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High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews

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High-resolution Y chromosome haplotype analysis was performed in 143 paternally unrelated Israeli and Palestinian Moslem Arabs (I&P Arabs) by screening for 11 binary polymorphisms and six microsatellite loci. Two frequent haplotypes were found among the 83 detected: the modal haplotype of the I&P Arabs (approximately 14%) was spread throughout the region, while its one-step microsatellite neighbor, the modal haplotype of the Galilee sample (approximately 8%), was mainly restricted to the north. Geographic substructuring within the Arabs was observed in the highlands of Samaria and Judea. Y chromosome variation in the I&P Arabs was compared to that of Ashkenazi and Sephardic Jews, and to that of North Welsh individuals. At the haplogroup level, defined by the binary polymorphisms only, the Y chromosome distribution in Arabs and Jews was similar but not identical. At the haplotype level, determined by both binary and microsatellite markers, a more detailed pattern was observed. Single-step microsatellite networks of Arab and Jewish haplotypes revealed a common pool for a large portion of Y chromosomes, suggesting a relatively recent common ancestry. The two modal haplotypes in the I&P Arabs were closely related to the most frequent haplotype of Jews (the Cohen modal haplotype). However, the I&P Arab clade that includes the two Arab modal haplotypes (and makes up 32% of Arab chromosomes) is found at only very low frequency among Jews, reflecting divergence and/or admixture from other populations.
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Abstract
High-resolution Y chromosome haplotype anal-
ysis was performed in 143 paternally unrelated Israeli and
Palestinian Moslem Arabs (I&P Arabs) by screening for
11 binary polymorphisms and six microsatellite loci. Two
frequent haplotypes were found among the 83 detected:
the modal haplotype of the I&P Arabs (~14%) was spread
throughout the region, while its one-step microsatellite
neighbor, the modal haplotype of the Galilee sample
(~8%), was mainly restricted to the north. Geographic
substructuring within the Arabs was observed in the high-
lands of Samaria and Judea. Y chromosome variation in
the I&P Arabs was compared to that of Ashkenazi and
Sephardic Jews, and to that of North Welsh individuals.
At the haplogroup level, defined by the binary polymor-
phisms only, the Y chromosome distribution in Arabs and
Jews was similar but not identical. At the haplotype level,
determined by both binary and microsatellite markers, a
more detailed pattern was observed. Single-step micro-
satellite networks of Arab and Jewish haplotypes revealed
a common pool for a large portion of Y chromosomes,
suggesting a relatively recent common ancestry. The two
modal haplotypes in the I&P Arabs were closely related to
the most frequent haplotype of Jews (the Cohen modal
haplotype). However, the I&P Arab clade that includes
the two Arab modal haplotypes (and makes up 32% of
Arab chromosomes) is found at only very low frequency
among Jews, reflecting divergence and/or admixture from
other populations.
Introduction
The analysis of variable loci in the non-recombining part
of the Y chromosome, which contains a record of many
past mutational events, facilitates the tracing of paternal
lineages. Over the last few years, an increasing number of
informative Y chromosome polymorphisms, which can be
typed following PCR, have become available (Jobling and
Tyler-Smith 1995; Underhill et al. 1997; Hammer and Ze-
gura 1997). Furthermore, extensive data have been assem-
bled on the geographic distribution of different Y-specific
markers among various contemporary populations (de
Knijff et al. 1997; Karafet et al. 1997; Kayser et al. 1997;
Skorecki et al. 1997; Hammer et al. 1997, 1998). Com-
pound Y chromosome haplotypes comprising both binary
and microsatellite polymorphisms have proved to be espe-
cially powerful tools for the investigation of population
substructure (Thomas et al. 1998) and, possibly, of rela-
tionships between groups that have become obscured
through considerable admixture (Thomas et al. 2000).
Some high frequency modal haplotypes (signature haplo-
types) may be representative of particular communities,
for instance, the Cohen modal haplotype (CMH) appears
to be associated with the paternally inherited Jewish
priesthood (Thomas et al. 1998). Binary markers repre-
sent rare, in most cases probably unique, event polymor-
phisms in human evolution and, thus, allow identification
of deep splits in the Y chromosome genealogy (Jobling
and Tyler-Smith 1995). In contrast, microsatellite loci
have a much faster mutation rate (Kayser et al. 2000) and
Almut Nebel · Dvora Filon · Deborah A. Weiss ·
Michael Weale · Marina Faerman · Ariella Oppenheim ·
Mark G. Thomas
High-resolution Y chromosome haplotypes
of Israeli and Palestinian Arabs reveal geographic substructure
and substantial overlap with haplotypes of Jews
Hum Genet (2000) 107:630–641
DOI 10.1007/s004390000426
Received: 12 July 2000 / Accepted: 10 October 2000 / Published online: 21 November 2000
ORIGINAL INVESTIGATION
URLs for computer programs in this article are as follows:
Arlequin, http://anthropologie.unige.ch/arlequin;
BATWING, http://www.maths.abdn.ac.uk/~ijw;
Microsat, http://lotka.stanford.edu/microsat.html;
PHYLIP, http://evolution.genetics.washington.edu/phylip.html;
TreeView, http://taxonomy.zoology.gla.ac.uk/rod/rod.html
A. Nebel · D. Filon · A. Oppenheim ()
Department of Hematology, Hebrew University,
Hadassah Medical School and Hadassah University Hospital,
Jerusalem 91120, Israel
e-mail: Ariella@md.huji.ac.il,
Tel.: +972-2-6776753, Fax: +972-2-6423067
D.A. Weiss
Department of Anthropology, University of California,
Davis, USA
M. Weale · M.G. Thomas
Department of Biology, University College London, London, UK
M. Faerman
Laboratory of Biological Anthropology and Ancient DNA,
Hebrew University, Hadassah School of Dental Medicine,
Jerusalem, Israel
© Springer-Verlag 2000
reflect more recent genealogical events (Roewer et al.
1996; Bosch et al. 1999).
Historically, the origin of the Arab population residing
in Israel and the Palestinian Authority Area (I&P Arabs)
is complex and diverse. Located at the crossroads of three
continents, the Southern Levant has, throughout history,
attracted many waves of immigrants and conquerors alike.
Permanent human settlement in the region dates back to
the Natufian Period (~12,500–10,000
BP
). Based on an-
thropological evidence, it has been suggested that the
Natufians and their descendants formed a ‘core’ popula-
tion that can be traced to recent times, but was mixed with
incoming groups (Arensburg 1973). According to histori-
cal records, major demographic events took place in the
Israelite Period and during the Jewish Kingdom Period
(1200–586
BC
): the Assyrian and Babylonian invasions
were followed by the deportation of locals and the settle-
ment of foreign peoples (Bachi 1974). The Roman Judean
Wars (66–135
AD
) culminated in the destruction of the
Second Temple and led to the annihilation or exile of a
large portion of the Jewish population (Anderson 1995).
By the fifth century
AD
, the majority of non-Jews and
Jews had become Christians by conversion (Bachi 1974).
The first millennium
AD
was marked by the immigration
of Arab tribes, reaching its climax with the Moslem con-
quest from the Arabian Peninsula (633–640
AD
). This
was followed by a slow process of Islamization of the lo-
cal population, both of Christians and Jews (Shaban 1971;
Mc Graw Donner 1981). Additional minor demographic
changes might have been caused by subsequent invasions
of the Seljuks, Crusaders, Mongols, Mamelukes and Ot-
toman Turks. Recent gene-flow from various geographic
origins is reflected, for example, in the heterogenous
spectrum of β-globin mutations among Israeli Arabs
(Filon et al. 1994).
Israeli and Palestinian Arabs share a similar linguistic
and geographic background with Jews. Their genetic re-
lationship has been the focus of several investigations.
Comparative studies of classical markers (Bonné-Tamir
et al. 1979), mitochondrial DNA (mtDNA) restriction
haplotypes (Bonné-Tamir et al. 1986; Ritte et al. 1993),
HLA (Bishara et al. 1997) and disease-related mutations
(Filon et al. 1994; Peretz et al. 1997) revealed substantial
genetic affinities between the two populations, yet also
significant differences. Based on two Y chromosome
RFLP markers it was suggested that Ashkenazi and
Sephardic Jews are more closely related to Arabs from
Lebanon than to Czechoslovakians (Santachiara-Benere-
cetti et al. 1993). Moreover, a recent survey of 18 binary
Y-specific polymorphisms showed that Y chromosome
haplotypes of Middle Eastern non-Jewish populations are
almost indistinguishable from those of Jews (Hammer et
al. 2000).
In the present study, we performed an in-depth evalua-
tion of the Y chromosome affinity between Arabs and
Jews by analysis of high-resolution haplotypes compris-
ing both binary and microsatellite polymorphisms. This
approach also allowed us to characterize in detail the I&P
Arab population with regard to their genetic composition,
lineage diversity, geographic substructure and possible
origins.
Subjects and methods
Subjects
Y chromosomes of 143 Moslem Arabs from Israel and the Pales-
tinian Authority Area (I&P Arabs), unrelated at the paternal great-
grandfather level, were analyzed. Druze and Bedouins were ex-
cluded from this study. Most of the subjects come from rural areas
where their families have lived for generations. DNA was obtained
anonymously from thalassemia patients or their relatives (carriers
as well as non-carriers). For the purpose of the present study, we
consider this sample to be representative of the general Moslem
Arab population in Israel and the Palestinian Authority Area be-
cause: (1) thalassemia is unlinked to the Y chromosome, is spread
throughout the country and is not restricted to specific regions; (2)
the spectra and frequencies of thalassemia mutations in any subset
of males classified here according to their Y chromosomes (i.e.,
haplogroups) was found to be similar to each other and to the spec-
trum and frequency of thalassemia mutations in the general popu-
lation, as previously reported (Filon et al. 1994); (3) a significantly
different proportion of YAP
+
chromosomes was observed in one of
the regional Arab subpopulations, the Highlands people (see Re-
sults). We used this finding to obtain independent evidence that the
entire sample was not biased. We randomly collected 24 additional
DNA specimens from the Highlands population. No statistical dif-
ference was detected between this control group and the Highlands
sample used in the study, neither at the haplogroup level (popula-
tion differentiation test: P>0.9) nor at the haplotype level
(AMOVA: Φ
ST
value = 0.003; P>0.27).
Data on Y chromosomes of Ashkenazi and Sephardic Jews
(collected in Israel, Canada and the UK) were the same as previ-
ously reported (Thomas et al. 1998). Male Jews are traditionally
divided into Israelites, Levites and Cohanim. In this study, only Is-
raelites were considered. They comprise approximately 90% of the
Jews and are, therefore, most representative of the Jewish popula-
tion. During the diaspora, Sephardic Jews lived mostly in Arab
countries (in North Africa and the Middle East) or in countries un-
der strong Arab influence (in Spain and other regions in southern
Europe), while Ashkenazim mainly resided in northern and central
Europe. To ascertain that any genetic similarity between Arabs and
Jews seen in this study is not due to recent admixture of Sephardim
with Arabs, Ashkenazi and Sephardic Jews were treated sepa-
rately.
The North Welsh, a representative European Caucasian popu-
lation (Darke et al. 1998; Sellers et al. 1999), were included in the
analysis because they do not have a known history of admixture
with Jewish communities. The data obtained from the Welsh there-
fore allowed us to examine possible gene flow from Europeans to
Ashkenazi Jews during the diaspora. The group of Welsh analyzed
included 94 males unrelated at the paternal grandfather level. The
samples were collected from villages around Llangefni, a town in
North Wales.
The study was approved by the Hebrew University Committee
for Ethics in Research.
Typing of Y chromosome DNA polymorphisms
The DNA samples, prepared from peripheral blood by standard
protocols, were typed for 17 different Y chromosome DNA poly-
morphisms in three multiplex PCRs as described (Thomas et al.
1999): UEP1-PCR: YAP (DYS287; Hammer 1994), 92r7 (Mathias
et al. 1994), SRY4064 (Whitfield et al. 1995), SRY+465 (Shinka
and Nakahori, personal communication), sY81 (DYS271; Seielstad
et al. 1994), Tat (Zerjal et al. 1997); UEP2-PCR: M9, M13, M17,
M20 (Underhill et al. 1997), SRY10831 (Whitfield et al. 1995);
MS-PCR: DYS19, DYS388, DYS390, DYS391, DYS392, DYS393
(Jobling and Tyler-Smith 1995).
631
Since the Y chromosomes of Jews had not been typed for the
five markers in UEP2-PCR, the Arab chromosomes were, for the
purpose of Arab-Jewish comparisons, classified into three hap-
logroups based on the allelic state of the six binary markers in
UEP1-PCR. For intra-population analysis, the Arab chromosomes
were classified into six haplogroups based on all 11 binary mark-
ers. Haplogroups were defined using the nomenclature presented
in Tables 1 and 2.
Statistical and genealogical analyses
Genetic identity (I), haplotype diversity (h) and its sampling vari-
ance were calculated as described by Nei (1987), using unbiased
estimates. Interpopulation comparisons were made using the exact
test of population differentiation (Raymond and Rousset 1995) and
the analysis of molecular variance (AMOVA; Excoffier et al.
1992) included in the software package Arlequin (Version 1.1;
Schneider et al. 1997). Φ
ST
values in AMOVA were calculated us-
ing the sum of squared allele size differences (R
ST
) as a measure of
microsatellite haplotype distance (Michalakis and Excoffier 1996).
Microsat (Version 1.5d; Minch 1997) was used to compute the ge-
netic distance measure average square distance (ASD; Goldstein et
al. 1995). UPGMA and unrooted neighbor joining (NJ) haplotype
trees based on ASD were drawn with the phylogeny inference
package, PHYLIP (Version 3.5c; Felsenstein 1995) and displayed
using TreeView (Version 1.5). Relationships of haplotypes were
also visualized by constructing networks of microsatellite haplo-
types for each haplogroup (Cooper et al. 1996). In these networks,
all haplotypes are linked to one or more other haplotypes without
inferring unobserved intermediate states. This method excluded all
those haplotypes (44 of the 140 different haplotypes found in
Arabs and Jews) that were at least two microsatellite mutational
steps removed from their nearest link in the network. We note that,
with the exception of three, all unlinked haplotypes were single-
tons. Tests for differences in genetic distance of populations X and
Y from a third population Z were carried out by bootstrapping a
relevant statistic D and deriving a 95% confidence interval for the
difference D
XZ
-D
YZ
.
Estimate of population expansion date
In order to estimate dates for the start of population growth
amongst the I&P Arabs, we carried out full-likelihood Bayesian
analysis using the BATWING (Bayesian Analysis of Trees With
Internal Node Generation) program (Wilson and Balding 1998).
The extended version of the program used here assumes an un-
bounded single stepwise mutation model (Moran 1975) for the mi-
crosatellite loci and a coalescent process under a model of expo-
nential population growth from an initially constant-size popula-
tion. Binary polymorphisms were used only to condition the space
of permissible trees, but otherwise did not contribute to the likeli-
hood. Informative priors were based on previous data or reason-
able ranges. The initial effective population size was given a prior
distribution of Gamma(4,0.001), which has 2.5%, 50% and 97.5%
quantiles of 1090, 3672 and 8767. The population growth rate (r)
per generation was given a Gamma(1.5,100) prior (2.5%, 50%,
97.5% quantiles = 0.0011, 0.012, 0.047). The microsatellite muta-
tion rate per generation,
µ
, was given a Gamma(12,5862) prior
632
Table 1 Y chromosome haplogroup distribution in Arabs, Jews and Welsh (P YAP insert present, N no YAP insert, A adenine, C cyto-
sine, G guanine, T thymine)
Population I&P Arabs Ashkenazi Jews
a
Sephardic Jews
a
North Welsh
b
Haplogroup n Frequency n Frequency n Frequency n Frequency
1 NCGCAT
c
100 0.699 42 0.618 32 0.628 7 0.074
2 NTGCAT
c
14 0.098 12 0.176 12 0.235 84 0.894
3 PCACAT
c
29 0.203 14 0.206 7 0.137 3 0.032
Total 143 1.000 68 1.000 51 1.000 94 1.000
a
Data on Ashkenazi and Sephardic Israelites as reported (Thomas
et al. 1998)
b
Data on Welsh are available upon request from one of the authors
(M.G.T.)
c
Haplogroups are defined by the allele status at six binary markers
in the following order: YAP, 92r7, SRY4064, SRY+465, sY81,
Tat
Table 2 Y chromosome haplogroup distribution in four I&P Arab subpopulations (P YAP insert present, N no YAP insert, A adenine,
C cytosine, G guanine, T thymine, G+ guanine present, G- guanine deleted)
Population I&P Arabs (total) North Lowlands Gaza Highlands
Haplogroup n Frequency n Frequency n Frequency n Frequency n Frequency
1 NCGCAT
a
100 0.699 39 0.722 23 0.793 15 0.714 23 0.589
1A CGG+AG
b
88 0.615 35 0.648 20 0.690 12 0.571 21 0.538
1B GGG+AG
b
10 0.070 4 0.074 3 0.103 1 0.048 2 0.051
1C CCG+AA
b
2 0.014 2 0.095
2 NTGCAT
a
14 0.098 8 0.148 4 0.138 1 0.048 1 0.026
2A GGG+AG
b
12 0.084 6 0.111 4 0.138 1 0.048 1 0.026
2B GGG-AA
b
2 0.014 2 0.037 -
3 PCACAT
a
29 0.203 7 0.130 2 0.069 5 0.238 15 0.385
CGG+AG
b
Total 143 1.000 54 1.000 29 1.000 21 1.000 39 1.000
a
Haplogroups are defined by the allele status at six binary markers in the following order: YAP, 92r7, SRY4064, SRY+465, sY81, Tat
b
Haplogroups are additionally defined by the allele status at five binary markers in the following order: M9, M13, M17, M20, SRY10831
(2.5%, 50%, 97.5% quantiles = 0.0011, 0.0020, 0.0034). This prior
is based on data from four published studies (Heyer et al. 1997;
Bianchi et al. 1998; Kayser et al. 1997; Kayser et al. 2000), re-
stricted to the same microsatellite loci as those used here. The 12
observed mutational events out of 5862 meioses were combined
with an (improper) uniform pre-prior. Generation time was set at
25 years.
Results
Genetic composition of the I&P Arab population
The six binary markers YAP, 92r7, SRY4064, SRY+465,
sY81 and Tat defined three haplogroups among the I&P
Arabs (Table 1). Haplogroups 1 and 2 lack the YAP inser-
tion, while haplogroup 3 is YAP
+
/sY81-A. The additional
five polymorphisms, M9, M13, M17, M20 and SRY10831
further divided haplogroups 1 and 2 into three and two
groups, respectively (Table 2). The two sets of binary
markers together with the six microsatellites defined 83
different compound haplotypes, as listed in the appendix.
No instance of homoplasy of microsatellite haplotypes
across haplogroups was observed. The large number of
singletons (73.5%) contributed to the high haplotype di-
versity (h) of 0.971±0.008 for all the Arab samples. Hap-
lotype 25 was the most common (~14%) and was, there-
fore, called the modal haplotype of the Israeli and Pales-
tinian Arabs. Haplotype 21, one of its single-step neigh-
bors, was observed almost exclusively in individuals from
the Lower Galilee area, where it was the modal haplotype.
It made up 18.5% of the samples from the Galilee. Together
with their one-step neighbors, both modal haplotypes com-
prise 31% of the sample.
Using BATWING analysis, the median estimate for the
start of exponential population growth from an initially
constant-size population was 7780 years
BP
(95% credi-
bility interval = 2780–22856 years
BP
). The proportion of
the posterior distribution for population expansion dates
that is post the onset of the Neolithic Period in the South-
ern Levant (10,300
BP
; Bar-Yosef 1995) is 69.2%. The
median estimate for the population growth rate during the
expansion period was 0.76% per generation (95% credi-
bility interval = 0.26%–2.24% per generation).
Genetic affiliation of Arabs with Jews
For the Jews, data on only six binary polymorphisms and
six microsatellites were available (Thomas et al. 1998).
Therefore, a comparison of the Arab and Jewish samples
was performed using 12-marker haplotypes.
The population differentiation test based on haplo-
group frequencies (Table 1) showed a statistically signifi-
cant difference between Arabs and Sephardic Jews
(P<0.05) due to a higher frequency in Sephardic Jews of
haplogroup 2, but no significant differences were found
between Arabs and Ashkenazi Jews nor between the two
Jewish communities. However, all three were distin-
guished from the Welsh (P<0.0005). Table 1 shows that
the major proportion of Y chromosomes of Arabs and
Jews belonged to haplogroup 1, while most of the Welsh
chromosomes were of haplogroup 2. The frequency of
haplogroup 2 chromosomes in Arabs (~10%) was signifi-
cantly lower than that in Sephardic Jews (~24%,
P<0.018), and lower, but not significantly so, than that in
Ashkenazi Jews (~18%, P>0.05).
Table 3 presents the extent of I as pairwise compar-
isons between populations based on the frequencies of bi-
nary plus microsatellite haplotypes. Using bootstrap tests
on I values, we found that both Sephardic and Ashkenazi
Jews were significantly closer to I&P Arabs than Arabs
were to Welsh (P<0.001 in both cases), and no significant
difference was found in the genetic identity of Arabs to
one Jewish group compared to the other (P=0.816).
Sephardic Jews were less distant to Arabs than to
Welsh. However, Ashkenazi Jews and Welsh were closer
to one another than Ashkenazim and Arabs. Examination
of the data revealed that this finding is due to the fact that
two Ashkenazi individuals carried the most common
Welsh haplotype (~27%). This haplotype has also been
observed at high frequencies in other European countries,
including England (~15%), Frysland (~13%) and Norway
(~6%) (manuscript in preparation). We note that 8 of the
12 chromosomes shared between Jews (both Ashkenazim
and Sephardim) and Welsh belonged to haplogroup 2,
which was found in the Welsh at a frequency of ~89%
(Table 1). In contrast, most chromosome sharing between
Arabs and Jews involved haplogroup 1. Neither of the two
Arab modal haplotypes were detected in Jews. However,
three Arab individuals from different regions carried the
CMH (haplotype 27). None of these three modal haplo-
types were seen in the Welsh sample.
The genetic differences among the four populations
were assessed by AMOVA, including chromosomes from
633
Table 3 Genetic identity (I) between populations
Population Sephardic Jews Ashkenazi Jews North Welsh
I&P Arabs 0.144 0.134 0.018
Sephardic Jews 0.706 0.093
Ashkenazi Jews 0.174
Table 4 Y chromosome variation between populations estimated
by AMOVA (Φ
ST
)
a
Population I&P Ashkenazi Sephardic
Arabs Jews Jews
Φ
ST
b
P
c
Φ
ST
b
P
c
Φ
ST
b
P
c
Ashkenazi Jews 0.067 <0.001
Sephardic Jews 0.055 0.002 0.001 0.330
North Welsh 0.391 <0.001 0.290 <0.001 0.376 <0.001
a
AMOVA was performed on chromosomes from all three hap-
logroups
b
Φ
ST
: ratio of variance component due to differences among popu-
lations over the total variance
c
P the probability of observing a more extreme Φ
ST
after 1000 ran-
domizations than those generated in the analysis
all three haplogroups (Table 4). The Φ
ST
values (the pro-
portion of total variance attributable to inter-population
differences) between Arabs and both Jewish communities
were significant, yet low relative to the values obtained in
the analysis of the Welsh outgroup with the three other
populations. The Φ
ST
values calculated for Ashkenazi and
Sephardic Jews revealed no significant difference.
High repeat numbers for DYS388 (15) were common
in Arabs and both Jewish populations. Europeans have
been shown to exhibit mainly DYS388 alleles with short
repeat lengths (Kayser et al. 1997; Kittles et al. 1998,
1999). High repeat numbers for DYS388 (15) have, so
far, been found at high frequency only in populations
originating in the Middle East (Thomas et al. 2000) and
are restricted to haplogroup 1. Compared to 54% of the
Ashkenazi and 53% of the Sephardic Jews, 72% of Arabs
with a haplogroup 1 chromosome carried a DYS388 repeat
number 15. In the Welsh, only one of the seven individ-
uals belonging to haplogroup 1 had a high repeat number
for DYS388.
Genealogical trees of Arab, Jewish and Welsh haplo-
types were constructed separately for each haplogroup,
using both UPGMA and NJ on ASD distances. The NJ
tree for haplogroup 1 is presented as an example in Fig.1.
The haplotypes of Arabs, Jews and Welsh were intermin-
gled and no population-specific clustering was observed,
with the exception of a single branch in haplogroup 1.
This branch or clade, which was identical in both UP-
GMA and NJ trees, comprised almost exclusively Arab
haplotypes, including the modal haplotypes of the I&P
Arabs and the Galilee sample (Fig.1). 32% of the 143
Arab chromosomes belonged to this “I&P Arab clade”
that contained only one non-Arab chromosome, that of a
Sephardic Jew. Bootstrap analysis on 500 resamplings
showed support for the Arab clade of about 50% (NJ) and
10% (UPGMA), respectively.
Evidence for an Arab clade can also be seen in the sin-
gle-step network of haplogroup 1 chromosomes in which
the haplotypes were linked to each other without inferring
unobserved intermediate states (Fig.2). The network ex-
cluded all those haplotypes that could not be linked and
therefore comprised fewer haplotypes than the corre-
sponding trees. The bottom part of the network with the
two Arab modal haplotypes and their one-step neighbors
634
Fig.1 Unrooted neighbor joining tree based on ASD was drawn
for haplogroup 1 haplotypes of Arabs, Jews and Welsh. Bootstrap
analysis on 500 resamplings showed support for the Arab clade of
about 50% (marked with an asterisk). The numbers of the 12 Arab
haplotypes that define the Arab clade are: 7–9, 18–26 (as listed in
the appendix). (A I&P Arab, AJ Ashkenazi Jew, SJ Sephardic Jew,
W Welsh, MH I&P Arabs modal haplotype of the I&P Arabs, MH
Galilee modal haplotype of the Galilee sample, CMH Cohen
modal haplotype)
contains 9 of the 13 haplotypes of the Arab clade. The
other Arab clade haplotypes, including the one of the
Sephardic Jew, are not present as they were at least two
microsatellite mutational steps removed from their nearest
link in the network. Networks were also constructed sep-
arately for the other two haplogroups (not shown). Apart
from the Arab clade, Jewish, Arab and shared Y chromo-
somes were, to a substantial extent, intermingled through-
out the networks of all three haplogroups.
Is there a geographic substructure
in the Arab population?
Most Arab families in the rural regions have lived in the
same local area for generations. Although Israel and the
Palestinian Authority Area are relatively small, it was of
interest to investigate whether there was evidence of any
geographic structure within the Arab population. Four re-
gions were designated as previously described (Filon et
al. 1994): the North comprises the mountainous region of
the Upper and the Lower Galilee; the fertile plain along
the Mediterranean Sea is divided into the central Low-
lands and the Gaza area; the Highlands to the east of the
coastal plain are a mountain range that covers Samaria
and Judea (including Jerusalem).
The analysis of the four Arab subpopulations was
based on the 17-marker haplotypes (Table 2). At the hap-
logroup level, the Y chromosome distribution was similar
for all populations, except for the Highlands people. As
shown by the population differentiation test, they were
distinguished from those in the Lowlands (P<0.01) and
the North (P<0.05), but not from those in the Gaza area.
The Highlands people are also the only population who
differed significantly from the Ashkenazi (P<0.05) and
Sephardic Jews (P<0.001). If haplogroup 3 (YAP
+
) chro-
mosomes are excluded from the analysis, the only signifi-
635
Fig.2 Network of haplogroup 1 Y chromosome haplotypes of
Arabs and Jews. Alleles for the microsatellite loci are listed in the
order DYS19, DYS388, DYS390, DYS391, DYS392, DYS393. Lines
represent single microsatellite mutation steps. The network was
drawn manually by starting with the most common haplotype and
sequentially adding adjacent ones. All possible adjacent relation-
ships were indicated by connecting lines. The arrangement of the
haplotypes within the network is arbitrary. The length of the lines
connecting haplotypes as well as the distance between unlinked
haplotypes do not reflect phylogenetic proximity. Colour indicates
the population in which the haplotype is present. The box area sur-
rounding each haplotype is proportional to its frequency in both
populations. Numbers in parenthesis under shared haplotypes de-
note the proportion of Arab chromosomes. The haplotype marked
with an asterisk was also found in a single Welsh individual. (MH
I&P Arabs modal haplotype of the I&P Arabs, MH Galilee modal
haplotype of the Galilee sample, CMH Cohen modal haplotype)
636
cant difference that remains is between the Highlands and
Sephardic Jews, P<0.05. Thus, the higher frequency of
haplogroup 3 is the principal distinguishing feature of the
Highlands population. In a genealogical tree including all
YAP
+
haplotypes, no association between haplotypes and
a particular subpopulation was observed (not shown). All
four Arab subpopulations were distinguished from the
Welsh (P<0.0005).
The close relationship of the four Arab subpopulations
is reflected in the high proportion of shared chromo-
somes. Each had between 36% (the Highlands) and 52%
(the Gaza area) of the Y chromosomes in common with
the other Arab subpopulations. The modal haplotype of
the I&P Arabs was detected in all four subpopulations.
Discussion
Geographic origin of haplogroups
The largest proportion (~62%) of Arab Y chromosomes
belonged to haplogroup 1A, the most geographically
widespread haplotype today (Underhill et al. 1997; Ham-
mer et al. 1998). Haplogroup 1C, represented by two Arab
chromosomes in this study, has so far only been reported
in Sudan (Underhill et al. 1997). Haplogroup 3 (chromo-
somes with the SRY4064-A polymorphism on a YAP
+
background), estimated to have arisen about 30,000 years
BP
in Africa (Hammer et al. 1998), constitutes about 20%
of the overall Arab sample.
The most recent YAP
+
haplotype, with the A to G tran-
sition at sY81, has been estimated to have originated in
sub-Saharan Africa between 10,000 and 20,000 years
BP
(Hammer et al. 1998). Outside its area of origin, the pres-
ence of this haplogroup is thought to indicate admixture
with sub-Saharan Africans. It has been reported, for ex-
ample, in Egypt (2%) and the Arabian Peninsula (5%;
Hammer et al. 1998). Other sub-Saharan markers have
been documented in the I&P Arabs, including mtDNA
RFLP defined haplotypes, blood groups and sickle cell
anemia (Sandler et al. 1979; Bonné-Tamir et al. 1986;
Rund et al. 1990; Ritte et al. 1993). It is, therefore, in-
triguing that this YAP
+
haplotype with the A to G transi-
tion at sY81 was not observed in the I&P Arabs sampled
in this study.
Haplogroups 1B and 2, which comprise about 17% of
the examined Arab Y chromosomes, are likely to be of
Eurasian origin (Underhill et al. 1997; Hurles et al. 1998).
In Europe, the 92r7 T-allele, which distinguishes hap-
logroup 2 from haplogroup 1, shows a decreasing north-
south gradient, ranging from 89% in Welsh (this study) to
48% in north Italians and 20% in Greeks (Mitchell et al.
1997). It would seem that the Arabs, with a haplogroup 2
frequency of 10%, represent a population in the southern
part of the geographic cline.
Of the polymorphic variants particularly associated
with Asian populations (SRY4064-G/YAP
+
, SRY+465-T,
Tat-C, M20-G and M17-G
-
) only the last was detected
here, in two individuals (haplogroup 2B). To date, M17-G
-
has been observed at high frequency in central and west-
ern Asia and in India/Pakistan (Underhill et al. 1997).
Our median estimate for the start of exponential popu-
lation growth falls within the Neolithic Period. Although
this was unsurprising, given that population growth is ex-
pected to follow the development of farming, the credibil-
ity interval is wide, with only 69.2% of the posterior dis-
tribution falling on or after the onset of the Neolithic Pe-
riod in the Southern Levant. This reflects, to some extent,
the limited information contained in a sample of only 143
chromosomes. However, recent admixture events may
also contribute to this wide estimate.
I&P Arab population structure
The similarity of the four Arab subpopulations is attested
by the large extent of Y chromosome and haplotype shar-
ing among the people residing in the various regions. This
homogeneity is not surprising given that the studied area
is relatively small and that there are no natural geograph-
ical barriers. However, the haplotype distribution also re-
flects a certain degree of regional isolation. This is seen in
the Highlands people, who differ from two of the three
other subpopulations by a significantly higher frequency
of YAP
+
chromosomes. The genetic distinctiveness of the
Highlands people has also been noted with regard to mu-
tations in the β-globin gene. The predominant β-tha-
lassemia mutation in the region, IVS 1–6, reaches 40%,
which is fourfold higher than in any other part of the
country, where another mutation, IVS 1–110, predomi-
nates (Filon et al. 1994). The locally restricted modal hap-
lotype of the Galilee sample also suggests possible geo-
graphic structuring, although this is not statistically estab-
lished. A possible explanation for the restricted presence
of this haplotype could be a recent, localized population
expansion in the Galilee. The observed regional differ-
ences in the distribution of Y chromosome haplotypes
may be the result of drift and/or founder effect and may
subsequently have been enhanced by traditional endoga-
mous marriage practices, such as intrafamilial marriages,
male polygamy and patrilocality.
Genetic affinities of Arabs to Jews
Arabs are more closely related to Jews than they are to the
Welsh, indicating a more recent common ancestry. At the
haplogroup level, the Y chromosome distribution was
similar in both Arabs and Jews, although a significant dif-
ference was found between Arabs and Sephardic Jews in
haplogroup 2 frequencies. This finding does not necessar-
ily conflict with the results of Hammer et al. (2000), who
found no significant differences between Jews and non-
Jewish Middle-Eastern populations, as the difference re-
ported here was only just significant (P<0.05) and Ham-
mer et al. used a lower significance level (α=0.03).
The incorporation of microsatellites in the analysis re-
vealed a more complex pattern of genetic affinities and
637
differences among the populations. Arabs and Jews had
approximately 18% of their chromosomes in common. In
addition, they were characterized by closely related modal
haplotypes, each displaying a high repeat number DYS388
allele typical of Middle Eastern populations (Thomas et
al. 2000). Furthermore, with the exception of the Arab
clade, the haplotypes of the two populations appeared in-
terspersed throughout the NJ and UPGMA trees of all
three haplogroups, reflecting a close genealogical rela-
tionship given the high observed mutation rate of Y chro-
mosome microsatellites (Kayser et al. 2000). In the haplo-
type networks, Jewish chromosomes provided connecting
links that were missing in the Arab-only networks and
vice versa. A substantial portion of Arab (82%) and Jew-
ish Y chromosomes (70%) comprised the mixed chromo-
some pools of each of the three haplogroups (as inferred
from the networks). Our findings corroborate previous
studies that suggested a common origin for Jewish and
non-Jewish populations living in the Middle East (San-
tachiara-Benerecetti et al. 1993; Peretz et al. 1997; Ham-
mer et al. 2000).
However, the present study, using high-resolution hap-
lotypes, also revealed statistically significant differences
between Arabs and Jews. Both populations were charac-
terized by distinct modal haplotypes that were infrequent
in the other population. Notably, about one third of the
Arab individuals carried I&P Arab clade haplotypes that
were observed once in the Sephardic Jews studied here
and in a single Ashkenazi Cohen out of 306 male Jews
tested (Thomas et al. 1998). Although Arabs and Jews
showed a high frequency of haplotypes with a DYS388 re-
peat number 15, the distribution of the alleles was differ-
ent in each population. DYS388 allele 17 was found al-
most exclusively in Arabs, while allele 16 was common
among Jews. In addition, both Sephardic and Ashkenazi
Jews had higher frequencies of haplogroup 2 chromo-
somes than Arabs. These differences presumably reflect
divergence over time due to genetic drift and/or gene-flow
from other populations. Both Ashkenazi and Sephardic
Jews are likely to have experienced admixture with vari-
ous populations during the 2000 years of diaspora. The
higher frequency of haplogroup 2 chromosomes in Jews
may reflect the influx of foreign lineages. Two Ashkenazi
Jews in our sample were found to share the most common
haplotype of the Welsh, a frequent and widespread haplo-
type in northern Europe. The presence of European Y
chromosomes in Ashkenazi Jews has also been reported
previously based on two RFLP markers (Santachiara-
Benerecetti et al. 1993).
The occurrence of less than 1% of I&P Arab clade
chromosomes in the Ashkenazi and Sephardic samples is
noteworthy since they shared many other haplotypes with
Arabs. The low haplotype diversity of the Arab clade
chromosomes, as seen in the network (Fig.2), suggests
that they descended from a relatively recent common an-
cestor. Arab clade chromosomes could have been present
in the common ancestral population of Arabs and Jews,
and drifted to high frequencies in one of the subgroups
following population isolation. The event leading to this
isolation might have been the acceptance of the monothe-
istic Jewish religion by a subset of the population, or geo-
graphic separation due to the expulsion of Jews after the
destruction of the Second Temple in
AD
79. Alternatively,
the Arab clade could have been introduced through gene-
flow, perhaps by the immigration of Arab tribes in the
first millennium
AD
. In this regard, it is of interest that
Arab clade chromosomes were observed in 8 out of 49
Moslem Arabs (16%) from the Hadramaut in Yemen
(Thomas et al. 2000). Further studies are needed to clarify
the origin of the Arab clade.
According to historical records part, or perhaps the ma-
jority, of the Moslem Arabs in this country descended
from local inhabitants, mainly Christians and Jews, who
had converted after the Islamic conquest in the seventh
century
AD
(Shaban 1971; Mc Graw Donner 1981).
These local inhabitants, in turn, were descendants of the
core population that had lived in the area for several cen-
turies, some even since prehistorical times (Gil 1992). On
the other hand, the ancestors of the great majority of pre-
sent-day Jews lived outside this region for almost two
millennia. Thus, our findings are in good agreement with
historical evidence and suggest genetic continuity in both
populations despite their long separation and the wide ge-
ographic dispersal of Jews.
Acknowledgements We wish to thank Prof. Patricia Smith for
stimulating discussions and encouragement and Prof. Hagai Ben-
Shamai for providing the historical insight. We are grateful to Dr.
Moien Kanaan and Mahmoud Abd El-Latif for supplying control
DNA samples. This work was partially supported by a research
grant from the Israeli Ministry of Science, Culture and Sport, and
by funding to M.G.T. from the Nuffield Foundation (NUF-NAL).
638
Appendix
Distribution of Y chromosome haplotypes in four I&P Arab subpopulations
Haplotype Allele status at Arab subpopulations
a
No.
DYS19 DYS388 DYS390 DYS391 DYS392 DYS393 NLGHTotal
Haplogroup 1A
1161523101112 1 1
2161424101112 1 1
3161324111113 1 1
4 16 13 23 10 12 14 1 1
5161223101112 1 1
6161222101114 1 1 2
7151823121113 1 1
8151723111112 1 1
9151722111112 1 1
10 15 16 24 10 11 12 1 1
11 15 15 24 11 11 12 1 1
12 15 15 24 10 11 12 3 1 1 5
13 15 15 22 10 8 12 1 1
14 15 13 25 10 11 12 1 1
15 15 13 23 10 12 12 1 1
16 15 12 22 11 11 14 2 2
17 15 10 23 10 12 13 2 2
18 14 17 24 11 11 12 1 1
19 14 17 23 13 11 12 1 1
20 14 17 23 11 11 11 1 1
21 14 17 23 11 11 12 10 2 12
22 14 17 23 10 11 12 2 1 3
23 14 17 22 12 11 13 1 1
24 14 17 22 11 12 12 1 1
25141722111112 546520
26 14 17 22 10 11 12 1 2 3
27 14 16 23 10 11 12 1 1 1 3
28 14 16 23 9 11 16 1 1
29 14 16 22 11 11 12 1 1
30 14 16 22 10 11 12 1 1
31 14 15 26 10 11 12 2 2
32 14 15 23 10 11 14 1 1
33 14 15 23 10 11 13 2 2
34 14 15 23 10 11 12 1 1 2
35 14 15 22 11 11 13 2 2
36 14 15 22 9 11 12 1 1
37 14 14 25 11 11 12 1 1
38 14 14 24 10 11 12 1 1
39 14 14 23 11 11 12 1 1
40 14 14 23 10 11 12 1 1
41 14 12 22 11 11 14 1 1
Haplogroup 1B
42 15 12 24 10 14 13 1 1
43 15 12 23 11 13 15 1 1
44 15 12 23 10 13 13 1 1
45 15 12 23 9 13 13 1 1
46 14 12 23 10 14 13 1 1
47 14 12 23 10 14 12 1 1
48 14 12 22 10 14 11 1 1
49 14 12 22 10 13 13 1 1
50 13 12 24 10 13 13 1 1 2
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... A high-resolution Y chromosome haplotype analysis on unrelated Israeli and Palestinian Moslem Arabs showed a common pool for the male lineages. However, some significant differences were also detected between Jews and Arabs, suggesting a recent divergence of the Arab clade from the common ancestral population (Nebel et al., 2000). ...
... The IPD of the Israeli population appears to be similar to the Arab population (60.9 ± 3.0 in females and 62.0 ± 2.6 in males 4 ), which could be due to the fact that our cohort included 53 Israeli Arabs and that the two ethnic groups are genetically similar. 65,66 ...
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Background Interpupillary distance (IPD) is important in developmental anatomy, genetics, design of optical instrumentation, ocular diagnostics, and optical prescribing. IPD frequently is measured on different days, and by either automatic pupillometers (physiological measurement) or manual ruler (anatomical measurement). Therefore, there is importance in the agreement and inter-session repeatability of manual and automatic IPD measurements. Methods Monocular distance from the bridge of the nose and binocular distance and near binocular IPD were randomly measured, using a millimeter ruler and the Essilor Pupillon pupillometer. Gender effects were assessed using Wilcoxon and Mann-Whitney tests, respectively. Agreement was assessed using Spearman correlation and Bland-Altman (B&A) plots. Thirty additional participants were tested within 1–2 weeks to determine the inter-session repeatability. Results The agreement study included 199 participants (mean age: 24.1 ± 5.0 range: 19−53, 58 male, 141 female) and the repeatability sub- study included 30 (mean age: 27.9 ± 4.5, range: 23–39, 6 male, 24 female). Males and females significantly differed in age (<2 year mean difference (md)) and IPD (monocular md: < 1 mm, binocular md: < 2 mm). Manual vs. automatic measurements were significantly different for all conditions (md: <1 mm for all) except for distance left eye male PD. There was no significant difference between the session for both methods. Conclusions Binocular and monocular manual and automatic measurements were significantly different statistically, but not clinically. Distance binocular IPD was approximately 3 mm wider than near IPD. Male binocular IPD was approximately 2 mm wider than the female IPD. Both methods had good inter-session repeatability.
... 11 In addition, the absence of populations from key corridors and centers of Jewish settlement, such as Belarus, Lithuania, and Poland, could have influenced the results of the study, which favored a Levantine origin for Eastern European Jews. Y-chromosome studies by Nebel et al. (2000Nebel et al. ( , 2001Nebel et al. ( , 2005 also supported the suggestion that Ashkenazi males were more closely related to "Middle Eastern" populations than to "host" European populations (Rhine French, German, and various Eastern European groups). In this regard, the range of NRY haplogroups present in Jewish populations was broad. ...
... Based on the predominance of M17 lineage among diverse linguistic families (Indo-European, Altaic, Uralic and Caucasian) and geographic regions (Central Asia, Europe, Caucasus, Middle East), Underhill et al. 2000;Karafet et al. 1999;Rosser et al. 2000;Nebel et al. 2000) it has been associated with the Kurgan culture, domestication of horses and spread of Indo-European languages, all which supposedly originated in southern Russia/Ukraine and subsequently extended to Europe, Central Asia around 3000 B.C . Its presence in India has been linked to the "Aryan" migration and subsequent spread of Indo-European languages, appearance of iron and Painted Grey Ware culture in North West frontier (Cavalli-Sforza et al. 1994). ...
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Thesis
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