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Population history of the Red SeaЧgenetic exchanges between the Arabian Peninsula and East Africa signaled in the mitochondrial DNA HV1 haplogroup.

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Population History of the Red Sea—Genetic Exchanges
Between the Arabian Peninsula and East Africa Signaled
in the Mitochondrial DNA HV1 Haplogroup
Eliška Musilová,1 Verónica Fernandes,2,3 Nuno M. Silva,2 Pedro Soares,2 Farida Alshamali,4
Nourdin Harich,5 Lotfi Cherni,6,7 Amel Ben Ammar El Gaaied,6 Ali Al-Meeri,8
Luı́sa Pereira,2,9 and Viktor Černý10*
Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, UK
Dubai Police GHQ, General Department of Forensic Sciences & Criminology, Dubai, United Arab Emirates
Laboratoire d’Anthropogénétique, Départment de Biologie, Université Chouaı̈b Doukkali, El Jadida, Morocco
Faculty of Sciences of Tunis, Laboratory of Genetics Immunology and Human Pathology, Tunis, Tunisia
Higher Institute of Biotechnology of Monastir, Tunisia
Department of Clinical Biochemistry, Faculty of Medicine and Health Sciences, University of Sana’a, Sana’a, Yemen
Faculdade de Medicina da Universidade do Porto, Portugal
Archaeogenetics Laboratory, Institute of Archaeology, Prague, Academy of Sciences of the Czech Republic,
Czech Republic
mtDNA genomes; HV1 haplogroup; Arabian Peninsula; East Africa
Archaeological studies have revealed cultural connections between the two sides of the Red Sea
dating to prehistory. The issue has still not been properly addressed, however, by archaeogenetics. We focus
our attention here on the mitochondrial haplogroup HV1
that is present in both the Arabian Peninsula and East
Africa. The internal variation of 38 complete mitochondrial DNA sequences (20 of them presented here for the
first time) affiliated into this haplogroup testify to its
emergence during the late glacial maximum, most probably in the Near East, with subsequent dispersion via
population expansions when climatic conditions
improved. Detailed phylogeography of HV1 sequences
shows that more recent demographic upheavals likely
contributed to their spread from West Arabia to East
Africa, a finding concordant with archaeological records
suggesting intensive maritime trade in the Red Sea from
the sixth millennium BC onwards. Closer genetic
exchanges are apparent between the Horn of Africa and
Yemen, while Egyptian HV1 haplotypes seem to be more
similar to the Near Eastern ones. Am J Phys Anthropol
145:592–598, 2011. V 2011 Wiley-Liss, Inc.
The recent advances in sequencing technology enable
us to get a much better picture of human population history than before. This is being achieved in part through
the highly resolved phylogenetic inferences based on
complete mitochondrial DNA (mtDNA) genomes. In fact,
the association of these detailed phylogenies with a molecular clock allows us to focus on a specific time-frame
of human evolution occurring in a particular geographic
context and to disentangle information for diverse migrations which followed the same pathways.
One important geographic route that has become a
focus of interest in recent years is the one linking East
Africa with the Arabian Peninsula through the Bab elMandeb strait. Some genetic studies inferred that this
route has played a main role not only in the first successful out-of-Africa migration of modern humans some
50–70 thousand years ago (KYA) (Macaulay et al., 2005;
Thangaraj et al., 2005) but also in more recent occurrences such as the back to Africa migrations from Arabia
revealed in the analysis of the Yemeni maternal gene
pool (Černý et al., 2011) and in human movements
resulting from the Arab slave trade from the seventh
century onwards, further contributing to the spread of L
haplogroups into Arabia (Richards et al., 2003; Kivisild
et al., 2004; Harich et al., 2010).
Archaeology has demonstrated several important periods of common history between East Africa and the Arabian Peninsula. There are two archaeological sites in the
C 2011
Additional Supporting Information may be found in the online
version of this article.
Grant sponsors: Ministry of Education of the Czech Republic,
Grant number: KONTAKT ME 917; the Council of American Overseas Research Centers; the American Institute for Yemeni Studies;
the Portuguese Fundação para a Ciência e a Tecnologia (project PTDC/ANT/66275/2006; post-doc grant - SFRH/BPD/64233/2009;
PhD grant - SFRH/BD/61342/2009); IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and
Higher Education, and is partially supported by FCT; the Portuguese Foundation for Science and Technology.
*Correspondence to: Viktor Černý, Archaeogenetics Laboratory,
Institute of Archaeology, Academy of Sciences of the Czech Republic,
Prague 11801, Czech Republic. E-mail:
Received 24 November 2010; accepted 7 February 2011
DOI 10.1002/ajpa.21522
Published online 9 June 2011 in Wiley Online Library
Yemeni highlands attesting to an Early Holocene ‘‘PreNeolithic’’ settlement throughout the eastern Yemen Plateau and a single continuum from Pre-Neolithic to Neolithic, with features of the Pre-Neolithic industry displaying hints of similarities with East Africa rather than
the Fertile Crescent (Fedele, 2009). Another study
(McCorriston and Martin, 2009) focused on the Early
Holocene pastoralists along the desert margins of southern Arabia and found evidence for cattle introduction
from the Levant or possibly from northeastern Africa by
the sixth millennium BC, if not earlier. Moreover, many
important trade links connected the two Red Sea coasts,
including the obsidian trade network between the Horn
of Africa and Arabia, which arose as early as the seventh
to fourth millennia BC and continued up to the first millennium BC (Zarins, 1989). In the mid-first millennium
BC, a south Arabian commercial network was established under the control of the so-called caravan kingdoms, especially that of Saba (Breton, 1999). At this
time, a group of Semitic-speaking peoples—immigrants
from Southern Arabia—arrived to Eritrea and Ethiopia
to expand their commercial activities (Munro-Hay, 1991).
It has been suggested that these trading colonists, who
maintained their contact with their country of origin for
centuries, brought not only a sea-based trading network
but also a Semitic cultural tradition into the Cushitic
substrate (Newman, 1995).
Archaeogenetics has started revealing the importance
of the period encompassing the end of the Pleistocene
and Early Holocene, when major population expansions
occurred in South Arabia, leaving evidence in the form
of the internal diversification of mtDNA haplogroup R0a
(Černý et al., 2011). Considering the paleoclimatic data
(Rose and Petraglia, 2009), the post-late glacial maximum (LGM) expansion around 16 KYA seemed to be
especially important within southeast parts of Yemen
(such as Al Mahra and Hadramawt) known as the South
Arabian refugium. This climatically favorable period,
coinciding roughly with the Bölling-Allerød interstadial,
was only interrupted with the onset of the Younger
Dryas 13.5 KYA, but was re-established in the Early
Holocene when monsoon precipitation increased again
some 9 KYA. Present climatic conditions started to develop from about 5 KYA onward (Parker, 2009). An
example of the later demographic expansion was the development of R0a1a1a and R0a2f1 lineages especially in
Soqotra Island, between 6 and 3 KYA (Černý et al.,
2011), chronologically matching the earliest evidence for
seafaring activity in the area (Boivin et al., 2009). Naturally, some of the R0a branches emerging in the Arabian
Peninsula spread to East Africa as well.
Together with R0a, HV1 lineages attain a frequency of
15.7% in Yemen (Černý et al., 2008), 18.4% in Saudi Arabia (Abu-Amero et al., 2008), 4.9% in Sudan (unpublished), 11.2% in Ethiopia (Kivisild et al., 2004), and
unpublished), and 9.5% in Somalia (unpublished). There
is not much information about the HV1 haplogroup,
which is defined by a transversion (A to T) at position
hypervariable region I
inverse distance weighted
thousand years ago
maximum likelihood
mitochondrial DNA
polymerase chain reaction
time of the most recent common ancestor
8,014 and two substitutions at positions 15,218 and
16,067 (van Oven and Kayser, 2009), except that it
appeared contemporaneously with its sister clade R0a,
around 20 KYA in the Near East. In this work, we focus
on HV1 lineages found in Arabia, Eastern, and Northern
Africa, and perform complete sequencing of 20 HV1 haplotypes to add new information to what is known on the
population history of both sides of the Red Sea.
Complete mtDNA sequencing
A total of 20 HV1 haplotypes were selected for complete mtDNA sequencing from available datasets of
hypervariable region I (HVRI) sequences (Černý et al.,
2008; Cherni et al., 2009; Harich et al., 2010; and
articles under preparation), previously defined as HV1
for displaying a transition at control region position
16,067; the sample represents 12 haplotypes from
Yemen, one from Sudan, one from Ethiopia, three from
Somalia, two from Tunisia, and one from Morocco.
Whole genome sequencing was conducted under conditions already published (Maca-Meyer et al., 2001; Pereira et al., 2007). Polymerase chain reaction (PCR)
products were purified and sequenced using the forward
primers only. However, in cases of the poly-C stretch
between positions 568–573 and 16,184–16,193, the
reverse primers were used as well. Sequencing was performed on an ABI 3100 DNA Analyzer (Applied Biosystems, Foster City, CA). Chromatograms were evaluated
by two independent observers with the help of SeqScape
(Applied Biosystems) and BioEdit version (Hall,
1999). In cases of ambiguous results, new PCR amplification and sequencing reactions were performed. The complete mtDNA sequences are deposited in GenBank database with accession numbers JF260932–JF260951.
Phylogenetic analyses
A preliminary reduced-median network analysis (Bandelt et al., 1995) led to a suggested branching structure
for the tree of complete sequences, which was then
checked and constructed by hand. All variable positions
were used except 16182C, 16183C, and 16519, as they
are inconsistently reported in the literature and are too
recurrent. We also used 18 previously published whole
HV1 genome sequences [AY738942 and AY738943
(Achilli et al., 2004), EF556168, EF556182, and
EF556190 (Behar et al., 2008), FJ460547 (Costa et al.,
2009), EF660935 and EF660936 (Gasparre et al., 2007),
EU935461 (Kujanová et al., 2009), FJ210914, EF421157,
HM998901, HQ165756, and HQ326986 from Family Tree
DNA. In calculating the q statistic (mean divergence
from inferred ancestral haplotype) for the time of the
most recent common ancestor (TMRCA) of specific clades
in the phylogeny, the complete sequence mutation rate
estimates used were one substitution in every 3,624
years corrected for purifying selection, and one substitution in every 7,884 years for synonymous substitution
(Soares et al., 2009), by using the calculator provided in
that article. Standard errors were calculated as in Saillard et al. (Saillard et al., 2000). We obtained maximum
likelihood (ML) estimates of branch lengths using PAML
3.13 (Yang, 1997), assuming the HKY85 mutation model
with c-distributed rates (approximated by a discrete distribution with 32 categories). We converted mutational
American Journal of Physical Anthropology
Fig. 1. Interpolation map for HV1 haplogroup.
distance in ML into time using the complete mitochondrial genome clock (Soares et al., 2009).
We also constructed a reduced-median network, with a
reducing threshold of two, for HVRI diversity of HV1
haplotypes described in the literature (references presented in Supporting Information 1). The fastest sites
[16,093, 16,129, 16,189, 16,311, and 16,362 (Soares et al.,
2009)] were down-weighted to 5 from an overall value of
10 for all the remaining sites. Age estimates using the q
statistic were obtained using the mutation rate of 1 substitution every 16,667 years for the HVRI region
between positions 16,051 and 16,400 (Soares et al.,
Interpolation map
To determine and visualize the geographical distribution of HV1, an interpolation map was drawn using the
‘‘spatial analyst extension’’ of ArcView version 3.2
( The ‘‘inverse distance
weighted’’ (IDW) option with a power of two was used
for the interpolation of the surface. IDW assumes that
each input point has a local influence that decreases
with distance. The geographic location used is the center
of the distribution area from where individual samples
of each population were collected.
The geographic distribution of HV1 frequencies was
plotted across the Arabian Peninsula, East Africa, and
neighboring regions (see Fig. 1). Very high frequencies of
HV1 are found around the Near East (including northeast Africa as well), where this haplogroup probably originated (see also the geographic location of the ancestral
American Journal of Physical Anthropology
haplotype in Fig. 3). The highest HV1 frequency was
detected in Somalia, where, however no ancestral haplotypes were found.
The HV1 phylogeny drawn based on information from
38 complete mtDNA sequences (see Fig. 2) shows an
early split, with two Yemeni sequences missing the substitution (a medium recurrent mutation) at position
15,218 (Pereira et al., 2009; Soares et al., 2009).
Although we have considered, based on the geography,
the possibility that 15,218 might have back-mutated, the
argument is not really strong enough to lead us not to
present a parsimonious reconstruction. In either case,
these sequences represent an extra HV1 branch—HV1
proper is thus split into two main branches each defined
by a single coding region transition: a transition at position 8277 defining HV1a, and position 12,696 enclosing
HV1b lineages. Three other rarer lineages derive from
the root of HV1. An extra main branch of HV1 could be
considered if we assume that 15,218 reverted in the
above-mentioned branch. Group HV1a is further split
into three sub-haplogroups—the previously defined
HV1a1 (with transition at positions 150, 15,927, and
16,355), HV1a2 (transition at 4,596), and the newly designated HV1a3 (transition at 3,421 and transversion C
to A at 16,327). The three Yemeni sequences described in
this work belonging to sub-haplogroup HV1a1 present
the common 9bp deletion (Cann and Wilson, 1983),
sometimes defined between positions 8,281–8,289 (Kong
et al., 2006) but here more parsimoniously defined
between positions 8,272–8,280, since it is missing the
haplogroup defining position 8,277. The HV1b group has
a main branch—sub-haplogroup HV1b1—bearing transitions at positions 2,626, 4,739, 7,598, and 16,274. The
sub-haplogroup HV1b2 presents substitutions at positions 152, 3,547, 6,023, and 16,189.
From the complete mtDNA tree (see Fig. 2), HV1a3
and HV1b1 seem to be restricted to Yemen and East
Africa. It is noteworthy that although the first branch
split of the HV1 haplogroup does not show diversity in
HVRI, most of its internal branches can be differentiated
according to the variants in this region (except most of
HV1a2). This allowed us to search in the HVRI datasets,
which have a much larger number of samples, for
sequences with substitution at positions 16,067 (HV1)
and 16,355 (HV1a1) or 16,327A (HV1a3), 16,192 (a subbranch of HV1a2), 16,274 (HV1b1), 16,189 (HV1b2),
16,234 (a sub-branch of HV1b), 16,172 (HV1c), and
16,242 (a sub-branch of HV1). We must take into account
that some of these are fast-evolving sites and that they
could be defining false monophyletic clades. A total of
187 HV1 sequences with known geographical origin
were collected. The haplotypes are displayed in the network in Figure 3. In fact, sub-haplogroup HV1a3 has
been observed only in Africa (in one Egyptian and one
Ethiopian sample) and in Arabia (one Saudi and four
Yemeni); sub-haplogroup HV1b1 was also mainly found
in Africa (10 Somali, two Nubian, one Egyptian, and one
Ethiopian) and Arabia (12 Yemeni Jewish, seven Yemeni,
and one Bedouin), with a few instances in other places
(one Caucasus and one Near Eastern). Sub-haplogroup
HV1a1 is geographically widespread (five Caucasus, one
Egyptian, one European, 43 Caucasus Jewish, four Near
Eastern, and three Yemeni). Curiously, the HV1 root
haplotype with substitution at position 16,067 was not
observed in the Arabian Peninsula except in four Yemeni
Jews, but was observed in 11 Caucasus, four Egyptian,
one European, two Maghreb, and six Near Eastern
Fig. 2. Phylogeny of the complete HV1 mtDNA sequences. Integers represent transition, only when a suffix ‘‘A,’’ ‘‘G,’’ ‘‘C,’’ or ‘‘T’’
is appended, then it indicates a transversion. Deletions are indicated by a ‘‘del’’ following the deleted nucleotide position. Integers
in bold indicate synonymous substitutions. Dates indicated are based on diversity for the complete molecule, only synonymous polymorphisms (in bold) and ML estimates (underlined). ‘‘rCRS’’—revised Cambridge Reference Sequence; the insertion at 3151C was
left out.
samples, thus supporting a possible origin in the Near
East. Haplotype 16,067–16,362, possibly defining a preHV1 haplogroup, has so far been observed in Dubai
(one), Ethiopia (four), Maghreb (one), and Yemen (three).
The complete sequencing allowed the application of
the mutation rate estimate with a correction for purifying selection, as well as a clock based only on synonymous mutations, both recently published (Soares et al.,
2009). The TMRCA estimate for HV1 was 22,350
(14,737–30,227) years when taking into consideration
the sequences without the polymorphism at 15,218—a
figure which closely matches the estimate of 18,695
(13,094–24,449) years when not considering those two
sequences. The control region age estimate of HV1 also
presents a similar age, dating to 19,430 (6,840–32,023)
years. Age estimates of HV1 daughter sub-haplogroups
are only slightly lower—15,178 (8,893–21,671) years
for HV1a and 17,682 (10,320–25,316) years for HV1b.
The common Arabian Peninsula and East African
sub-haplogroups HV1a3 and HV1b1 share a close age of
6,549 (2,456–10,746) years and 10,268 (4,792–15,918)
years, respectively. Sub-haplogroups HV1a1 and HV1a2,
American Journal of Physical Anthropology
Fig. 3. Network for HVRI diversity in several regional populations.
which despite being rare seem to have a wider geographical distribution, have TMRCA of 10,268 (3,602–17,194)
years and 9,518 (3,963–15,255) years, respectively. The
ratio of the dates based on the q statistic for the synonymous clock relative to the complete sequence was 1.24,
closely overlapping in most branches except for HV1a1
which has a very broad age estimate based only on synonymous diversity [23,616 (4,917–42,315) years]. When
testing ML estimates for the complete molecule, better
concordance (0.96) was obtained with the ratio between
ML and the q statistic.
The mtDNA gene pool of the West Arabian Peninsula
displays signs of population expansions in lineages
which have most probably been introduced here from
the Near East. This is the pattern observed for HV1,
which, together with R0a, constitute a considerable proportion of R and even N haplogroups observed in this
geographic region [respectively, 63% and 22% in Saudi
Arabia (Abu-Amero et al., 2008); and 76% and 25% in
Yemen (Černý et al., 2008)]. HV1 presents an age overlapping the LGM period [22,350 (14,737–30,227) years],
coincident with the age obtained for R0a haplogroup
[22,588 (20,886–24,290) years; Černý et al., 2011]. Y
chromosome diversity also reveals that the Arabian Peninsula mainly received its lineages from the Near East
from the LGM onwards (Abu-Amero et al., 2009). It has
been shown that Y chromosome population structure
across the Peninsula was modulated by geography, along
a west-east axis (Abu-Amero et al., 2009; Alshamali
et al., 2009).
Local population expansions in the post-LGM and
early Holocene seem to have occurred in the Near East
American Journal of Physical Anthropology
(Roostalu et al., 2007) and the Arabian Peninsula (Černý
et al., 2011). The HV1 tree also shows branching in starlike sub-haplogroups matching these periods, such as in
HV1a [15,178 years (8,893–21,671)] and HV1b [17,682
years (10,320–25,316)]. These dates overlap the dates for
the main R0a branches (Černý et al., 2011): 11,489 years
(9,503–13,475) for R0a1a; 15,608 years (13,742–17,474)
for R0a2; and 12,455 years (5,801–19,109) for R0a3.
HV1 can be interpreted as a haplogroup whose geographic spread was facilitated by migration activity
across the Red Sea as part of the post-LGM expansions
occurring in the West of the Arabian Peninsula. Most
probably some lineages of HV1 such as HV1a3 and
HV1b1 passed from South Arabia to East Africa during
the periods of intense commercial network activity that
might have started, as is suggested by the archaeological
evidence (Boivin et al., 2009), already in the sixth millennium BC. The fact that the East African lineages are
not derivative of the Arabian ones, but diverge from the
root of the sub-haplogroups, seems to indicate that the
migration toward Africa happened soon after the emergence of the sub-haplogroups rather than recently. This
pattern is similar to the one displayed by some R0a
branches such as R0a2b [10,063 (5,467–14,659) years]
and R0a2g [6,094 (1,558–10,630) years], published earlier (Černý et al., 2011). Intense maritime activity led
not only to the expansion of lineages from the Arabian
Peninsula to East Africa but also to the settlement of
Soqotra Island in the Arabian Sea (Černý et al., 2009;
Černý et al., 2011). Interestingly, the flow of migrations
from East Africa to the Arabian Peninsula seem to have
been more recent, occurring mainly during the Arab-conducted slave trade initiated only in the seventh century
AD (Richards et al., 2003; Kivisild et al., 2004). Curiously, Kivisild et al. (2004) detected a high proportion
(12%) of the sub-Saharan L6 sequences in their Yemeni
sample, suggesting that these sequences could be
explained by an earlier gene flow across the Red Sea;
this observation was not reproduced, however, in other
and larger Yemeni sample sets (Černý et al., 2008; Černý
et al., 2009).
It appears that Egypt received some N lineages directly
from the Near East after the LGM, as is testified to by the
higher match of Egyptian HV1 lineages with widespread
haplotypes found in this study, as well as by genetic evidence collected earlier (Rowold et al., 2007). The close connection of HV1 between Egypt and the Near East, together with the geographical distribution of other haplogroups such as J, T, R0a, U6, H1, H3, or V show that
North Africa can be genetically divided into an eastern
and a western part. Although the first was influenced by
Near Eastern population expansions in the end of the
Pleistocene and in the Holocene, the western part seems
to show mainly post-LGM population expansions of the
by-that-time autochthonous lineage U6 (Pereira et al.,
2010a) and of European lineages such as H1, H3, and V
that probably stemmed from the Iberian refugium (Cherni
et al., 2009; Ennafaa et al., 2009; Pereira et al., 2010b).
The question of how far the Near Eastern influence in
North Africa extends remains. According to some genetic
data, the imaginary line could be detected somewhere
between Libya and Algeria (Dupanloup et al., 2000).
Unfortunately, Libyan mtDNA sequences are still not currently available to address these issues. Notwithstanding,
the distribution of HV1 haplogroup in Arabian and African populations would very well fit these expectations.
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exchanger, population, haplogroup, signalen, dna, red, history, east, arabian, hv1, africa, peninsular, seaчgenetic, mitochondria
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