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ARCHAEOLOGY,
ETHNOLOGY
& ANTHROPOLOGY
OF EURASIA
Archaeology Ethnology & Anthropology of Eurasia 43/4 (2015) 144–150
E-mail: Eurasia@archaeology.nsc.ru
Copyright © 2016, Siberian Branch of Russian Academy of Sciences, Institute of Archaeology and Ethnography of the Siberian Branch of the Russian
Academy of Sciences. Published by Elsevier B.V. All rights reserved
doi:10.1016/j.aeae.2016.02.015
144
A.S. Pilipenko1–3, R.O. Trapezov1, 2, and N.V Polosmak2
1Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences,
Pr. Akademika Lavrentieva 10, Novosibirsk, 630090, Russia
E-mail: alexpil@bionet.nsc.ru; Rostislav@bionet.nsc.ru
2Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences,
Pr. Akademika Lavrentieva 17, Novosibirsk, 630090, Russia
E-mail: polosmaknatalia@gmail.com
3Novosibirsk State University,
Pirogova 2, Novosibirsk, 630090, Russia
A PALEOGENETIC STUDY OF PAZYRYK PEOPLE BURIED
AT AK-ALAKHA-1, THE ALTAI MOUNTAINS*
The study outlines the results of a molecular-genetic analysis of two males from a Pazyryk burial at Ak-Alakha-1,
Ukok Plateau, the Altai Mountains, relating to mitochondrial DNA, the polymorphic part of the amelogenin gene,
autosomal STR-loci, and STR-loci of the Y-chromosome. Major lineages of both mtDNA and the Y-chromosome
are identical, indicating kinship. However, more detailed results exclude ¿ rst-degree (father–son) kinship in favor
of a more distant relationship. Phylogenetic and phylogeographic implications of the ¿ ndings are discussed. The
study demonstrates the capacities of modern paleogenetic methods and the urgent necessity of including them in
archaeological reconstructions.
Keywords: Paleogenetics, ancient DNA, mitochondrial DNA, sex-related genetic markers, autosomal STR-loci,
Y-chromosome STR-loci, Altai Mountains, Pazyryk culture.
*Supported by the Russian Science Foundation, project
No. 14-18-03124.
Introduction
Numerous Pazyryk burial mounds of the Scythian period
studied by archaeologists in Southern Siberia and the Altai
Mountains have gained the widest prominence, owing
to their unique preservation of the remains of humans,
animals, and items made of organic materials, which is
determined by favorable conditions for the environment
in burials (low average temperature, weak intensity of
microbial activity, the presence of frozen earth in some
burials, etc.). The variability of the construction of burial
facilities, the number and nature of people buried in the
mound, and the variety of grave goods and everyday
objects found in the burials, allow reconstruction of
different aspects of the social order of Pazyryk society,
special features of family organization, and related
elements of funeral practices.
At the same time, the high survival rate for remains
of the Pazyryk people (both mummified bodies and
skeletons) makes them promising objects for scienti¿ c
studies—primarily for those based on paleogenetic
methods. Apart from studying the general structure of
the gene-pool of Pazyryk populations and searching for
their genetic roots and genetic heritage in later groups
ANTHROPOLOGY AND PALEOGENETICS
A.S. Pilipenko et al. / Archaeology, Ethnology and Anthropology of Eurasia 43/4 (2015) 144–150 145
of the Eurasian population, one of the most promising
avenues in the use of paleogenetic methods comprises
reconstruction of such aspects as the degree of kinship
between humans buried in communal graves or burial
grounds, and the sexual identity of some individuals.
We have already conducted a number of studies in this
area (see, e.g., (Pilipenko, Trapezov, Polosmak, 2015;
Pilipenko et al., 2010)).
Now our attention is focused on the remains of the
Pazyryk people from mound 1 of the Ak-Alakha-1 burial
ground (Polosmak, 1994: 16–60; Naseleniye..., 2003:
17–21). The site is located in the valley of the eponymous
river at the Ukok Plateau (the Altai Mountains, Russia).
It consisted of ¿ ve mounds, three of which were studied
under the supervision of N.V. Polosmak. Mound 1, with a
diameter of 18 m (which belongs to the medium grade in
terms of size), contained the remains of two individuals.
The rather high status of the buried people, who obviously
belonged to the elite of Pazyryk society, is evidenced by a
number of features in the construction of the burial facility
and in the burial rite: presence of two log structures, the
outer structure with seven-joist À oors and the inner one
with ¿ ve-joist À oors; an accompanying burial of nine
horses in a special compartment of the outer log structure;
placement of both buried people in special cists at least
equal in their size to those from the “royal” Pazyryk
mound 4 (Rudenko, 1953: 44). Interestingly, both cists
contained armories including iron pick-axes with wooden
handles, iron daggers in wooden scabbards, gorytoi with
arrows, and bows. In the studies of the Pazyryk culture,
this mound was the ¿ rst intact and “frozen” burial of noble
equestrian warriors with fully preserved grave-goods and
fragments of costume.
Using physical anthropology techniques, it has been
established that a 45-to-50-year-old man was buried in
the ¿ rst cist, and a young woman (16- or 17-year-old) in
the second one (Chikisheva, 1994). Hence, this burial was
considered an argument for weapons-training practice and
involvement of both men and women in warlike activities;
though it was emphasized that this case was unique for the
Pazyryk culture (Polosmak, 2001: 276).
The study outlines the results of analysis of two
Pazyryk people from mound 1 of the Ak-Alakha-1 burial
ground by paleogenetic methods in order to clarify their
phylogenetic and phylogeographic characteristics (using
the mtDNA and Y-chromosome markers), the possible
degree of kinship, and sexual identity.
Materials and methods
Paleoanthropological samples. Two bones
characterized by the best macroscopic integrity were
taken from the postcranial skeleton of each of the buried
people: namely, femurs of individual 1 and a femur and
a tibia of individual 2. The different bones of each buried
person were treated a fairly large time apart, so as to
preclude the possibility of any cross-over contamination
and ensure maximum independence of results. Also,
special measures were implemented to eliminate the
possibility of cross-over contamination between the
samples taken from individuals 1 and 2.
Pre-treatment of paleoanthropological material
and DNA extraction. The methods were performed as
described previously in our studies (Pilipenko et al.,
2010, 2015; Pilipenko, Trapezov, Polosmak, 2015).
The surface of the bones was treated with bleach (5 %
solution) to destroy possible contamination from modern
DNA. Then, the external layer (approximately 1–2 mm
thick) was mechanically removed, and the sample was
irradiated with UV light for at least one hour. Fine
powder, to be used for extraction of total DNA, was
drilled from the internal layer of compact bone tissue.
The bone-powder was incubated with a 5M guanidinium
thiocyanate buffer at 65 ºC and under continuous
stirring with the use of a thermal shaker for 36–48 hours
(Pilipenko et al., 2010, 2015). DNA was isolated using
phenol/chloroform extraction, followed by precipitation
with isopropanol.
Analysis of genetic markers. The research includes
analysis of four systems of molecular-genetic markers
such as mitochondrial DNA (HVR I sequence, a kinship
marker through the female line, a phylogenetically and
phylogeographically informative marker); a portion of the
amelogenin gene (a marker used to determine the sexual
identity of remains); highly variable autosomal STR-
loci (universal markers of the degree of kinship between
the individuals); and STR-loci of the Y-chromosome
(kinship markers through the male line, phylogenetically
and phylogeographically informative markers being also
independent male sex-markers). Thus, the sex of the
buried people was identi¿ ed on the basis of analysis of
two independent marker systems (amelogenin gene and
STR-loci of the Y-chromosome), and their kinship on
the basis of three marker systems (autosomal STR-loci,
STR-loci of the Y-chromosome, and mtDNA). Two of
them (mtDNA and STR-loci of the Y-chromosome) are
phylogenetically and phylogeographically informative,
thus reflecting the genetic history of the Pazyryk
populations for female and male lineages, respectively.
The methods for genotyping each system of markers
being analyzed are presented below.
MtDNA sequence analysis. Ampli¿ cation of HVR I of
the mtDNA was performed using two different methods:
ampli¿ cation of four short overlapping fragments in one-
round PCR (Haak et al., 2005), and ampli¿ cation of one
long fragment by nested PCR (consisting of two reaction
rounds) (Pilipenko et al., 2008).
Nucleic-acid sequencing was performed with an
ABI Prism BigDye Terminator Cycle Sequencing
146 A.S. Pilipenko et al. / Archaeology, Ethnology and Anthropology of Eurasia 43/4 (2015) 144–150
Ready Reaction Kit (Applied Biosystems, USA). The
products of the sequencing reaction were analyzed with
an ABI Prism 3100 Genetic Analyzer automatic capillary
sequencer (Applied Biosystems, USA) at the SB RAS
Genomics Core Facility (Novosibirsk) (http://sequest.
niboch.nsc.ru).
The obtained sequences were compared with the
revised Cambridge Reference Sequence of human
mitochondrial DNA (rCRS) (Andrews et al., 1999).
Phylogenetic interpretation of sequences was performed
based on the current classi¿ cation of mitochondrial DNA
variability (http://www.phylotree.org) (van Oven, Kayser,
2009). The obtained results were further veri¿ ed using
the HaploGrep software tool (Kloss-Brandstatter et al.,
2011) (http://haplogrep.uibk.ac.at/). Phylogeographic
analysis of the obtained results was carried out using
data from the existing literature on mitochondrial DNA
HVR I variability in modern populations of Eurasia,
which consist of more than 25 thousand samples.
Pro¿ ling of nine autosomal STR-loci and analysis
of polymorphism of the site of the amelogenin gene
(the sex-marker of the remains) were conducted using
an AmpFlSTR® Profiler® Plus PCR Amplification
Kit (Applied Biosystems, USA) according to the
manufacturer’s instructions. Pro¿ ling of 17 STR-loci of
the Y-chromosome was conducted using an AmpFlSTR®
Y-¿ ler® PCR Ampli¿ cation Kit (Applied Biosystems,
the USA) according to the manufacturer’s instructions.
Membership of the studied STR haplotypes of the
Y-chromosome in certain haplogroups was established
using the free Haplogroup predictor software (http://www.
hprg.com/hapest5/).
Precautions against contamination and veri¿ cation
of results. All stages of work with ancient materials were
conducted in laboratory rooms especially equipped for
paleogenetic research. All laboratory staff used special
protective clothing for the clean rooms. All work
surfaces and equipment were routinely cleaned with a
5 % solution of bleach and irradiated by UV light. The
ancient samples, and tubes containing blank controls
(without adding ancient materials), underwent DNA
extraction and ampli¿ cation procedures simultaneously
in order to identify possible contamination of the
reagents and equipment used. Three independent
DNA extractions were conducted for each individual.
Ampli¿ cation was conducted several times for each
extract. The mtDNA HVR I was sequenced for all
paleogenetic laboratory staff who had access to the
clean rooms, in order to identify possible contamination
of the ancient materials. The implementation of the
above measures, with the details of the research
results, together imply the validity of the obtained
paleogenetic data.
Results and discussion
A series of seven DNA extracts was obtained for each
individual (three extracts from each ¿ rst bone and four
extracts from each second bone). The analysis has allowed
information to be obtained about the mitochondrial DNA
HVR I sequence, the presence of the amelogenin gene
allelic variants specific for sex-chromosomes in the
remains, and the allelic variants of autosomal STR-loci
and STR-loci of the Y-chromosome (Tables 1, 2).
Degree of DNA preservation in the remains and
ef¿ ciency of the marker-genotyping systems used. In
the course of the experimental works, we have obtained
abundant testimony of different degrees of DNA
preservation in the remains under study, the preservation
being substantially lower in individual 2 as compared
to individual 1. Ampli¿ cation of mtDNA by the nested
PCR method, implementation of which requires the
presence of fragments having a length of more than 300
base-pairs, has yielded positive results for all DNA
samples of individual 1, and only four out of seven for
the samples of individual 2. Meanwhile, ampli¿ cation
by short overlapping fragments was successfully
conducted for all samples, which is indicative of a
suf¿ ciently high degree of authentic DNA preservation
for ancient skeletal materials. Similar results have been
obtained for other marker systems: complete allelic
profiles of autosomal STR-loci and STR-loci of the
Y-chromosome have been reconstructed for individual 1;
while ampli¿ cation for individual 2 was less effective
(especially for loci whose ampli¿ cation products far
exceeded the length of 250 base-pairs), giving no way
of reproducing complete pro¿ les of alleles (Tables 1, 2).
Amplification of the amelogenin gene (sex-marker)
fragments was unstable as well. It is precisely with
regard to the relatively low degree of DNA preservation
in the remains of individual 2 that we decided to increase
the number of independent extracts for each individual
from two or three (the standard number) to seven. In this
context, the reproducibility of the results from different
parts of the skeleton is of particular importance. The valid
data obtained have allowed the drawing of conclusions
with the use of all four analyzed systems of genetic
markers.
Sexual identity of the buried people. The problem
of determining the sexual identity of an individual
reduces to ascertaining the presence or absence of
authentic DNA of the Y-chromosome in the remains.
The two following approaches to this problem have
been implemented within the framework of our
research: analysis of alleles of the amelogenin gene
(its variants differ for human X- and Y-chromosomes),
and genotyping of STR-loci of the Y-chromosome. For
A.S. Pilipenko et al. / Archaeology, Ethnology and Anthropology of Eurasia 43/4 (2015) 144–150 147
Table 2. Results of genotyping of pro¿ le of Y-chromosome STR-loci
Locus Genotype
Skeleton 1 Skeleton 2
DYS19 14 14
DYS385a/b 12/13 N/A
DYS389I 13 13
DYS389II 29 N/A
DYS390 23 23
DYS391 10 10
DYS392 14 N/A
DYS393 13 13
DYS437 14 14
DYS438 10 10
DYS439 10 10
DYS448 18 N/A
DYS456 15 15
DYS458 16 16
DYS635 24 24
YGATAH4 12 12
Table 1. Results of genotyping of autosomal STR-loci pro¿ le in DNA samples
Locus Genotype
Skeleton 1 Skeleton 2
D3S1358 15/16 14/15
vWA 18/18 14/16
FGA 22/22* 23/23*
D8S1179 13/13 14/18
D21S11 31/32.2 29/30
D18S51 N/A N/A
D5S818 11/12 11/11
D13S317 10/13 N/A
D7S8 8/8 N/A
Amelogenin (male) XY (male) XY (male)
Note: Genotypes indicating the absence of first-degree kinship between the buried people are
highlighted with bold.
*There is a probability of the absence of signal from the second allele (with a large number of repeats),
which would not have been ampli¿ cated owing to the degraded state of DNA.
the AmpFlSTR® Pro¿ ler® Plus PCR Ampli¿ cation Kit
(Applied Biosystems, USA), which allows simultaneous
analysis of the amelogenin gene alleles and the
profile of autosomal STR-loci, we have revealed a
considerable dependence of the ampli¿ cation-ef¿ ciency
on the degree of DNA preservation in the remains. This
method has allowed the obtaining of stable, properly
reproducible results both for the amelogenin gene and
for the STR-loci of individual 1. Ampli¿ cation of the
markers for individual 2 was unstable. Similar results
have been obtained using the AmpFlSTR® Y-filer®
PCR Ampli¿ cation Kit (Applied Biosystems, USA).
Nevertheless, both approaches have demonstrated the
presence of DNA of the Y-chromosome in the remains.
Thus, molecular-genetic data bear evidence of the male
sex of both buried people from mound 1 of the Ak-
Alakha-1 burial ground; which is inconsistent with the
results of sexual identi¿ cation of individual 2 by the
148 A.S. Pilipenko et al. / Archaeology, Ethnology and Anthropology of Eurasia 43/4 (2015) 144–150
physical anthropology techniques (Naseleniye..., 2003:
19). In our opinion, this may be caused by a young
age for this individual (16 years old), since the sexual
identi¿ cation of buried adolescents by their skeletal
morphology is rather dif¿ cult in certain cases. Thus,
the obtained data allow the conclusion that mound 1 of
the Ak-Alakha-1 burial ground accommodates a paired
burial of 45–to-50-year-old and 16-year-old men.
Results from the analysis of the structure of
mtDNA samples. The studied individuals were
characterized by an identical structure of DNA
HVR I. The HVR I haplotype structure 16093C-16129A-
16223T-16298C-16327T gives unambiguous evidence
that this structural variant of mtDNA belongs to the
Eastern Eurasian haplogroup C (most probably, to
haplogroup C4a1), falling into macrohaplogroup M.
According to the results of phylogeographical analysis,
variants of haplogroup C4 with an identical or similar
structure of haplotypes are common both among the
population of Southern Siberia (including Altai) and
Central Asia (including Northern China), and also among
the autochthonous populations of more remote northern
regions of Siberia (Pilipenko, Trapezov, Polosmak,
2015; Derenko et al., 2003, 2007; Starikovskaya et al.,
2005; Metspalu et al., 2004). Thus, the revealed variant
is characteristic of modern indigenous peoples of the
region under consideration.
Analysis of data on the composition of mtDNA
lineages among the tribes of the Pazyryk culture has
demonstrated that the discovered variant is common
in the gene-pool of the Pazyryk people, and presents
one of its typical components. In particular, similar and
identical variants of haplogroup C4 have been revealed
among the people buried in the Ak-Alakha-3 (Pilipenko,
Trapezov, Polosmak, 2015) and Ak-Alakha-5 sites
located at a small distance from the Ak-Alakha-1 burial
ground; and also in other, more geographically remote
Pazyryk burial grounds, such as Alagail in the Middle
Chuya River (unpublished data of the authors). The
high frequency of occurrence of the considered mtDNA
variant in the gene-pool of the Pazyryk people in Altai
diminishes its signi¿ cance as a possible kinship marker
through maternal lineage between the individuals buried
in mound 1 of the Ak-Alakha-1 burial ground.
Allelic pro¿ le of STR-loci of the Y-chromosome.
This has been used within our research as one of the sex-
markers of the remains (see above), as a kinship marker
between the individuals through the male lineage,
and as a phylogenetically and phylogeographically
informative marker reÀ ecting the history of the male
part of the Pazyryk population. We have succeeded in
reconstructing the complete pro¿ le of 17 STR-loci of the
Y-chromosome for individual 1. Owing to a relatively
low degree of DNA preservation in the remains of
individual 2, the data for him were only obtained
on the basis of 12 STR-loci out of 17 (Table 2). The
allelic variants for STR-loci successfully genotyped in
both cases are identical. This suggests that the studied
individuals are very likely to belong to the same lineage
of Y-chromosome, which implies their close kinship
through the male line.
The Y-chromosome structure can be studied by two
methods for the purpose of conducting phylogenetic
and phylogeographic analysis. One of them consists in
analyzing the SNPs of the Y-chromosome, which are
the markers of its membership in speci¿ c haplogroups
and subgroups; another consists in genotyping the set of
STR-loci and determining the phylogenetic membership
using special software, which reveals correlation
between STR-pro¿ les and phylogenetic clusters of the
Y-chromosome. We have used the latter. The complete
allelic pro¿ le obtained based on 17 STR-loci has made
it possible to determine that the studied variant of the
Y-chromosome belongs to haplogroup N (according to
the data of Haplogroup Predictor software, the probability
is 100 %). This haplogroup appeared in Southeastern
Asia, but subsequently had been evolving in Southern
Siberia for a long time (Kharkov, 2012). The pathway
of distribution of its subgroups across other Eurasian
regions, predominantly at the northern latitudes from
Eastern Europe to the Far East, ran exactly through the
Altai-Sayan highlands. Subgroups of haplogroup N have
their phylogeographic speci¿ cs, many of them formed
in the Southern Siberia, and it is exactly in this region
that the greatest variety of variants of this haplogroup is
observed. Accurate ascertaining of whether the studied
variant of the Y-chromosome belongs to subgroups of
haplogroup N requires additional analysis of its SNP
markers. This problem will be solved in the course of
large-scale studies of the variety of Y-chromosome
lineages in the gene-pool of the Pazyryk populations
in Altai, which are currently under way. At this stage,
we restrict ourselves to stating that the Y-chromosome
variant revealed in the buried people from mound 1
of the Ak-Alakha-1 burial ground is characteristic for
the studied region, and adjoining regions, of Northern
Eurasia; which is in good agreement with the above data
on their mtDNA structure.
Thus, on the basis of the results of analysis of
markers with uniparental inheritance (mtDNA and
Y-chromosome), we have established the probability
of close kinship between the studied individuals from
the paired burial both through the female and male
lineages. In such a situation, data on the pro¿ le of
autosomal STR-loci can be of crucial importance.
They suggest that the individuals under study could not
be relatives in direct descent; and in this case, taking
into account the sex of buried men, they could not be
father and son. This may be a different variant of close
kinship.
A.S. Pilipenko et al. / Archaeology, Ethnology and Anthropology of Eurasia 43/4 (2015) 144–150 149
Burial in mound 1
of the Ak-Alakha-1 burial ground
in the light of molecular-genetic data
The obtained molecular-genetic data allow interpretation
of the special features of burial in mound 1 of the Ak-
Alakha-1 burial ground in a new fashion. Of great
importance is identi¿ cation of the male sex of the young
individual. In this regard, it becomes apparent that both the
men’s clothes in which the buried individual was dressed
(woolen breaches, a belted fur coat, and a felt helmet with
wooden ¿ gures of animals) and men’s headdress (that
is, the absence of a wig, a women’s headdress) are sex-
markers in disputed cases. Earlier, based on the physical
anthropology data, this individual was considered a young
woman. However, her physical traits approaching male
characteristics were emphasized, “the skull is very large
and seems to be massive... the brain-case is very long and
very high... the jaw bone is very massive... The bones of
the postcranial skeleton are very long and compare well
with the bones of a male skeleton in terms of absolute
dimensions and massiveness index... The body is very
long” (Chikisheva, 1994: 173).
The new data also allow revision of the possible kinship
relationship between the buried people. The paired burial
of an adult man and a young woman was considered as a
burial of either spouses, or a father and his daughter. The
genetic data rule out both of these proposals. Obviously, the
men buried together are indeed related by a certain degree
of kinship. This is evidenced by a rather rare situation
when individuals from a paired burial demonstrate identical
variants of both mtDNA and the Y-chromosome, which
points to a potential kinship through the maternal and
paternal lineages, respectively. Taking into account the sex
of the buried people, it can be assumed that they are father
and son. However, the data on autosomal STR-loci, which
allow checking of the fact of ¿ rst-degree kinship, rule out
this proposal. Obviously, the relationship between the
studied individuals is more distant (and dif¿ cult to analyze)
(for example, uncle and nephew)*. Detailed reconstruction
and probabilistic assessment of such kinship requires
representative data on the frequencies of allelic variants of
STR-loci and the Y-chromosome in the Pazyryk population,
to which the buried men belong. At present, we have
proceeded to accumulate these data in order to improve
the probability of establishing a distant degree of kinship
between individuals from Pazyryk burials.
The situation in which all basic variants of kinship
relationship between the buried men were rejected
subsequent to the results of paleogenetic analysis
demonstrates the urgent necessity of making such
archaeological reconstructions more objective. This can
be achieved through widespread use of paleogenetic
methods, which, in spite of the existing restrictions, allow
testing of the simplest kinship models. It is just these
models that are generally used by archaeologists in such
reconstructions.
Notably, two men were placed in the same grave as
a consequence of both their kinship and a certain social
standing. However, their burial together was caused by
the existing situation: both of them (probably, each for his
own reason) did not survive the winter and were buried
in the spring, when this became possible. Most likely, the
Ukok paired burials are explained by these circumstances.
And now we have the possibility of verifying this fact.
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Received October 26, 2015.
