First ancient DNA analysis of mummies from the post-Scythian Oglakhty cemetery in South Siberia

doi:10.21203/rs.3.rs-1993191/v1

Download PDF

Article

First ancient DNA analysis of mummies from the post-Scythian Oglakhty cemetery in South Siberia

https://doi.org/10.21203/rs.3.rs-1993191/v1

This work is licensed under a CC BY 4.0 License

Version 1

posted

You are reading this latest preprint version

The Minusinsk Basin in Southern Siberia had unique conditions for the development of ancient societies, thanks to its geographical location, favorable climatic conditions, and relative isolation. Located at the northern periphery of the eastern Eurasian steppe, surrounded by the Altai-Sayan Mountains this area witnessed numerous ancient human migrations with specific types of interaction between outside and local archaeological cultures.

The genomic history of the human population of Southern Siberia from the Chalcolithic to the middle Bronze Age has been relatively well described in the recent genome-wide studies, while the genetic ancestry of populations, represented by diverse archaeological cultures of the Late Bronze and Early Iron Ages, remains a blank spot for modern paleogenomics.

Here, for the first time, we present two ancient nuclear genomes of the individuals buried in the Oglakhty cemetery (early Tashtyk culture, 2nd to 4th centuries AD). Our pilot study is undertaken within a multidisciplinary project on this noteworthy site with well-preserved organic remains and provides fresh paleogenomic data on the ancient societies of Southern Siberia.

Ancient DNA studies of geographically and chronologically disparate human population groups are of the utmost importance for understanding their development and interactions which led eventually to the contemporary picture of human diversity and resettlement. Despite significant progress and accumulation of genomic data for ancient archaeological cultures in Eurasia ^1–4, detailed data describing the genesis and evolution of populations associated with single archaeological culture and their sequences in certain historical regions are still insufficient ^5–7.

Anatomically modern humans have inhabited the semi-arid steppe and forest-steppe regions of Southern Siberia since the Late Paleolithic period ⁸. During the Chalcolithic, the Bronze and Early Iron Age, this region became home to several human populations who greatly influenced the cultural and technological development and exchange processes in the middle latitudes of Eurasia and left a rich archaeological heritage ⁹.

The Minusinsk Basin is a mountainous-steppe area in the northern part of the Altai-Sayan plateau, which is situated at the juncture of the Siberian taiga and the mountains and steppe of Central Asia, on both sides of the middle reaches of the Yenisei River. This region corresponds to the modern territories of the Republic of Khakassia and the southern part of the Krasnoyarsk region in Russia. The Minusinsk Basin’s ancient human history had much in common with other ancient societies of the Altai-Sayan plateau but stood out from them due to its milder climate and less accessible location. The Minusinsk Basin facilitated a complex economy and relatively safe life for many ancient human societies because of its favorable conditions and abundance of natural resources ¹⁰.

The Minusinsk Basin was a place where different archaeological cultures with complex ideologies, advanced technologies and distinctive artistic activity flourished. This region is world-famous for its rich and elaborate rock art of various epochs, e.g. the monumental steles of the Okunev culture ^9,11−14 or bronze artefacts of the Tagar culture ^15,16. The Tes’ and early Tashtyk cultures in the later historical period are also well-known on account of their elaborate funeral customs including mummification, recreating the bodies, head modification, and face masks (Fig. 1B; Fig. 1C) ^17–19. Interactions between archaeological cultures from adjacent and remote regions, including the Eastern European steppe, Central Asia, and the Chinese plain have been reliably attested by parallels in the local material culture, arts and ritual traditions since the Chalcolithic period ¹².

The Minusinsk Basin has always been a well-populated area, leading to a very high density of archaeological sites ^20,21. Many of them are still clearly visible in the steppe due to an age-old tradition of creating enclosures or other above-ground constructions from large stones and slabs. Notably, the Minusinsk Basin became the first region in Russia where archaeological excavations were carried out –as far back as 1722 ²². The first periodization of antiquities from the Early Bronze to the Middle Ages was established in the 1920s based on local material culture ²⁰, laying a reliable foundation for the modern chronological system of archaeological sites/artefacts of the Eurasian steppe. Moreover, this system is still in use for the study of the archaeology of the Eurasian steppe. The material culture, art and burial rituals of the ancient societies in this part of Southern Siberia have been extensively studied whereas the human population history is still somewhat sparsely established for different historical periods ¹².

Patterns of interaction between migrant and local human populations changed over time in Southern Siberia²³. Recent studies, which combined genetical, archaeological and physical anthropological data, have shown that the exchange of local populations caused by migrations into the Minusinsk Basin was almost total during the Chalcolithic Period and the Early Bronze Age. In the Late Bronze Age (LBA), however, the character of interaction between local and incoming groups changed, and more genetic and cultural continuity of ancient societies can be observed from the mid-2nd millennium BC ¹². Extensive archaeological data from the period between the LBA (represented by several archaeological horizons previously known as the Karasuk culture) and the Early Iron Age (Tagar and Tes’ cultures) suggest several local migrations into this region, and archaeological materials indicate both local and outside ancestry for each of the corresponding chronological horizons. Genetic information is very scarce for them, and nuclear genomic data from the LBA and Early Iron Age archaeological cultures of the Minusinsk Basin are of utmost importance for building the overall picture of the genomic ancestry in this region.

The Tashtyk culture is the post-Scythian Iron Age archaeological culture of the Minusinsk Basin which followed the Tagar culture ¹⁸. It is viewed as having had a nomadic pastoralist economy supplemented by hunting-gathering and small-scale agriculture. Cultural innovations and a slight admixture of East Asian craniological features on early Tashtyk skulls and funeral masks led to the idea of some mass migration from Central Asia which possibly took place at the turn of the Christian era ^24–26. This East Asian craniological impact is now seen as considerably exaggerated for the early Tashtyk population ²⁷ and requires further study. The interactions between local and various incoming human groups at that time are currently seen as a complex phenomenon, suggesting their co-existence in Southern Siberia during this historical period ^28,29. Significant innovations documented in the burial rituals and grave goods of the early Tashtyk sites are still considered to be the result of migrations from Central Asia, likely from the areas adjacent to the Tarim Basin, but the question remains open ³⁰.

To date, only a few studies on the genetic ancestry of the early Tashtyk culture have been carried out using Y-chromosome short tandem repeat (STR) analysis and mtDNA hypervariable region 1 (HVR1) sequencing. A study of 4 female and 1 male individuals from the Abakano-Pérévoz I cemetery provided information on their mitochondrial DNA (mtDNA) and Y-chromosome haplogroups³¹. C, HV, H, N9a, and T1 mtDNA and R1a Y-chromosome haplogroups were described for these individuals³¹.

The Oglakhty cemetery is one of the well-studied Tashtyk burial complexes, situated 40 km north of the city of Abakan (Fig. 1A). This archaeological site with well-preserved organic artefacts and anthropological remains provides exceptionally detailed information on funeral rituals and peculiarities of material culture, which is usually lost. People were buried in the Oglakhty graves according to different rites – mummification and cremation with the cremated remains (cremains) being placed into full-size human-like mannequins made from leather and grass ^30,32,33. The graves are thought to be family ones as opposed to the previous and following periods’ collective burials containing tens or hundreds of dead. The biritualism of the early Tashtyk graves is a unique feature and possible evidence of the complex structure of this society made up of people with different origins and traditions.

Methods of archaeology and craniometry have up to now been unable to trace the core region, cultural and biological characteristics of the incoming human group that was incorporated into the early Tashtyk society. The family kinship of the dead from the Oglakhty graves cannot be established by these methods either, nor can the continuity of the early Tashtyk population from the previous local groups. Genetic studies of the individuals from the Oglakhty cemetery are capable of shedding light on these crucial questions.

Here we present nuclear genomes of two human mummies of the early Tashtyk culture (1st − 4th centuries AD) buried in the Oglakhty cemetery, grave 4 (Fig. 1D). A child mummy from the same grave has also been analyzed but its endogenous DNA content proved insufficient for cost-effective DNA sequencing, so we cannot take that information into consideration. In addition, the ancient DNA identification of animal leather and fur found in grave 4 in elements of the clothing and a mannequin was covered in this study.

DNA sequencing statistics

Anthropological material from male (KE9609), female (LC8544), and child (PI5222 and QR6400) human individuals was selected for the sampling of bone powder. We carried out several extractions that were used for library preparation and DNA sequencing. The child (PI5222 and QR6400) was excluded from further analysis after test-sequencing because it had a low percentage of endogenous DNA (Supplementary Table 1). The total number of reads generated for two DNA libraries varied from 99 Gb (LC8544) to 148 Gb (KE9609) per DNA library (Supplementary Table 1). The proportion of nucleotides with a quality of at least 30 (Phred ≥ 30) was 93% and 94% for KE9609 and LC8544 specimens, respectively. The high-quality SNPs (with p-value < 0.05; coverage > 5×) were identified against the human reference genome (GRCh37.p13). A total of 97,037 and 150,663 SNPs for KE9609 and LC8544 specimens were found, respectively.

Mitochondrial DNA and Y-chromosome haplogroup identification

MtDNA haplogroup analysis of the two adult Oglakhty individuals showed that they had a potential maternal kinship and belonged to the same I4a1 subclade of mtDNA haplogroup I. Previously, this subclade had been detected only once in the Minusinsk Basin – in an individual of the Karasuk culture (RISE 493, Sabinka II, grave 20) from the LBA (Supplementary Table 2) ¹. It has not yet been found in any other analyzed individuals from the period of the Tashtyk culture or its immediate predecessor. Nevertheless, the I4 haplotype was described in an individual of the Tagar culture (Tchernogorsk archaeological site) ³¹. Interestingly, this haplogroup was also found in Viking graves of the 9th–12th centuries and is currently represented in Europe, North Africa, and Western Asia ³⁴.

The Y-chromosome haplogroup was identified for the male individual (KE9609) as R1a1a subclade based on M738, CTS3230, M747 polymorphisms. The R1a haplogroup was common for the Eurasian steppe and North Caucasus populations during the Bronze and Early Iron Ages. It became widely spread from the Andronovo cultural-historical commonality (17th − 15th centuries BC) onwards. This haplogroup is usually associated with the Indo-European migrations across Eurasia. The R1a haplogroup was identified in ancient burials at the Scythian and Sarmatian archaeological sites of the 1st millennium BC – first centuries AD ^2,3,35−37

In the Minusinsk Basin, the R1a haplotype has been found in representatives of the Andronovo culture and subsequent population groups from the LBA and the Tagar cultures ^1,31,38 (Supplementary Table 3).

Genome-wide autosomal marker data analysis

We merged the newly generated SNPs dataset for the two Oglakhty individuals with previously published genotypes of ancient inhabitants of the Eurasian steppe and Central Asia from the 1240K + HO database. We limited the study through the selection of those who are possibly more closely genetically/historically/geographically related to the Tashtyk culture individuals than others (Supplementary Dataset 1–2). This combined dataset was used for PCA, ADMIXTURE, and f3-statistics analyses to assess the genetic relationship between two Oglakhty individuals and other ancient Eurasian archaeological cultures.

Based on the PCA plot, we clearly showed that the Tashtyk specimens were genetically close to individuals from the precedingTagar culture as well as to inhabitants of Eastern Kazakhstan (in the period 1000 BC – early centuries AD) and Kyrgyzstan (first half of the 1st millennium AD) (Fig. 2; Supplementary Fig. 2). Interestingly, among modern populations Tashtyk individuals (KE9609 and LC8544) share genetic ancestry with the present-day Chuvash people (Fig. 2B) who are predominantly native to the Volga-Ural region of Russia and are related to the Finno-Ugric group ³⁹.

A comparable picture was obtained from the ADMIXTURE analysis. The two Oglakhty individuals share a similar genetic profile with representatives of the preceding Tagar culture and people from the Tian Shan foothills (modern territory of Eastern Kazakhstan and Kyrgyzstan) who lived in these territories during the foregoing or adjacent historical periods (Fig. 3). F3-statistics analysis was carried out with the African Mbuti population as an outgroup could not identify any ancient genotype or group of ancient genotypes that had a significant genetic influence on the two Oglakhty specimens (Supplementary Dataset 3). It follows that further more detailed genome-wide data are needed from other Tashtyk individuals from the Minusinsk Basin, as well as other specimens from Central Asia, especially the Tarim Basin with historically close dating due to the previously described parallels between the material culture of Tashtyk and Tarim cultures ³⁰.

The Tashtyk archaeological culture is one of the post-Scythian Iron Age cultures of Southern Siberia that left numerous archaeological sites ¹⁸. To date, information about the genetic origin, kinship analysis and genetic diversity of Tashtyk culture has been limited to only one published study based on mtDNA and Y-chromosome haplogroup analyses ³¹. However, these types of genetic markers do not allow us to evaluate several questions raised by archaeologists^1,31,40,41.

In this study, we present the first nuclear genome analysis of early Tashtyk culture individuals buried in the Oglakhty cemetery in the 3rd century CE. We reconstructed the ancient genomes of two individuals – male (KE9609) and female (LC8544) –from grave 4, while a third aDNA analysis – of a child – was unsuccessful.

MtDNA haplogroup I4a1, which was identified in both studied individuals from grave 4 of the Oglakhty cemetery, may point to maternal kinship between the two mummies. However, genome-based kinship analysis between individuals from grave 4 of the Oglakhty cemetery was not carried out because it requires additional nuclear genomes from the Tashtyk culture as a referral group. The I4a1 mtDNA haplotype has been previously observed in a member of the Karasuk culture (RISE 493, Sabinka II, grave 20) and another sub-haplotype (I4) was found for Tagar culture from the Minusinsk Basin (Supplementary Table 2) ^1,31. Notably, C, HV, H, N9a, and T1 mtDNA haplogroups were described for the early Tashtyk culture individuals from the Abakano-Pérévoz I cemetery. The same haplogroups were observed in human specimens from the preceding Tagar culture ^2,31,40 and they are widespread across Eurasia ^1,4,35,42. Both Tagar and Tashtyk culture individuals have mixed Western (European) and East Asian mtDNA pools ^31,41.

The KE9609 male individual has R1a1a Y-chromosome haplogroup, which is common for the Eurasian steppe population from the middle Bronze Age to the Early Iron Age (Supplementary Table 3) and is usually associated with the Indo-European migrations ^2,3.

In general, the genomic data of two Oglakhty mummies presented together with previously published genetic information on the early Tashtyk culture individuals ³¹ demonstrate their genetic connections with members of the preceding local Siberian cultures – Karasuk and the Tagar archaeological cultures. It seems, that the Oglakhty specimens also have a genetic contribution from the ancient inhabitants of Eastern Kazakhstan (in the period 1000 BC – early centuries AD) and Kyrgyzstan (first half of the 1st millennium AD), which is consistent with the archaeological data ³⁰.

Our preliminary results are consistent with the idea that people buried as inhumations or mummies in the Early Tashtyk cemeteries followed the funerary traditions of the previous population of the Minusinsk Basin associated with the Scythian-type Tagar culture and could therefore be their cultural successors ^25,26. Whether the cultural heritage corresponds to the genetic ancestry is still a matter for discussion, and more paleogenomic data of Tashtyk individuals from the Minusinsk Basin, as well as other genomic datasets of specimens from Central Asia, especially from the Tarim Basin in historically close periods, are required to trace the genetic ancestry of the early Tashtyk mummies. The genetic kinship between individuals buried using different rites (mummified and cremated) in the Oglakhty cemetery (grave 4) is still under question. We anticipate that further efforts and novel methods of ancient DNA extraction from the cremains will allow us to shed light on this archaeological riddle.

Sample description. Anthropological material

The proximal phalanx of the little finger of the left hand from the male individual (KE9609), the middle phalanx of the little finger of the left hand from the female (LC8544), and a tooth (PI5222) and a metatarsal bone (QR6400) of a child were taken for ancient DNA (aDNA) analysis (Supplementary Table 1). A description of the Oglakhty cemetery and grave 4 and its chronology are presented in Supplementary Notes 1–2 and Supplementary Fig. 1.

Ancient DNA extraction, DNA library preparation, and genome sequencing

The anthropological material was used for meticulous sampling and grinding to small fragments in the extra-clean room DNA facilities of Genotek Ltd. (Moscow, Russia). Ancient DNA was extracted from the bone powder using a phenol-chloroform extraction method with prior demineralization. Several independent ancient DNA extractions were performed. The concentration of DNA extracts was measured using Qubit 3.0 (Thermo Fisher Scientific, USA). Custom Illumina library preparation method, including preliminary uracil DNA glycosylase, UDG (New England Biolabs, USA) treatment, was used (Supplementary Note 3). The amplified DNA libraries were quantified using a High Sensitivity DNA Kit on a 2100 Bioanalyzer instrument (Agilent Technologies, USA). Multiple negative controls were used during the aDNA extraction and DNA library amplification. The negative controls did not contain DNA after the DNA extraction, and the DNA libraries prepared from the negative controls were not amplified. DNA of all researchers involved in this study at the aDNA facilities was taken to analyze potential contamination of the DNA extracts. The results showed that the mtDNA and Y-chromosome haplogroups identified for the Oglahty individuals did not match those of any researchers. Rapid Run mode of Illumina HiSeq 2500 sequencing system (Illumina, USA) with paired-end reads of 150 bp length was used for whole-genome sequencing (WGS).

Bioinformatics and statistical analyses of ancient DNA sequencing data

The paired-end reads were obtained in FASTQ format. We used clumpify v38.91 from the BBMap package (www.sourceforge.net/projects/bbmap/) to remove PCR-duplicates from the sequencing data. Adapter sequences and low-quality DNA reads (phred ≤ 30) were trimmed with cutadapt v3.2 ⁴³. Paired DNA reads were merged using flash v1.2.11 ⁴⁴. Cleaned and merged reads were mapped to the human nuclear reference genome (GRCh37.p13) and human mitochondrial Cambridge Reference Sequence (NC_012920.1, rCRS) using bwa mem v0.7.17 ⁴⁵. Additional removal of duplicates was carried out after the mapping using GATK v4.1.9.0 ⁴⁶.

Mitochondrial DNA contamination test and mtDNA haplotype identification were carried out using the Haplocheck tool ⁴⁷ with the default parameters (--level 0.01, --mapQ 30, --baseQ 20, --deletions). MtDNA tree Build 17 (18 Feb 2016) database was also used for mtDNA haplotype identification. Autosome and Y-chromosome SNPs were called using samtools v1.11 (-C 30, -Q 20 parameters) ⁴⁸. Y-chromosome haplogroup was identified then by ISOGG v15.73 ⁴⁹.

Pseudo-haploid SNP calls were generated for randomly selected reads for each Oglakhty individual using apulldown.py script from the gdc3 package (https://github.com/mathii/gdc3) with default parameters. The 1240K database (1240K + HO) v44.3 (https://reich.hms.harvard.edu/) was selected as a reference panel of genotypes. We combined our newly generated ancient data for the two Oglakhty specimens with other ancient individuals from populations of Eurasian steppe and Central Asia and modern human populations. Two genotype datasets were used for PCA analysis. The first comprises a limited set of data (954), presumably the genetically closest genotypes to the Tashtyk individuals studied (Supplementary Dataset 1). The second includes an extended number of genotypes – 1504 (Supplementary Dataset 2). Genotype calling was carried out for v44.3_HO_public_modif.snp.

Pseudo-haploid VCF file for two Oglakhty individuals was converted to PED format in the plink v1.9 (--recode ped parameter), and then transformed to the EIGENSTRAT format using convertf and merged with previously selected genotypes from the 1240K database using mergeit tool from the EIGENSOFT package ^50,51. The smartpca tool from the EIGENSOFT package ^50,51 was used for principal component analysis (PCA) for a combined ancient individual genotype dataset inhabited Eurasian steppe and Central Asia and several modern human populations (Supplementary Dataset 1–2).

The qp3Pop tool with default parameters from ADMIXTOOLS v1.3.0 package ⁵² was used for f3-statistics analysis (Mbuti population genotypes were used as an outgroup). ADMIXTURE analysis was used to assess what contribution one of the K putative “donor” populations has made. To select the optimal K, the ADMIXTURE analysis was launched with 5-fold cross-validation and different values of K (3, 4, 6, 8, 10, 11, 12, 14) with the c (stop) parameter equal 0.9. Finally, ADMIXTURE analysis was performed with the number of ancestral populations (K) equal to 11. The ancient populations which have possible historical connections to the Tashtyk culture as well as populations which showed the least genetic distances from the Oglakhty individuals studied (based on PCA) were used for ADMIXTURE and f3-statistics analysis.

Author Contributions

A.V.N., S.V.P., A.S.R., A.Y.I. and V.V.I. conceived and designed experiments; S.V.P. and N.A.P. performed sampling; N.A.P., A.A.K., M.I.S., N.A.P. and A.Y.I. extracted ancient DNA, performed library preparation and sequencing; A.V.N., N.A.P., K.I.A., N.V.N. A.S.R. and E.O.V. analyzed the data, A.V.N., S.V.P. and A.V.P. wrote original draft; all authors participated in writing, review and editing.

Acknowledgements

The authors are grateful to Prof. Mikhail B. Piotrovsky (State Hermitage Museum, Saint-Petersburg, Russia), Aleksandr S. Voloshin, Oleg V. Zherebtsov (Solopharm (Grotex LLC), Saint-Petersburg, Russia), and Prof. Vadim V. Volkov (European University at St. Petersburg, Saint-Petersburg, Russia) for their ongoing support.

Author information

European University at St. Petersburg, Shpalernaya Ulitsa 1, 191187, Saint-Petersburg, Russia

Artem V. Nedoluzhko, Svetlana V. Pankova

State Hermitage Museum, Dvortsovaya nab. 34, 190000, Saint-Petersburg, Russia

Svetlana V. Pankova

Genotek Ltd., Nastavnicheskiy Lane 17-1, 105120, Moscow, Russia

Nikolay A. Plotnikov, Anna A. Kim, Mikhail I. Shulpin, Nadezhda A. Pogodina, Natalia V. Nenasheva, Alexander S. Rakitko, Ekaterina O. Vergasova, Kim I. Adameyko, Anna Y. Ilinskaya, Valery V. Ilinsky

Institute for the History of Material Culture, Russian Academy of Sciences, Dvortsovaya nab. 18, 191186, Saint-Petersburg, Russia

Andrei V. Poliakov

Data availability

All raw reads and BAM files for KE9609 and LC8544 individuals are publicly available at the NCBI BioProject: PRJNA872874

Competing interests

The authors declare that they have no competing interests.

Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172, doi:10.1038/nature14507 (2015).
Damgaard, P. B. et al. 137 ancient human genomes from across the Eurasian steppes. Nature 557, 369–374, doi:10.1038/s41586-018-0094-2 (2018).
Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211, doi:10.1038/nature14317 (2015).
Wang, C. C. et al. Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions. Nat Commun 10, 590, doi:10.1038/s41467-018-08220-8 (2019).
Fowler, C. et al. A high-resolution picture of kinship practices in an Early Neolithic tomb. Nature 601, 584–587, doi:10.1038/s41586-021-04241-4 (2022).
Erlikh, V. R. et al. Potential maternal kinship among humans from the Northern Caucasus “post-dolmen” burials. Journal of Archaeological Science: Reports 39, 103198, doi:10.1016/j.jasrep.2021.103198 (2021).
Schroeder, H. et al. Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave. Proc Natl Acad Sci U S A 116, 10705–10710, doi:10.1073/pnas.1820210116 (2019).
Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449, doi:10.1038/nature13810 (2014).
Polyakov, A. V. Overview of the Results of the Initial Stage of Paleogenetic Research Into the Population of the Minusinsk Hollow in the Bronze Epoch. Teoriya i praktika arkheologicheskikh issledovaniy 26, 91–108, doi:10.14258/tpai(2019)2(26).-<background-color:#D279AA;>08</background-color:#D279AA;> (2019).
Vadetskaya, E. B. Archaeological monuments in the steppes of the Middle Yenissey. (Nauka, 1986).
Leont'ev, N. V. & Kapel'ko, V. F. Steinstelen der Okunev-Kultur. (Verlag Philipp von Zabern, 2002).
Poliakov, A. V. Chronology and cultural genesis of the Paleometal epoch sites in Minusinsk basins. (Institute for the History of Material Culture RAS, 2022).
Poliakov, A. V. & Lazaretov, I. P. Current state of the chronology for the palaeometal period of the Minusinsk basins in southern Siberia. Journal of Archaeological Science: Reports 29, 102125, doi:10.1016/j.jasrep.2019.102125 (2020).
Poliakov, A. V. & S., S. Modern Data on the Bronze Age Radiocarbon Chronology in the Minusinsk Basins. Vestnik of St Petersburg University. History 66, 934–949, doi:10.21638/11701/spbu02.2021.314 (2021).
Piotrovsky, B. B. & Zavitukhina, M. P. Frozen Tombs: The Culture and Art of the Ancient Tribes of Siberia. 102 (British Museum Publications, 1978).
Zavitukhina, M. P. Ancient art of the Yenisey river. The Scythian time / Publication of one collection. (Iskusstvo, 1983).
Kuzmin, N. Y. Pogrebalnye pamyatniki khunno-syanbiiskogo vremeni v stepyakh Srednego Eniseya: Tesinskaya kultura. (Aising, 2011).
Vadetskaya, E. B. The Tashtyk epoch in the ancient histoty of Siberia. Vol. 7 440 (Petersburg's Oriental Studies Print, 1999).
Vadetskaya, E. B. Ancient Yenisey masks. (Verso, 2009).
Teploukhov, S. A. in Materialy po ethnographii Vol. 4 41–62 (1929).
Gryaznov, M. P. in Kompleks arkheologicheskikh pamyatnikov u gory Tepsei na Yenisee (ed M.P. Gryaznov) 89–146 (Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, 1979).
Tunkina, I. V., Savinov, D.G.. Daniel Gotlib Messerschmidt: at the dawn of the Siberian archaeology. (Eleksis, 2017).
Klein, L. S. Migraciia: arkheologicheskie priznaki. Stratum + 1, 52–71 (1999).
Debets, G. F. Paleoantropologiya SSSR. Vol. 4 (Izdatelstvo Akademii Nauk SSSR, 1948).
Kyzlasov, L. R. Tashtykskaya epokha v istorii Khakassko-Minusinskoy kotloviny [Tashtyk epoch in the history of the Khakass-Minusinsk depression]. (Moscow State University, 1960).
Kiselev, S. V. Ancient history of Southern Siberia (USSR Academy of Sciences, 1951).
Shirobokov, I. G. & Pankova, S. V. Dannye kompjuternoy tomografii v izuchenii golovy muzhskoy mumii iz pogrebeniya 4 Oglahtinskogo mogil’nika [Computer tomography datae for the research of the male mummy’s head from grave 4, Oglakhty cemetery]. Archaeological sites of Southern Siberia and Central Asia: from the appearance of the first herders to the epoch of the establishment of state formations. Transactions of the International Scientific Conference devoted to the 85th anniversary of Doctor of Historical Sciences Elga Borisovna Vadetskaya (1936–2018) and 90th anniversary of Doctor of Historical Sciences Gleb Alekseyevich Maksimenkov (1930–1986) April 19–21, 107–109 (2021).
Uchaneva, E. N., Kazarnitsky, A. A., Gromov, A. V. & Lazaretova, N. I. The Early Iron Age populations of the Minusinsk hollow: revisiting inter- and intragroup variations. Vestnik Arheologii, Antropologii i Etnografii 1, 78–87, doi:10.20874/2071-0437-2017-36-1-078-087 (2017).
Gromov, A. V., Lazaretova, N. I. & Uchaneva, E. N. in Kul'tury stepnoi Evrazii i ikh vzaimodeistvie s drevnimi tsivilizatsiiami 117–122 (Periferiia, 2012).
Pankova, S. V. in Masters of the Steppe: the Impact of the Scythians and Later Nomad Societies of Eurasia. Proceedings of a Conference Held at the British Museum, 27–29 October 2017 (eds S.V. Pankova & St.J. Simpson) 373–396 (2020).
Keyser, C. et al. Ancient DNA provides new insights into the history of south Siberian Kurgan people. Hum Genet 126, 395–410, doi:10.1007/s00439-009-0683-0 (2009).
Nikolaev, N. N. & Pankova, S. V. After the Scythians. Scythians: Warriors of Ancient Siberia, 322–351 (2017).
Tallgren, A. The South Siberian cemetery of Oglakty from the Han period. Eurasia Septentrionalis Antiqua 11, 69–90 (1937).
Margaryan, A. et al. Population genomics of the Viking world. Nature 585, 390–396, doi:10.1038/s41586-020-2688-8 (2020).
Boulygina, E. et al. Mitochondrial and Y-chromosome diversity of the prehistoric Koban culture of the North Caucasus. J Archaeol Sci-Rep 31, doi:10.1016/j.jasrep.2020.102357 (2020).
Krzewinska, M. et al. Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads. Sci Adv 4, eaat4457, doi:10.1126/sciadv.aat4457 (2018).
Underhill, P. A. et al. The phylogenetic and geographic structure of Y-chromosome haplogroup R1a. Eur J Hum Genet 23, 124–131, doi:10.1038/ejhg.2014.50 (2015).
Narasimhan, V. M. et al. The formation of human populations in South and Central Asia. Science 365, doi:10.1126/science.aat7487 (2019).
Stepanov, V. A. et al. Characteristics of Populations of the Russian Federation over the Panel of Fifteen Loci Used for DNA Identification and in Forensic Medical Examination. Acta Naturae 3, 56–67 (2011).
Bouakaze, C., Keyser, C., Amory, S., Crubezy, E. & Ludes, B. First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA. Int J Legal Med 121, 493–499, doi:10.1007/s00414-007-0177-3 (2007).
Pilipenko, A. S. et al. Maternal genetic features of the Iron Age Tagar population from Southern Siberia (1st millennium BC). PLoS One 13, e0204062, doi:10.1371/journal.pone.0204062 (2018).
Sokolov, A. S. et al. Six complete mitochondrial genomes from Early Bronze Age humans in the North Caucasus. Journal of Archaeological Science 73, 138–144, doi:10.1016/j.jas.2016.07.017 (2016).
Marcel, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12, doi:10.14806/ej.17.1.200 (2011).
Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963, doi:10.1093/bioinformatics/btr507 (2011).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760, doi:10.1093/bioinformatics/btp324 (2009).
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20, 1297–1303, doi:10.1101/gr.107524.110 (2010).
Weissensteiner, H. et al. Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome research 31, 309–316, doi:10.1101/gr.256545.119 (2021).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079, doi:10.1093/bioinformatics/btp352 (2009).
Genealogy, I. S. o. G. (2019).
Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet 2, e190, doi:10.1371/journal.pgen.0020190 (2006).
Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38, 904–909, doi:10.1038/ng1847 (2006).
Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093, doi:10.1534/genetics.112.145037 (2012).

No competing interests reported.

supplementaryfilesubmit.docx

Download PDF

Version 1

posted

You are reading this latest preprint version

First ancient DNA analysis of mummies from the post-Scythian Oglakhty cemetery in South Siberia

Status:

Version 1

Abstract

Figures

Introduction

Results

DNA sequencing statistics

Mitochondrial DNA and Y-chromosome haplogroup identification

Genome-wide autosomal marker data analysis

Discussion

Material And Methods

Sample description. Anthropological material

Ancient DNA extraction, DNA library preparation, and genome sequencing

Bioinformatics and statistical analyses of ancient DNA sequencing data

Declarations

References

Additional Declarations

Supplementary Files

Status:

Version 1