arabian Peninsula
singularity were the comparatively high frequency of
(preHV)1, J1b, T5 and M3 haplogroups and the population specificity for other haplogroups such as L4, L6, U9
or U6b. This result was similar to that obtained using classical markers [11]. Saudi and Bedouin samples were relatively homogenous; however, the Arabian Peninsula as a
whole was not homogenous because Yemenis were differentiated by a greater African component.

Discussion
MtDNA genetic analysis of this Saudi Arabian group
revealed almost exclusively contributions from Africa and
the Near East. All Saudi L, M and N lineages were derived
from clades with roots in Africa and west and south Asia.
The L4, L5, and L6 haplogroups recently found in Ethiopia and/or Yemen [19] were not detected in the Saudi
population. Half of the sub-Saharan African Saudi lineages had exact matches in Ethiopians and/or Yemeni,
pointing to these areas as the most likely source. The other
half belonged to haplogroups with an East Africa origin or
that reached the Red Sea in their eastern radiation [19,24].
The Arab slave trade and the expansion of empires from
the Sudan and Ethiopia [25] could explain this moderate

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Figure 3
Reduced median network relating (preHV)1 HVSI sequences
Reduced median network relating (preHV)1 HVSI sequences. The central motif (star) differs from rCRS at positions
16126 and 16362 in HVI control region. Numbers along links refer to nucleotide positions minus 16000. Positions not used in
diversity estimations are in italics. The broken lines are less probable links and/or recurrent mutations. Size of boxes is proportional to the number of individuals included. Codes are: ARA, Arab; BAL, Balkanian; BED, Bedouin; CAS, Caspian; CAU, Caucasus; DRZ, Druze; EGY, Egyptian; ETH, Ethiopian; EUR, European; IND, Indian; IP, Iberian Peninsula; IRK, Iraki; IRN, Iranian;
JBA, Baltic Jew; JET, Ethiopian Jew; JEU, European Jew; JIP, Iberian Jew; JIR, Iraki Jew; JOR, Jordanian; JRN, Iranian Jew; JYE,
Yemeni Jew; KEN, Kenian; KUR, Kurd; MAU, Mauritanian; MBE, Moroccan Berber; MOR, Moroccan; NUB, Nubian; PAK, Pakistani; PAL, Palestinian; SAH, Saharan; SEN, Senegalese; SOM, Somalian; SYR, Syrian; TUK, Turkish; TUN, Tunisian; and YEM,
Yemeni.

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Figure 4
Graphical relationships among the studied populations
Graphical relationships among the studied populations. Codes are as in Table 1. (A) MDS plot based on FST haplotypic
distances. Stress value is 0.086. Dimension 1 axe has been shortened to include the Druze sample. (B) PC analysis based on
haplogroup frequencies. The two components represent 37% of the total variance.

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sub-Saharan Africa maternal contribution to the present
Saudi Arabian gene pool.
The majority of M1 lineages in Saudi Arabia belonged to
the eastern Africa M1a sub-clade that is particularly frequent and diverse in Ethiopia [19,44]. Ethiopia was again
the most likely source. However, the sole M1b1 Saudi
sequence probably reached the Arabian Peninsula from
northwest Africa through the Levantine corridor because
this sequence has been reported repeatedly in west Africa,
the Iberian Peninsula, and Jordan [27], but not yet in Ethiopia. Based on Y-chromosome studies, this northern
route was proposed as an important path for bidirectional
human migration between north Africa and the Levant
[45,46]. The remaining M lineages detected in Saudi Arabs
had a clear Indian provenance. The basic Saudi M3 lineage
out of India was shared by Yemenis and Iranians. Relatively recent contacts between India and the Arabian
Peninsula by continental routes through Iran or by Indian
Ocean maritime routes could be responsible of this
Indian gene flow.
The overwhelming majority of N lineages present in Saudi
Arabia had a clear western Asia provenance. Giving priority to geographically closest neighbors, 47% of the N lineages in Saudi Arabs were shared with other Arabian
Peninsula neighbors (Bedouin from the Negev and Yemeni), 31% with Levantine populations, 16% with the Anatolian-Caucasus region, and only 6% with eastern Africa.
These data revealed only a modest backflow of Eurasian
lineages from Africa to the Arabian Peninsula. The close
affinity found among Arabian Peninsula populations was
due mainly to sharing Eurasian haplotypes and to similar
Eurasian haplogroup frequencies and not to the sub-Saharan African contribution that is prominent in the Yemeni
population.
The high frequency of (preHV)1 in Saudi Arabians was
not significantly different from that found in Bedouin
[18] and in Yemeni Jews (20%). However, this (preHV)1
frequency is significantly different of the non-Jewish Yemeni population [19] and may reflect strong genetic drift in
the founding population of Yemeni Jews. The frequencies
of L (10%) and J (26%) lineages deduced from published
sequences of Yemeni Jews [47] were also similar to
Bedouin from Negev desert and Saudi frequencies. In general, Jewish communities have evidenced strong maternal
founder effects [47,48]. However, they usually harbor
chromosome Y and mtDNA lineages that permit their
most probable origin to be traced to the Near East because
they share the most common haplotypes with those populations [47-50].
The majority of western Asia lineages found in the Arabian Peninsula had original Paleolithic and Neolithic

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expansions in the Near East [16] or in Caucasian and Caspian regions [26,51]. Most probably, these expansions
reached the Arabian Peninsula as secondary waves when
climatic conditions there or cultural improvements such
as herding allowed colonization. The Arabian Peninsula
has had a relatively low population density, and substantial demographic backflow to the Near East is improbable.
However, as for M1, minor N North-African influences
have been detected by the presence of an U6 lineage in our
Saudi sample. It has been suggested that the rare U9 clade
might be another interesting exception because it has
been detected only in Pakistan [26], Ethiopia, and Yemen
[19], and now in our Saudi sample. U9 occurs frequently
only among the Makrani population in Pakistan, which is
characterized by a large component of sub-Saharan African lineages, suggesting that U9 lineages in Pakistan
might also have an African origin [19]. Makrani sub-Saharan Africa lineages have exact matches in Africa, which is
compatible with a recent conection as the result of the
East African slave trade [26]. However, the entire
sequenced Ethiopian and Pakistani U9 lineages [37] are
separated by a mean of 4.5 coding mutations from the
common root, placing the split at Paleolithic times. Most
probably, Ethiopia received its U9 lineages from the Arabian Peninsula that, in turn, received them from northern
areas. The southern geographic distribution of U9 contrasts with the west-northern distribution U4, of its sister
clade [52], but this is a pattern shared with other Paleolithic U radiations such as U2, U7 [32], or U8 [53] that
have eastern and western branches. An original area west
to India and east to the Capsian sea would be an equidistant point to conciliate these early U radiations [54].
It is difficult to differentiate successive gene flows or
expansions at a population level because the most recent
migration could carry both early and derivative lineages.
However, the refined phylogenetic and phylogeographic
analysis carried out for haplogroup (preHV)1 allows some
inferences regarding Arabian Peninsula population history. The coalescence age for the entire (preHV)1 haplogroup was estimated at around 19,000 years ago, which is
coincident with the beginning of the last ice age recession.
However, in light of the peripheral distribution of the Arabian lineages in the phylogenetic tree (Figure 3), Arabian
Peninsula populations most likely did not actively participate in this Paleolithic expansion. The subsequent radiation of the (preHV)1a1 clade occurred around 10,000
years ago, a date that marks the transition from Mesolithic
to Neolithic in the Near East. The ancestral core of this
cluster was defined mainly by Near Eastern lineages with
important Arabian and Ethiopian participation. Finally, a
third detectable expansion involving lineages carrying the
16304 transition seemed to be largely restricted to the Arabian Peninsula. Its coalescence age, most probably placed
it in a period of empires flourishing in northern Arabia

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and on both shores of the Red Sea. The lack of archaic N
and/or M autochthonous lineages in the Arabian Peninsula do not offer support for the proposed southern route
of Homo sapiens sapiens outside Africa. Nevertheless, these
ancient lineages may become apparent in larger samples.

Conclusion
The majority of Saudi-Arab mitochondrial DNA lineages
(85%) have a western Asia provenance. All of the main
western Asia haplogroups were detected in the Saudi sample, including the rare U9 clade. The African contribution
totalled 12%, with the sub-Saharan Africa (7%) contribution, represented by L macrohaplogroup, being only
slightly higher than the M1 and U6 specific North-African
contribution (5%). A small Indian influence (3%) was
also detected; however, no archaic N and/or M autochthonous lineages in the Arabian Peninsula were found.
Although the still large confidence intervals, the coalescence and phylogeography of (preHV)1 haplogroup
(accounting for 18 % of Saudi Arabian lineages) matches
a Neolithic expansion in Saudi Arabia.

Methods
Study population
Buccal swabs or peripheral blood were obtained from 120
maternally unrelated Saudi Arabs, all whose known ancestors were of Saudi Arabian origin. All five major regions
were represented, although the central region was the best
represented [see Additional file 1]. Sequence analysis was
performed of mtDNA regulatory region hypervariable segment I (HVSI) and hypervariable segment II (HVSII) and
of haplogroup diagnostic mutations using RFLPs or partial sequencing when individual haplogroup assignment
remained ambiguous. Positions analyzed for each individual are detailed in [see Additional file 1]. For population and phylogeographic comparison, we used 2,204
published or unpublished partial sequences from the
Near East and 728 from East Africa, as detailed in Table 1
and [see Additional file 2]. In addition, complete mtDNA
sequences were obtained from nine subjects, eight
belonging to haplogroup (preHV)1 and one to macrohaplogroup M. Informed consent was obtained from all individuals.
MtDNA sequencing
Total DNA was isolated from buccal and blood samples
using the PURGENE DNA isolation kit from Gentra Systems (Minneapolis, USA). HVSI and HVSII segments were
PCR amplified using primer pairs L15996/H16401 and
L16340/H408, respectively, as previously described [54].
Complete mtDNA genomes and segments including diagnostic positions were amplified using a set of 24 separate
PCRs and single-set cycling conditions as detailed elsewhere [55]. Successfully amplified products were
sequenced for both complementary strands using the

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DYEnamic™ ET dye terminator kit (Amersham Biosciences), and samples were run on MegaBACE 1000
(Amersham Biosciences) according to the manufacturer
protocol.
Haplotype classification
Classification into sub-haplogroups was performed as
described previously for African [19,24] and for Eurasian
[29, 40, 56] sequences. Published sequences used for
comparative genetic analysis were re-classified into subclades using the same criteria in order to permit comparison.
Genetic analysis
Haplotypic diversity was calculated as h [57] and as K
(haplotype number/sample size quotient). Only HVSI
positions from 16069 to 16365 were used for genetic
comparisons of partial sequences with other published
data. Genetic variation was apportioned within and
among geographic areas using AMOVA by means of
ARLEQUIN2 [58]. Four regions were considered: Arabian
Peninsula (including Bedouin, Yemeni, and Saudi Arabian samples), Eastern Africa (including samples from
Egypt, Sudan, Ethiopia, and Kenya), Levant (containing
samples from Jordan, Palestine, Druze, Syria, and Iraq)
and Anatolia-Zagros (comprising samples from Turkey,
Iran, and Kurds). Pairwise FST distances between populations were calculated from haplogroup and haplotype frequencies, and their significance assessed by a
nonparametric permutation test (ARLEQUIN2). Principal
component (PC) and multidimensional scaling (MDS)
plots were obtained with SPSS version 13.0 (SPSS Inc.,
Chicago, Illinois). Phylogenetic relationships among partial and complete mtDNA sequences were established
using the reduced median network algorithm [59]. In
addition to our nine complete sequences, five published
complete or nearly complete sequences were used to
establish (preHV)1 phylogeny: one European (EU258)
[13]; one Pakistani (Pak1) [60]; one Indian (In180) [41],
one Bedouin (Bd38) [61], and one Eritrean (Ert41) [61].
A previously compiled database of published and unpublished Eurasian and African sequences [53] was augmented with additional sequences [26,29] and used for
(preHV)1 phylogeography.
Time estimates
Only substitutions in the coding region were taken into
account for complete sequences, excluding insertions and
deletions. The mean number of substitutions per site
compared to the most common ancestor (ρ) of each clade
was calculated [62] and converted into time using a substitution rates of 1.26 × 10-8 [63]. For HVSI, the age of clusters or expansions was calculated as the mean divergence
(ρ) from inferred ancestral sequence types [62] and converted into time by assuming that one transition within

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np 16090–16365 corresponds to 20,180 years [64]. The
standard deviation of the ρ estimator was calculated as
previously described [65}.

7.

Authors' contributions

8.

KKA was in charge of carrying out the sequences, collecting samples, haplogrouping, and writing part of the manuscript. AMG, JML and VMC were in charge of
haplogrouping, designing the experiments, and writing
the manuscript. TMB was in charge of writing the manuscript and commenting on historic matters related to this
region. All authors read and approved the final manuscript.

6.

9.
10.

11.

Additional material
12.

Additional File 1
Haplotypes of 120 Saudi Arabs
Click here for file
[http://www.biomedcentral.com/content/supplementary/14712148-7-32-S1.xls]

13.

14.

Additional File 2
Refernces used in Haplogroup frequencies comparisons
Click here for file
[http://www.biomedcentral.com/content/supplementary/14712148-7-32-S2.doc]

Additional File 3
Matrix of Fst haplotypic distances
Click here for file
[http://www.biomedcentral.com/content/supplementary/14712148-7-32-S3.xls]

15.

16.
17.

Acknowledgements
The authors would like to thank Mr. Mazen Osman for his help in recruiting
individuals for this study. This research was supported by grants from the
Resaerch Center at King Fasisal Specilaist hospital awrded to KKA and
Spain Ministry of Education and Science (BFU2006-04490/BMC) to JML.

References
1.

2.
3.

4.
5.

Clark JD, Beyene Y, WoldeGabriel G, Hart WK, Renne PR, Gilbert
H, Defleur A, Suwa G, Katoh S, Ludwig KR, Boisserie JR, Asfaw B,
White TD: Stratigraphic, chronological and behavioural contexts of Pleistocene Homo sapiens from Middle Awash, Ethiopia. Nature 2003, 423(6941):747-752.
White TD, Asfaw B, DeGusta D, Gilbert H, Richards GD, Suwa G,
Howell FC: Pleistocene Homo sapiens from Middle Awash,
Ethiopia. Nature 2003, 423(6941):742-747.
Walter RC, Buffler RT, Bruggemann JH, Guillaume MM, Berhe SM,
Negassi B, Libsekal Y, Cheng H, Edwards RL, von Cosel R, Neraudeau
D, Gagnon M: Early human occupation of the Red Sea coast of
Eritrea during the last interglacial.
Nature 2000,
405(6782):65-69.
Stringer C: Palaeoanthropology. Coasting out of Africa. Nature
2000, 405(6782):24-5, 27.
Petraglia M: The Middle Palaeolithic of Arabia: implications for
modern human origin, behaviour and dispersals. Antiquity
2003, 77:671-684.

18.
19.

20.

21.
22.

23.

24.

McCorriston J: Early settlement in Hadramawt: preliminary
report on prehistoric occupation at Shi'b Munayder. Arab
Arch EPIG 2000, 11:129-153.
Redman CL: The rise of civilization. From early farmers to
urban society in the ancient Near East. San Francisco , WH
Freeman and Company; 1978.
Newman JL: The peopling of Africa: A geographic interpretation. New Haven and London , Yale University Press; 1995.
Cavalli-Sforza LL, Menozzi P, Piazza A: The history and geography
of human genes. Princeton, NJ , Princeton University Press; 1994.
Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman
E, Bonne-Tamir B, Bertranpetit J, Francalacci P, Ibrahim M, Jenkins T,
Kidd JR, Mehdi SQ, Seielstad MT, Wells RS, Piazza A, Davis RW, Feldman MW, Cavalli-Sforza LL, Oefner PJ: Y chromosome sequence
variation and the history of human populations. Nat Genet
2000, 26(3):358-361.
Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, Anderson C,
Ghosh SS, Olefsky JM, Beal MF, Davis RE, Howell N: Reducedmedian-network analysis of complete mitochondrial DNA
coding-region sequences for the major African, Asian, and
European haplogroups. Am J Hum Genet 2002, 70(5):1152-1171.
Cinnioglu C, King R, Kivisild T, Kalfoglu E, Atasoy S, Cavalleri GL, Lillie
AS, Roseman CC, Lin AA, Prince K, Oefner PJ, Shen P, Semino O,
Cavalli-Sforza LL, Underhill PA: Excavating Y-chromosome haplotype strata in Anatolia. Hum Genet 2004, 114(2):127-148.
Maca-Meyer N, Gonzalez AM, Pestano J, Flores C, Larruga JM,
Cabrera VM: Mitochondrial DNA transit between West Asia
and North Africa inferred from U6 phylogeography. BMC
Genet 2003, 4:15.
Richards M, Macaulay V, Hickey E, Vega E, Sykes B, Guida V, Rengo C,
Sellitto D, Cruciani F, Kivisild T, Villems R, Thomas M, Rychkov S,
Rychkov O, Rychkov Y, Golge M, Dimitrov D, Hill E, Bradley D,
Romano V, Cali F, Vona G, Demaine A, Papiha S, Triantaphyllidis C,
Stefanescu G, Hatina J, Belledi M, Di Rienzo A, Novelletto A, Oppenheim A, Norby S, Al-Zaheri N, Santachiara-Benerecetti S, Scozari R,
Torroni A, Bandelt HJ: Tracing European founder lineages in
the Near Eastern mtDNA pool. Am J Hum Genet 2000,
67(5):1251-1276.
Underhill PA, Passarino G, Lin AA, Shen P, Mirazon Lahr M, Foley RA,
Oefner PJ, Cavalli-Sforza LL: The phylogeography of Y chromosome binary haplotypes and the origins of modern human
populations. Ann Hum Genet 2001, 65(Pt 1):43-62.
Di Rienzo A, Wilson AC: Branching pattern in the evolutionary
tree for human mitochondrial DNA. Proc Natl Acad Sci U S A
1991, 88(5):1597-1601.
Kivisild T, Reidla M, Metspalu E, Rosa A, Brehm A, Pennarun E, Parik
J, Geberhiwot T, Usanga E, Villems R: Ethiopian mitochondrial
DNA heritage: tracking gene flow across and around the
gate of tears. Am J Hum Genet 2004, 75(5):752-770.
Rosa A, Brehm A, Kivisild T, Metspalu E, Villems R: MtDNA profile
of West Africa Guineans: towards a better understanding of
the Senegambia region. Ann Hum Genet 2004, 68(Pt 4):340-352.
Knight A, Underhill PA, Mortensen HM, Zhivotovsky LA, Lin AA,
Henn BM, Louis D, Ruhlen M, Mountain JL: African Y chromosome
and mtDNA divergence provides insight into the history of
click languages. Curr Biol 2003, 13(6):464-473.
Pereira L, Macaulay V, Torroni A, Scozzari R, Prata MJ, Amorim A:
Prehistoric and historic traces in the mtDNA of Mozambique: insights into the Bantu expansions and the slave trade.
Ann Hum Genet 2001, 65(Pt 5):439-458.
Salas A, Richards M, De la Fe T, Lareu MV, Sobrino B, Sanchez-Diz P,
Macaulay V, Carracedo A: The making of the African mtDNA
landscape. Am J Hum Genet 2002, 71(5):1082-1111.
Richards M, Rengo C, Cruciani F, Gratrix F, Wilson JF, Scozzari R,
Macaulay V, Torroni A: Extensive female-mediated gene flow
from sub-Saharan Africa into near eastern Arab populations.
Am J Hum Genet 2003, 72(4):1058-1064.
Quintana-Murci L, Chaix R, Wells RS, Behar DM, Sayar H, Scozzari R,
Rengo C, Al-Zahery N, Semino O, Santachiara-Benerecetti AS, Coppa
A, Ayub Q, Mohyuddin A, Tyler-Smith C, Qasim Mehdi S, Torroni A,
McElreavey K: Where west meets east: the complex mtDNA
landscape of the southwest and Central Asian corridor. Am J
Hum Genet 2004, 74(5):827-845.
Larruga JM, Gonzalez AM, Abu-Amero K, Shi Y, Pestano J, Cabrera
VM: Mitochondrial linegae M1 traces an early human backflow to Africa. Genome Research (Submitted) 2006.

Page 14 of 15
(page number not for citation purposes)

BMC Evolutionary Biology 2007, 7:32

25.

26.

27.

28.

29.

30.

31.

32.

33.

34.

35.

36.

37.

38.

39.

Bamshad M, Kivisild T, Watkins WS, Dixon ME, Ricker CE, Rao BB,
Naidu JM, Prasad BV, Reddy PG, Rasanayagam A, Papiha SS, Villems R,
Redd AJ, Hammer MF, Nguyen SV, Carroll ML, Batzer MA, Jorde LB:
Genetic evidence on the origins of Indian caste populations.
Genome Res 2001, 11(6):994-1004.
Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, Kaldma K,
Serk P, Karmin M, Behar DM, Gilbert MT, Endicott P, Mastana S,
Papiha SS, Skorecki K, Torroni A, Villems R: Most of the extant
mtDNA boundaries in south and southwest Asia were likely
shaped during the initial settlement of Eurasia by anatomically modern humans. BMC Genet 2004, 5:26.
Barnabas S, Shouche Y, Suresh CG: High-resolution mtDNA
studies of the Indian population: implications for palaeolithic
settlement of the Indian subcontinent. Ann Hum Genet 2006,
70(Pt 1):42-58.
Sharma S, Saha A, Rai E, Bhat A, Bamezai R: Human mtDNA
hypervariable regions, HVR I and II, hint at deep common
maternal founder and subsequent maternal gene flow in
Indian population groups. J Hum Genet 2005, 50(10):497-506.
Kivisild T, Kaldma K, Metspalu M, Parik J, Papiha S, Villems R: The
place of the Indian mitochondrial DNA variants in the global
network of maternal lineages and the peopling of the old
world. In Genomic Diversity Edited by: Deka R, Papiha S. New York ,
Kluwer Academic Plenum Publishers; 1999:135-152.
Cordaux R, Saha N, Bentley GR, Aunger R, Sirajuddin SM, Stoneking
M: Mitochondrial DNA analysis reveals diverse histories of
tribal populations from India.
Eur J Hum Genet 2003,
11(3):253-264.
Rajkumar R, Banerjee J, Gunturi HB, Trivedi R, Kashyap VK: Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages. BMC Evol
Biol 2005, 5(1):26.
Sun C, Kong QP, Palanichamy MG, Agrawal S, Bandelt HJ, Yao YG,
Khan F, Zhu CL, Chaudhuri TK, Zhang YP: The dazzling array of
basal branches in the mtDNA macrohaplogroup M from
India as inferred from complete genomes. Mol Biol Evol 2006,
23(3):683-690.
Thangaraj K, Chanbey G, Singh VK, Vanniarajan A, Thanseem I, Reddy
AG, Singh L: In situ origin of deep rooting lineages on Indian
mitochondrial macrohaplogroup M in India. BMC Genomics
2006, 7:151.
Palanichamy MG, Sun C, Agrawal S, Bandelt HJ, Kong QP, Khan F,
Wang CY, Chaudhuri TK, Palla V, Zhang YP: Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South
Asia. Am J Hum Genet 2004, 75(6):966-978.
Reidla M, Kivisild T, Metspalu E, Kaldma K, Tambets K, Tolk HV, Parik
J, Loogvali EL, Derenko M, Malyarchuk B, Bermisheva M, Zhadanov S,
Pennarun E, Gubina M, Golubenko M, Damba L, Fedorova S, Gusar V,
Grechanina E, Mikerezi I, Moisan JP, Chaventre A, Khusnutdinova E,
Osipova L, Stepanov V, Voevoda M, Achilli A, Rengo C, Rickards O,
De Stefano GF, Papiha S, Beckman L, Janicijevic B, Rudan P, Anagnou
N, Michalodimitrakis E, Koziel S, Usanga E, Geberhiwot T, Herrnstadt
C, Howell N, Torroni A, Villems R: Origin and diffusion of
mtDNA haplogroup X. Am J Hum Genet 2003, 73(5):1178-1190.
Quintana-Murci L, Semino O, Bandelt HJ, Passarino G, McElreavey K,
Santachiara-Benerecetti AS: Genetic evidence of an early exit of
Homo sapiens sapiens from Africa through eastern Africa.
Nat Genet 1999, 23(4):437-441.
Cruciani F, La Fratta R, Santolamazza P, Sellitto D, Pascone R, Moral
P, Watson E, Guida V, Colomb EB, Zaharova B, Lavinha J, Vona G,
Aman R, Cali F, Akar N, Richards M, Torroni A, Novelletto A, Scozzari R: Phylogeographic analysis of haplogroup E3b (E-M215)
y chromosomes reveals multiple migratory events within
and out of Africa. Am J Hum Genet 2004, 74(5):1014-1022.
Luis JR, Rowold DJ, Regueiro M, Caeiro B, Cinnioglu C, Roseman C,
Underhill PA, Cavalli-Sforza LL, Herrera RJ: The Levant versus the
Horn of Africa: evidence for bidirectional corridors of
human migrations. Am J Hum Genet 2004, 74(3):532-544.
Thomas MG, Weale ME, Jones AL, Richards M, Smith A, Redhead N,
Torroni A, Scozzari R, Gratrix F, Tarekegn A, Wilson JF, Capelli C,
Bradman N, Goldstein DB: Founding mothers of Jewish communities: geographically separated Jewish groups were independently founded by very few female ancestors. Am J Hum
Genet 2002, 70(6):1411-1420.

http://www.biomedcentral.com/1471-2148/7/32

40.

41.

42.

43.

44.
45.

46.

47.
48.
49.
50.

51.
52.

53.

54.
55.

Hammer MF, Redd AJ, Wood ET, Bonner MR, Jarjanazi H, Karafet T,
Santachiara-Benerecetti S, Oppenheim A, Jobling MA, Jenkins T,
Ostrer H, Bonne-Tamir B: Jewish and Middle Eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes. Proc Natl Acad Sci U S A 2000, 97(12):6769-6774.
Nebel A, Filon D, Brinkmann B, Majumder PP, Faerman M, Oppenheim A: The Y chromosome pool of Jews as part of the
genetic landscape of the Middle East. Am J Hum Genet 2001,
69(5):1095-1112.
Behar DM, Metspalu E, Kivisild T, Achilli A, Hadid Y, Tzur S, Pereira
L, Amorim A, Quintana-Murci L, Majamaa K, Herrnstadt C, Howell N,
Balanovsky O, Kutuev I, Pshenichnov A, Gurwitz D, Bonne-Tamir B,
Torroni A, Villems R, Skorecki K: The matrilineal ancestry of
Ashkenazi Jewry: portrait of a recent founder event. Am J
Hum Genet 2006, 78(3):487-497.
Tambets K, Kivisild T, Metspalu E, Parik J, Kaldma K, Laos S, Tolk HV,
Golge M, Demirtas H, Geberhiwot T: The topology of the maternal lineages of the Antolian and trans-caucasus populations
and the peopling of Europe: Some prelininary considerations. In Archaeogenetics: DNA and the population prehistory of Europe. Edited by: Renfrew C, Boyle K. Cambridge, UK. ,
McDonald Institute for Archaeological Resaerch, University of Cambridge; 2000:219-235.
Maca-Meyer N, Gonzalez AM, Larruga JM, Flores C, Cabrera VM:
Major genomic mitochondrial lineages delineate early
human expansions. BMC Genet 2001, 2:13.
Rieder MJ, Taylor SL, Tobe VO, Nickerson DA: Automating the
identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial
genome. Nucleic Acids Res 1998, 26(4):967-973.
Macaulay V, Richards M, Hickey L, Vega E, Cruciani F, Guida V, Scozzari R, Bonne-Tamir B, Sykes B, Torroni A: The emerging tree of
west Eurasian mtDNAs: a synthesis of control-region
sequences and RFLPs. Am J Hum Genet 1999, 64:232-249.
Nei M: Molecular evolutionary genetics. New York , Columbia
University Press; 1987.
Schneider S, Roessli D, Excoffier L: Arlequin: A software for population genetics data analysis. 2.0th edition. Geneva , Genetics
and Biometry Laboratory, University of Geneva, Switzerland; 2000.
Bandelt HJ, Forster P, Rohl A: Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 1999, 16(1):37-48.
Achilli A, Rengo C, Battaglia V, Pala M, Olivieri A, Fornarino S, Magri
C, Scozzari R, Babudri N, Santachiara-Benerecetti AS, Bandelt HJ,
Semino O, Torroni A: Saami and Berbers--an unexpected mitochondrial DNA link. Am J Hum Genet 2005, 76(5):883-886.
Gonzalez AM, Garcia O, Larruga JM, Cabrera VM: The mitochondrial lineage U8a reveals a Paleolithic settlement in the
Basque country. BMC Genomics 2006, 7:124.
Morral N, Bertranpetit J, Estivill X, Nunes V, Casals T, Gimenez J, Reis
A, Varon-Mateeva R, Macek M Jr., Kalaydjieva L, et al.: The origin of
the major cystic fibrosis mutation (delta F508) in European
populations. Nat Genet 1994, 7(2):169-175.
Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, Hosseini S,
Brandon M, Easley K, Chen E, Brown MD, Sukernik RI, Olckers A,
Wallace DC: Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci U S A 2003, 100(1):171-176.
Forster P, Harding R, Torroni A, Bandelt HJ: Origin and evolution
of Native American mtDNA variation: a reappraisal. Am J
Hum Genet 1996, 59(4):935-945.
Saillard J, Forster P, Lynnerup N, Bandelt HJ, Norby S: mtDNA variation among Greenland Eskimos: the edge of the Beringian
expansion. Am J Hum Genet 2000, 67(3):718-726.

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(page number not for citation purposes)

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