AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 136:1118 (2008)
Alu Insertion Polymorphisms and an Assessment of the
Genetic Contribution of Central Asia to Anatolia With
Respect to the Balkans
Ceren Caner Berkman,* Havva Dinc, Ceran Sekeryapan, and Inci Togan
Department of Biological Sciences, Middle East Technical University, 06531 Ankara, Turkey
KEY WORDS Alu insertion; Anatolian population; admixture; Turkic language
ABSTRACT In the evolutionary history of modern
humans, Anatolia acted as a bridge between the Cauca-
sus, the Near East, and Europe. Because of its geographi-
cal location, Anatolia was subject to migrations from
multiple different regions throughout time. The last, well-
known migration was the movement of Turkic speaking,
nomadic groups from Central Asia. They invaded Anatolia
and then the language of the region was gradually
replaced by the Turkic language. In the present study,
insertion frequencies of 10 Alu loci (A25 5 0.07, APO 5
0.96, TPA25 5 0.44, ACE 5 0.37, B65 5 0.57, PV92 5
0.18, FXIIIB 5 0.52, D1 5 0.40, HS4.32 5 0.66, and
HS4.69 5 0.30) have been determined in the Anatolian
population. Together with the data compiled from other
databases, the similarity of the Anatolian population to
that of the Balkans and Central Asia has been visualized
Anatolia (the Asian segment of modern day Turkey)
has been occupied by modern humans since the lower
Paleolithic times (Kuhn, 2002). Geographically, Anatolia
is at the junction between the Balkans, the Near East
and the Caucasus, it has acted as a bridge and a reser-
voir for numerous movements of modern human beings
since very early times. It provided a suitable refuge dur-
ing the Last Glacial Maximum where modern humans
could survive (Cinnioglu et al., 2004) and it was an im-
portant passageway for the emergence and spread of the
farming industry (Renfrew, 2000; Cinnioglu et al., 2004).
Excavations on Catal Hoyuk, one of the oldest settle-
ment areas in Anatolia, revealed the presence of devel-
oped agricultural communities residing in this area as
early as 9000 BCE (Before Common Era) (Hodder, 2006).
Anatolia was populated by various civilizations, such
as the Hattians, the Hurries, the Hittites, the Phrygians,
the Lydians, the Urartians, the Medes, the Romans, the
Sassanids, the Byzantines, the Seljuk Turks, and the
Ottomans (Tambets et al., 2000). As a bridge between
the West and the East, Anatolia continued to be subject
to migrations from multiple regions throughout time.
The most recent migration took place with the Turkic
speaking nomadic groups, the part of Oghuz Turks.
Starting from the 10th Century CE, they spread away
from their homeland on the north bank of Syr Darya
(Cahen, 1968). Conventionally, the date of their arrival
to Anatolia was 1071 and was formally referred to as
Seljuks (Toynbee, 1970; Lewis, 1995). Because of these
migrations, the language of the region started to be
replaced by the Turkic language. Furthermore, migra-
tions of Turkic tribes to and around Anatolia did not
cease after the arrival of the Seljuks. Perhaps, the ear-
C 2007
V WILEY-LISS, INC.
by multidimensional scaling method. Analysis suggested
that, genetically, Anatolia is more closely related with the
Balkan populations than to the Central Asian popula-
tions. Central Asian contribution to Anatolia with respect
to the Balkans was quantied with an admixture analy-
sis. Furthermore, the association between the Central
Asian contribution and the language replacement episode
was examined by comparative analysis of the Central
Asian contribution to Anatolia, Azerbaijan (another
Turkic speaking country) and their neighbors. In the
present study, the Central Asian contribution to Anatolia
was estimated as 13%. This was the lowest value among
the populations analyzed. This observation may be
explained by Anatolia having the lowest migrant/resident
ratio at the time of migrations. Am J Phys Anthropol
136:1118, 2008. V 2007 Wiley-Liss, Inc.
C
lier movement was a facilitator for further Turkic tribe
migrations (Benedetto et al., 2001) because of the
Turkic language spoken in the region. Turkic tribal
migration into the Anatolian region continued for more
than two centuries after the Seljuks (Toynbee, 1970;
Roux, 1997). Hence, genetic contribution from the
tribes was expected to be relatively high within the
region compared with other neighboring, non-Turkic
speaking regions.
Before Seljuks, Anatolia was under the rule of Eastern
Romans but was mainly inhabited by people of Greek ori-
gin for nearly two millennia (Toynbee, 1970). The process
of change of language and religion by the Seljuks that is
assimilation of the residents but not the invaders in Ana-
tolia, was one of the puzzles of history (Toynbee, 1970).
As the part of puzzle, estimation of the relative size of
arriving nomads was the concern of many studies.
In earlier studies different molecular markers such
as proteins (Brega et al., 1998), mitochondrial DNA
Grant sponsor: Middle East Technical University Research Fund;
Grant numbers: BAP-2003-07-02-00-39 and BAP-2004-07-04-02.
*Correspondence to: Ceren Caner Berkman, Department of Bio-
logical Sciences, Middle East Technical University, 06531 Ankara,
Turkey. E-mail: cerenberkman@gmail.com
Received 31 May 2007; accepted 5 November 2007
DOI 10.1002/ajpa.20772
Published online 27 December 2007 in Wiley InterScience
(www.interscience.wiley.com).
12 C.C. BERKMAN ET AL.
Fig. 1. Map of Anatolia with the locations of the studied samples marked.
(mtDNA) (Calafell et al., 1996; Comas et al., 1996, 1998),
and Y-chromosomal markers (Wells et al., 2001; Cinnioglu
et al., 2004) were used to compare Anatolian population
with populations from Europe and Asia. Results sug-
gested that Anatolians are more closely related to Euro-
pean populations than Central Asian populations, sug-
gesting that migrations stemming from Central Asia had
little genetic effect on the current day Turkish gene pool.
Some of the newly developed computational methods
allowed scientists to investigate past population proc-
esses more deeply. For example, contribution by migra-
tions to the gene pool of populations can be partitioned
by analyzing the current pattern of genetic variation
with an admixture analysis. Many statistical methods
[ex: Roberts and Hiorns (1965), Longs (1991), Chakra-
bortys (1992), Bertorelle and Excofers (1998), and Chi-
khi et al.s (2001) methods] have been developed to esti-
mate admixture proportions from genetic data (Jobling
et al., 2004). The only prior study that used an admix-
ture analysis method to quantify Central Asian contribu-
tion to Anatolia, with respect to Balkans, was that of
Benedetto et al. (2001).
In the attempts to quantify the Central Asian contri-
bution to the Anatolian gene pool, generally unilinear
markers: maternally inherited mitochondrial DNA
(mtDNA) (Rolf et al., 1999; Benedetto et al., 2001) and
paternally inherited Y-chromosomal markers (Rolf et al.,
1999; Benedetto et al., 2001; Cinnioglu et al., 2004)
were analyzed. Estimates being between \9% (Cin-
nioglu et al., 2004) and 30% (Benedetto et al., 2001)
were in a wide range. Although these markers provide
some insights about the relative contributions of differ-
ent sexes they are haploid in nature therefore suffer
from genetic drift four times more than that of the
autosomal loci (Jobling et al., 2004). Furthermore,
migration being a population process needs to be ana-
lyzed by employing many autosomal loci to give a more
reliable genome wide estimate.
In the present study, the genetic diversity of Anatolia
based on Alu insertion polymorphisms was determined.
Then, together with the data compiled from databases,
multidimensional scaling (MDS) method was applied to
American Journal of Physical Anthropology
determine the relative similarity of the Turkish popula-
tion to that of the Balkans and Central Asia. To calcu-
late the proportion of Anatolians that can be traced to
Central Asians, Alu insertion polymorphisms, multiple
independent autosomal loci, were employed jointly thus
providing a general view of the genomic contribution of
the Turkic populations. Because the Alu markers repre-
senting unique insertions (Batzer et al., 1991) and being
under the effect of pure drift (Garcia-Obregon et al.,
2007) satised the assumptions of Chikhi et al.s (2001)
admixture method. Thus Chikhi et al.s (2001) method
was used to estimate the proportion Finally, to obtain a
more detailed perspective about the contribution of
Turkic speaking tribes within the Central AsianBalkan
region, as well as Anatolia, Azerbaijan (another Turkic
speaking population) and some other non-Turkic speak-
ing neighboring populations were also examined using
Chikhi et al.s (2001) method.
MATERIALS AND METHODS
Samples from Anatolia, DNA isolation, and Alu
insertion loci
In the present study, 10 Alu insertion polymorphisms,
namely A25, APO, TPA25, ACE, B65, PV92, FXIIIB, D1,
HS4.32, and HS4.69 were typed in 202 unrelated indi-
viduals from different regions of Anatolia (Fig. 1). Blood
or buccal samples were obtained from unrelated volun-
teer donors with their consents. The allele frequencies of
102 of the subjects had already been published (Dinc
and Togan, 2005).
Total genomic DNA from the blood samples was iso-
lated in accordance with the phenol-chloroform-isoamy-
lalcohol method (Sambrook et al., 1989). For the buccal
samples, epithelial cells were collected from inside of
both of the cheeks by scraping with a sterile brush. The
brush was placed into a 2X lysis buffer, the cells were
digested overnight by proteinase-K (20 mg/ml) and the
solution was extracted twice by phenol-chloroform-iso-
amylalcohol solution (25:24:1) by centrifuging at 10,000
rpm for 2 min at room temperature. One more extraction
 CENTRAL ASIAN ADMIXTURE IN ANATOLIA BASED ON Alu 13
TABLE 1. List of employed populations and their sample sizes
Average sample size
Region Population from 2Napopulation 2Naregion References
b
Parental Balkans Greece 212 462 Comas et al., 2004;
populations Mansoor et al., 2004
Albania 120 Comas et al., 2004
Romania 130 Comas et al., 2004
b
Central Asia Uighur 170 620 Xiao et al., 2002
Kazakhstan 155 Khitrinskaya et al., 2003
Kyrgyzstan 203 Khitrinskaya et al., 2003
Uzbekistan 92 Khitrinskaya et al., 2003
Admixed Anatoliab Anatolia 474 474 Dinc and Togan, 2005;
populations Comas et al., 2004;
Present study
Northern Ingushetia 94 373 Romualdi et al., 2002;
Caucasusb Nasidze et al., 2001
Kabardino-Balkaria 54 Romualdi et al., 2002
Cherkessia 161 Romualdi et al., 2002;
Nasidze et al., 2001
Dagestan 64 Romualdi et al., 2002;
Nasidze et al., 2001
Southern Georgiab 269 565 Romualdi et al., 2002;
Caucasus Nasidze et al., 2001
b
Azerbaijan 136 Romualdi et al., 2002;
Nasidze et al., 2001
Armeniab 160 Romualdi et al., 2002;
Nasidze et al., 2001
b
Near East Syria 137 137 Romualdi et al., 2002
a
Average sample sizes in number of chromosomes compiled for each locus.
b
Regional population that was used as a parent or an admixed population in analysis.

was performed by a chloroform-isoamylalcohol solution
(24:1), 3 M Sodium Acetate (NaAc) together with isopro-
panol were added and incubated overnight at 2208C.
The DNA was precipitated by centrifuging at 10,000 rpm
for 10 min.
The obtained DNA was used to genotype 10 Alu inser-
tion polymorphisms (A25, APO, TPA25, ACE, B65, PV92,
FXIIIB, D1, HS4.32, and HS4.69) as described in the
previous studies (Arcot et al., 1995; Batzer et al., 1996).
During amplication of the loci, hot start was applied to
improve the accuracy of primer annealing (Ueda et al.,
1996).
Compiled data for the other populations and the
loci used in comparative studies
Data for those populations from the Balkans, Central
Asia, the Near East, and the Caucasus were compiled
using the allele frequency database, ALFRED (Rajeevan
et al., 2005). Populations together with their sample
sizes are listed in Table 1.
In this study, as well as individual populations such as
the one from Syria, regional, composite populations
(such as the populations of the Northern Caucasus) were
considered (Table 1). In admixture analysis, Central Asia
was considered as one of the parental populations. The
Central Asian parental population was composed of sam-
ples from present day Kazakhstan, Kyrgyzstan, Uighur,
and Uzbekistan. These countries are located where long-
range spread of the Seljuks originated and/or these are
Turkic-speaking countries. Before the arrival of the Sel-
juks, Anatolia had a majority of Greek resident for more
than two millennia. Seljuk Turks arrived and settled in
Anatolia (Toynbee, 1970). Therefore, Balkans repre-
sented before the Turks state of Anatolia and remained
to be so after the arrival, hence, second parental popula-
tion was accepted as the Balkans. The composite popula-
tion of the Balkans was contained populations from pres-
ent day Greece, Albania, and Romania. Because no
genetic barrier was observed between these populations
(Comas et al., 2004) it seemed sensible to pool them.
Admixed populations represented present day Anatolia,
Azerbaijan, Armenia, Georgia, Syrian, and the Northern
Caucasus (which include Ingushetia, Kabardino-Balkaria,
Dagestan, Cherkessia).
Comparative studies were performed using seven of
the Alu insertion loci, which were common within the
populations under consideration, namely: A25, APO,
TPA25, ACE, B65, PV92, and FXIIIB polymorphisms.
Statistical analysis
The allele frequencies for the 10 Alu insertion poly-
morphisms (A25, APO, TPA25, ACE, B65, PV92, FXIIIB,
D1, HS4.32, and HS4.69) genotyped in Anatolia were
calculated by direct counting. The Hardy-Weinberg equi-
librium was assessed by the Fishers exact test to calcu-
late the P value using the Markov-Chain Monte Carlo
method (Guo and Thompson, 1992) provided by the Arle-
quin program (Excofer et al., 2005).
To measure the degree of genetic differentiation among
populations, GST values for seven Alu insertion polymor-
phisms (A25, APO, TPA25, ACE, B65, PV92, and
FXIIIB) were calculated using the DISPAN package pro-
gram (Ota, 1993). The GST value estimates the propor-
tion of total variance due to differences among popula-
tions. Therefore, higher GST values indicate higher
genetic differentiation among populations (Nei, 1987).
Furthermore, to visualize the genetic relatedness of the
examined populations a multidimensional scaling (MDS)

American Journal of Physical Anthropology

14 C.C. BERKMAN ET AL.

analysis (Kruskal, 1964) based on an R matrix, the nor- To compare the genetic similarity of the Anatolian pop-
malized covariance matrix of allele frequencies across ulation with that of the Central Asian populations and
populations (Harpending and Jenkins, 1973), was per- the Balkan populations seven of the 10 Alu insertion
formed using SPSS (version 13.0, SPSS, Inc., Chicago, polymorphisms (A25, APO, TPA25, ACE, B65, PV92, and
IL) statistical package. FXIIIB) which were common among the populations
In the presented study, Chikhi et al.s (2001) admix- were analyzed. For these seven loci, the frequencies of
ture estimation method implemented in LEA package the allele with Alu insertion in all of the studied popula-
program (Langella et al., 2001) was used. This method tions were given in the Table 3.
assumes that P1 and P2 are two independent parental The heterozygosity values of Anatolia (0.35 6 0.07),
populations, of size N1 and N2. These two parental popu- the Balkans (0.35 6 0.07), and the Southern Caucasus
lations contributed proportions p1 and p2 of the genes of (0.36 6 0.06) were very close to each other and lower
a third admixed population, H of size Nh, T generations than that of the Central Asian heterozygosity value
ago. The method further assumes that the parental and (0.39 6 0.06). The Northern Caucasus heterozygosity
admixed populations continued to evolve independently values with a mean of 0.31 6 0.06 were the lowest val-
after hybridization. The method estimates the admixture ues determined.
proportion (p1) of one of the parents (P1) by applying a The highest GST values were obtained for FXIIIB and
Bayesian and a coalescent-based approach. In the pres- PV92 loci (Table 3). This suggests that these two loci
ent study, P1 represents the Central Asian population have the highest power to differentiate populations/
and calculated admixture estimates (p1) based on the regions. In the present study, when populations were
posterior distribution curves correspond to the Central compared, the GST values ranged from 0.20 FXIIIB to
Asian genetic contribution to the admixed population. P2 0.02 for A25 and APO loci. On the other hand, the range
and H represent the Balkan and admixed populations of GST values of the regions (0.12 with FXIIIB0.01 with
respectively. Furthermore, for both the parental popula- A25) is narrower than that of populations. The GST aver-
tions and the admixed population, the amount of drift age over all loci between populations was 0.09 whereas
since admixture, (t1, t2, th) which is determined by the the GST average over all loci between regions was 0.06
time (T) scaled by the effective population size (Ni), was
obtained from the Chikhi et al. (2001) admixture method
and the posterior distributions were given. The highest TABLE 2. Alu insertion frequencies in Anatolia
posterior density (HPD) intervals and likelihood curves The frequency of
were obtained by using the R language (R Development Locus 2Na the Alu insert
Core Team, 2007).
A25 396 0.068
APO 394 0.957
RESULTS TPA25 402 0.435
Alu insertion frequencies ACE 404 0.371
B65 370 0.568
The Alu insertion frequencies for 10 Alu insertion PV92 372 0.183
polymorphisms in the Anatolian population are listed in FXIIIB 380 0.516
D1 366 0.396
Table 2. As can be noted, all 10 loci were polymorphic HS4.32 336 0.658
with APO (0.957) being the closest to xation. The popu- HS4.69 192 0.302
lation was found to be in Hardy-Weinberg equilibrium
a
for all analyzed loci. Sample size in number of chromosomes typed for each locus.

TABLE 3. The Alu insertion frequencies, associated heterozygosity (H) and the GST values for populations and regions
Population A25 APO TPA25 ACE B65 PV92 FXIIIB Ha
Albania 0.08 1.00 0.56 0.47 0.67 0.20 0.60 0.35 6 0.08
Romania 0.03 0.92 0.58 0.47 0.57 0.20 0.41 0.36 6 0.07
Greece 0.04 0.96 0.56 0.32 0.65 0.10 0.50 0.32 6 0.08
Balkans 0.06 0.96 0.55 0.40 0.62 0.16 0.50 0.35 6 0.07
Kazakhstan 0.07 0.92 0.53 0.60 0.35 0.55 0.53 0.39 6 0.07
Uighur 0.08 0.95 0.53 0.57 0.43 0.55 0.78 0.37 6 0.07
Uzbekistan 0.10 0.87 0.51 0.60 0.59 0.47 0.55 0.42 6 0.06
Kyrgyzstan 0.09 0.90 0.47 0.63 0.55 0.54 0.81 0.38 6 0.06
Central Asia 0.08 0.92 0.51 0.60 0.47 0.53 0.69 0.39 6 0.06
Azerbaijan 0.00 0.94 0.51 0.22 0.69 0.38 0.10 0.29 6 0.07
Armenia 0.06 0.87 0.43 0.48 0.45 0.01 0.34 0.33 6 0.08
Georgia 0.09 0.93 0.49 0.35 0.73 0.25 0.61 0.36 6 0.06
Southern Caucasus 0.06 0.92 0.48 0.35 0.64 0.22 0.43 0.36 6 0.06
Kabardino-Balkaria 0.11 0.93 0.29 0.27 0.43 0.15 0.14 0.31 6 0.05
Cherkessia 0.05 0.94 0.45 0.30 0.68 0.27 0.25 0.35 6 0.07
Dagestan 0.03 0.87 0.37 0.16 0.32 0.16 0.15 0.29 6 0.05
Ingushetia 0.07 0.94 0.22 0.34 0.21 0.13 0.00 0.23 6 0.06
Northern Caucasus 0.06 0.93 0.35 0.27 0.49 0.18 0.17 0.31 6 0.06
Syria 0.00 0.93 0.51 0.40 0.31 0.18 0.28 0.32 6 0.07
Anatolia 0.06 0.97 0.43 0.38 0.59 0.20 0.51 0.35 6 0.07
GST based on populations 0.02 0.02 0.04 0.07 0.09 0.14 0.20 Average 0.09
GST based on regions 0.01 0.01 0.02 0.04 0.05 0.09 0.12 Average 0.06
a
Average heterozygosity 6 standard error.

American Journal of Physical Anthropology

 CENTRAL ASIAN ADMIXTURE IN ANATOLIA BASED ON Alu 15

Fig. 2. Nonmetric multidimensional scaling (MDS) applied

on an obtained R matrix, based on seven Alu insertions to ana-
lyze genetic relationships among 16 populations. !: Central
Asia (present day Kazakhstan, Kyrgyzstan, Uighur, and Uzbe-
kistan); ~: The Balkans (present day Greece, Albania, and
Romania); n: The Northern Caucasus (present day Ingushetia,
Kabardino-Balkaria, Dagestan, and Cherkessia); &: The
Southern Caucasus (present day Azerbaijan, Armenia, and
Georgia); l: The Near East (present day Syria), *: Anatolia.

TABLE 4. Summary statistics for the posterior distributions of

Central Asian admixture estimates (p1) in admixed populations
Admixed population Median HPDa
Anatolia 0.127 0.0000.474
Azerbaijan 0.315 0.0000.843
Armenia 0.201 0.0000.707
Georgia 0.217 0.0000.596
Northern Caucasus 0.221 0.0000.771
Syria 0.326 0.0000.858
a
Highest posterior density intervals for p1.

indicating that the genetic variation between regions

was lower than that of the genetic variation between
populations.

Multidimensional scaling
To assess the population relationships, multidimen-
sional scaling (MDS) analysis was carried out. Popula-
tion relationships based on an R matrix (not shown)
were visualized on a two-dimensional genetic map shown
in Figure 2.
The two dimensional genetic map accounted for 94.8%
of the total variance. Central Asian populations (from
present day Kazakhstan, Kyrgyzstan, Uzbekistan, and
Uighur) were differentiated from the other populations.
The rst dimension separated the Central Asian popula-
tions from the populations of the Northern Caucasus.
Furthermore, the second dimension separated the Bal-
kan populations (from present day Greece, Romania, and Fig. 3. The posterior distribution curves of the ti 5 T/Ni
Albania) together with populations from Anatolia, Azer- distribution. (A) Central Asia, (B) Balkans, (C) admixed
baijan, Georgia, and Cherkessia from populations from populations.
Armenia, Central Asia, the Near Easter, and the North-
ern Caucasus.
mates (p1) for each of the admixed populations. Results
Admixture estimates indicated that the Central Asian contribution was 13%
for the Turkish population. Furthermore, it was observed
Table 4 presents the summary statistics for the poste- that the Central Asian contributions in the neighboring
rior distributions of the Central Asian admixture esti- regions were higher than that of Anatolia and ranged

American Journal of Physical Anthropology

16 C.C. BERKMAN ET AL.
between 20% and 33%. The Central Asian contribution
was highest in Syria and Azerbaijan. Moreover, the esti-
mates were approximately the same for Armenia, Geor-
gia, and the Northern Caucasus.
Genetic drift
Figure 3 displays the posterior distributions of the
genetic drift since admixture for the parental and
admixed populations. The same parent populations (Cen-
tral Asia and Balkans) were used for each admixed pop-
ulation. The method of Chikhi et al. (2001) gives three
estimates for drift corresponding to two parental popula-
tions and the admixed population. In the present study,
seven admixed populations were analyzed and hence
seven posterior distribution curves were obtained for
each of the parents. Therefore, for the parental popula-
tions (Fig. 3A,B) each curve corresponds to an estimate
of genetic drift obtained from the analysis of a particular
admixed population whereas the posterior distribution
curves for the admixed populations are represented sep-
arately in Figure 3C.
Almost identical and narrow curves are accepted as a
sign of limited genetic drift since the time of an admix-
ture event and thus indicate a large population size over
a long period of time (Chikhi et al., 2001). In the present
study, the posterior distribution curves for Central Asia
were wider (Fig. 3A) than the posterior distribution
curves of the Balkans (Fig. 3B).
In Figure 3C, each curve corresponds to the ti distribu-
tion of an admixed population. When the distributions
for the admixed populations were considered, the nar-
rowest posterior distribution curve was obtained for Ana-
tolia, suggesting that Anatolia had a large population
size and therefore was not greatly affected by drift (Fig.
3C). Excluding the distribution of the Anatolians, all of
the admixed populations distributions were wide (Fig.
3C).
DISCUSSION
Previous studies suggested that Anatolia had a step-
ping stone position between Asian and European popula-
tions and that it is closer to the European populations
(Calafell et al., 1996; Comas et al., 1996, 1998; Brega
et al., 1998; Wells et al., 2001; Cinnioglu et al., 2004). In
the present study, relative position of Anatolians was
addressed by employing Alu insertion polymorphisms.
The MDS plot depicted that the Anatolian population is
closest to the Balkan populations and hence results of
the present study supported the previous observations.
Furthermore, there was a clear differentiation of Central
Asian populations from Anatolian and all other analyzed
populations.
In the literature, there are attempts to quantify the
Asian genetic contribution in the Anatolian gene pool. In
these studies, Cinnioglu et al. (2004) and Rolf et al.
(1999) used the frequencies of Asian specic lineages to
quantify the Central Asian contribution to Anatolia.
Cinnioglu et al. (2004) determined the Central Asian
contribution as lower than 9% by comparing the frequen-
cies of Asian specic Y-chromosomal haplogroups C and
O3 in Asia and Anatolia. Based on mtDNA haplogroups
(H, U, K, T, and M) and allele frequencies of Y-chromo-
somal microsatellite (DXY156 13 repeat and DYS389
5 repeat) Rolf et al. (1999) also determined that there is
approximately 10% Central Asian contribution in Anato-
American Journal of Physical Anthropology
lia. To nd the Central Asian contribution to Anatolia,
an admixture analysis method has only been used in a
study by Benedetto et al. (2001). Benedetto et al. (2001)
analyzed mtDNA HVRI sequences, ve Y-STR (DYS19,
DYS390, DYS391, DYS392, DYS393) loci, and one auto-
somal microsatellite locus (TH01). On the basis of Ber-
torelle and Excofers (1998) admixture method, which
considers the effect of mutation as the main evolutionary
force, they estimated the Central Asian contribution to
Anatolia as approximately 30%.
Alu insertions are stable and selectively neutral
markers (Batzer et al., 1996). Without affects from muta-
tion and selection, Alu insertions reect the processes of
interaction between gene ow and genetic drift within
the past (Garcia-Obregon et al., 2007). Therefore, in the
present study, to quantify the Central Asian genetic con-
tribution to Anatolia instead of using the Bertorelle and
Excofers (1998) admixture method the Chikhi et al.s
(2001) admixture method was used. This method consid-
ers the effect of genetic drift as the main evolutionary
force. Through this method, the posterior distribution
curves for genetic drift were obtained. If curves for a
population are narrow and almost identical, then it is
suggested that the population experienced limited drift
since admixture. This suggests that the population has
rather large long-term population size (Chikhi et al.,
2001, 2002). For parent populations which were repre-
sented with pooled, composite populations (with 2N 5
620 for Central Asia and 2N 5 462 for the Balkans),
wide and variable posterior distribution curves were
obtained (Fig. 3A,B). Furthermore, much wider curves
were obtained for Central Asia than the Balkans sug-
gesting that Central Asia exhibited signs of higher
genetic drift than the Balkans between the time of
admixture and sampling. Previously, observation of low
diversity and high population specic Y-chromosomal
clusters in Central Asian populations lead Zerjal et al.
(2002) to a similar conclusion. For all of the examined
populations, heterozygosity levels (Table 3) were corre-
lated to the sample sizes of the populations (Table 1).
However, despite the relatively large sample size (aver-
age 2N 5 373) the lowest heterozygosity was observed in
the Northern Caucasus. Also, among the composite
populations, the Northern Caucasus displayed the high-
est effect of drift (Fig. 3). In parallel to the conclusion of
a previous study by Nasidze et al. (2001), it can be con-
cluded that isolation and genetic drift in the Northern
Caucasus are the causes of low levels of average hetero-
zygosity. Furthermore, excluding Anatolia, all of the
admixed populations exhibited effects from drift (Fig.
3C). Observing the effect of genetic drift in both parent
populations and the admixed populations supported the
decision to use Chikhi et al.s (2001) admixture method
in the present study.
The Central Asian contribution to Anatolia, with
respect to the Balkans, was determined as 13% with a
HPD interval of 0.0000.474. The calculated Central
Asian contribution was considerably lower than the esti-
mate (30%) made by Benedetto et al. (2001). At this
point of discussion, it must be emphasized that in addi-
tion to the use of a different admixture method, composi-
tion of the parent populations in Benedetto et al.s (2001)
study and that of the present study were different. On
the other hand, although the estimation methods and
analyzed molecular markers were different, the calcu-
lated admixture estimate was parallel to that of Cinnio-
glu et al. (2004) and Rolf et al. (1999).
 CENTRAL ASIAN ADMIXTURE IN ANATOLIA BASED ON Alu
It was hypothesized that if there was a specic contri-
bution related with the language replacement there
should be a higher contribution from Central Asia to
Anatolia and Azerbaijan than to that of Indo-European
speaking Armenia, Kartvelian speaking Georgia, Afro-
Asiatic (Arabic) speaking Syria, or the Caucasian speak-
ing Northern Caucasus. Hence, admixture estimates,
reecting the Central Asian contributions should be
higher in Anatolia and Azerbaijan and jointly should
appear as an island in a territory of non-Turkic speaking
populations. It was determined that the Central Asian
contribution to the other Turkic speaking population,
Azerbaijan, was 33%. Yet, the Central Asian contribution
of 13% to Anatolia was unexpectedly low when compared
with Azerbaijan and even other non-Turkic speaking
neighbors. A similar pattern was obtained when the
region was analyzed for the male-mediated Central
Asian contribution (Berkman, 2006). Did Anatolia
received fewer migrations from Central Asia compared
to the other admixed populations, or is there another
explanation?
The MDS plot clearly shows that there is a higher simi-
larity between the Balkan populations and Anatolia than
those of Azerbaijan or other non-Turkic speaking neigh-
bors (except for Georgia). In its past, Anatolia received
several migrations from the Balkans with the invasions of
the Phrygians, Ionian Greeks, Lydians, and Medes, and
with the expansions of Alexanders, the Roman and the
Byzantium Empires (Tambets et al., 2000). Therefore,
before the invasion of Turkic speaking tribes Anatolia
may have had a relatively high similarity to the Balkan
populations compared with the other admixed popula-
tions. When more recent historical relations are consid-
ered, it is suggested that the Janissaries, an army com-
posed of young, Christian boys from the Balkans, who
were employed for four centuries during the Ottoman
Empire (Goodwin, 1994) may have been partially respon-
sible for this homogenization. In the 19th century CE,
starting with the Greek war of independence (Quataert,
2004), migration movements between the Balkans and
Anatolia were accelerated. Thus these homogenization
events could be hindering the quantication of the Cen-
tral Asian genetic contribution in Anatolia. However,
another and probably more plausible explanation is that
in Anatolia the size of the population could have been rel-
atively high for multiple centuries which would increase
its resistance to large genetic effects from migration
movements. Indeed the population expansion during the
Bronze Age reached 12 million in the late Roman Period
(Russell, 1958). Hence, even if an equally high number of
migrants arrived in Anatolia, their relative contribution
would have been low. The narrowest posterior distribution
curve of genetic drift was determined for Anatolia which
supports this explanation.
The present study suggests that Central Asian contri-
bution was present in the analyzed region between the
Balkans and Central Asia with the peak in Azerbaijan.
Perhaps, Central Asian migrants arriving to the lands
between Central Asia and the Balkans were sometimes
absorbed by the host populations (such as the Northern
Caucasus), sometimes kept their identity as Turkic
speaking minorities (as is seen in Iran and Iraq today),
and other times, as seen only in Anatolia and Azerbai-
jan, managed to impose their language to a large popula-
tion. Political and military weakness of Byzantium at
the beginning of 11th Century CE (Toynbee, 1970) in
Anatolia might have facilitated the invasion of Seljuks,
17
and the adoption of Turkic language in contrast to their
neighbors.
It must be remembered that calculated contributions
are relative contributions. For example, in the present
study Central Asian contributions are in respect to the
Balkans. If they were calculated with respect to a more
Western European region, they could be higher than
those of the determined ones. Furthermore, before the
Central Asian contribution not all of the admixed popu-
lations had the equivalent gene pools, neither in number
nor in composition. Hence, estimates are not on the
same reference frame.
In conclusion, based on Alu insertion polymorphisms,
performed MDS analyses suggested that the genetic sim-
ilarity between Anatolia and the Balkans is high. Fur-
thermore, admixture analysis indicated that proportion
of Anatolians that can be traced to Central Asian is
minor (13%). Because the population size of Anatolia
was high since the Bronze Age, these observations may
be explained having the lowest migrant/resident ratio at
the time of migrations in Anatolia. Finally, the Central
Asian contributions ranging between 13% and 33% must
be considered with caution because of uncertainties
about the state of prenomadic invasions and further
local movements. Yet, a peak of Central Asian genetic
contribution in Azerbaijan might be related with lan-
guage dependent migration.
ACKNOWLEDGMENTS
We thank to C.O. Tan and O. Arun for their help in
some of the statistical analysis. We also thank to two
anonymous reviewers and E. Togan who provided con-
structive and helpful criticisms to improve the article.
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