Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians.

Biology Department Grand Valley State University 1 Campus Drive Allendale Michigan 49401 United States of America

Department of Archaeology and Classical Studies Stockholm University Wallenberglaboratoriet SE 106 91 Stockholm Sweden

Department of Biology and Environmental Studies Faculty of Education Charles University Prague Magdalény Rettigové 4 116 39 Prague Czech Republic

Department of Human Evolutionary Biology Institute of Anthropology Faculty of Biology Adam Mickiewicz University in Poznan Umultowska 89 61 614 Poznan Poland

Institute of Archaeology Faculty of History Adam Mickiewicz University in Poznan Umultowska 89D 61 614 Poznan Poland

Institute of Archaeology National Academy of Sciences of Ukraine Lanzheronivska Street 65026 Odessa Ukraine

Molecular Biology Techniques Laboratory Faculty of Biology Adam Mickiewicz University in Poznan Umultowska 89 61 614 Poznan Poland

Taras Shevchenko University in Tiraspol Taras Shevchenko University in Tiraspol October Street 25 33 00 Tiraspol Moldova

Zobrazit více v PubMed

Bokovenko N. A. The origins of horse riding and the development of ancient Central Asian nomadic riding harnesses. Kurgans Ritual Sites Settl. Eurasian Bronze Iron Age. BAR International Series 890, 304–310 (2000).

Parzinger H. Die Reiternomaden der eurasischen Steppe während der Skythenzeit. In Im Zeich. Goldenen Greifen Köönigsgräber Skythen (eds Menghin W. & Parzinger H.) 30–48 (Prestel, 2007).

Parzinger H. Die Skythen der ukrainischen Steppe und ihre Stellung in der Welt der eurasischen Reiterno- maden, In Im Gol- Dener Horiz. 4000 Jahre Ukr. (eds Leskovar J. & Zingerle M.-C.) 58–66 (Bibliothek der Provinz, 2010).

Rawlinson G. The History of Herodotus. (London: John Murray, Albemarle Street, 1859).

Skoryj S. A. Skify v Dneprovskoj Pravoberezhnoj stepi (problema vydeleniya iranskogo etnokul’turnogo elementa) (ed. Skoryj S. A.) (1A NANU, 2003).

Pipan M., Baradello L., Forte E. & Finetti I. Ground penetrating radar study of iron age tombs in southeastern Kazakhstan. Archaeol. Prospect. 8, 141–155 (2001).

Ricaut F.-X., Keyser-Tracqui C., Bourgeois J., Crubézy E. & Ludes B. Genetic analysis of a Scytho-Siberian skeleton and its implications for ancient Central Asian migrations. Hum. Biol. 76, 109–125 (2004). PubMed

Jordana X. et al.. The warriors of the steppes: osteological evidence of warfare and violence from Pazyryk tumuli in the Mongolian Altai. J. Archaeol. Sci. 36, 1319–1327 (2009).

Liberov P. D. & Gulyaev V. I. Problemy Skifskoj Archeologii (eds Liberov P. D. & Gulyaev V. I. (Nauka, 1971).

Tierenzokin A. I. Skifskaya kul’tura (ed. Tierenzokin A. I.) (MIA, 1976).

Gulyaev V. I. Skify: Rastsvet i padenie velikogo tsarstva (ed. Gulyaev V. I.) (Mocow: Aleteia, 2005).

Watt J. Y. C. Introduction, In Nomadic Art of the Eastern Eurasian Steppes: The Eugene V. Thaw and Other New York Collections (eds Bunker E. C., Watt J. C. Y., Sun Z.) 3 (Metropolitan Museum of Art, New York, 2002).

Der Sarkissian C. Mitochondrial DNA in ancient human populations of Europe (University of Adelaide, 2011).

Ricaut F.-X., Keyser-Tracqui C., Cammaert L., Crubézy E. & Ludes B. Genetic analysis and ethnic affinities from two Scytho-Siberian skeletons. Am. J. Phys. Anthropol. 123, 351–360 (2004). PubMed

González-Ruiz M. et al.. Tracing the origin of the east-west population admixture in the Altai region (Central Asia). PloS One 7, e48904 (2012). PubMed PMC

Chikisheva T. A. et al.. A paleogenetic study of the prehistoric populations of the Altai. Archaeol. Ethnol. Anthropol. Eurasia 32, 130–142 (2007).

Pilipenko A. S., Romaschenko A. G., Molodin V. I., Parzinger H. & Kobzev V. F. Mitochondrial DNA studies of the Pazyryk people (4th to 3rd centuries BC) from northwestern Mongolia. Archaeol. Anthropol. Sci. 2, 231–236 (2010).

Pilipenko A. S., Trapezov R. O., Zhuravlev A. A., Molodin V. I. & Romaschenko A. G. MtDNA Haplogroup A10 Lineages in Bronze Age Samples Suggest That Ancient Autochthonous Human Groups Contributed to the Specificity of the Indigenous West Siberian Population. PloS One 10, e0127182 (2015). PubMed PMC

Mathieson I. et al.. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015). PubMed PMC

Yang D. Y., Eng B., Waye J. S., Dudar J. C. & Saunders S. R. Technical note: improved DNA extraction from ancient bones using silica-based spin columns. Am. J. Phys. Anthropol. 105, 539–543 (1998). PubMed

Malmström H. et al.. More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA. Mol. Biol. Evol. 24, 998–1004 (2007). PubMed

Meyer M. & Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, pdb.prot5448 (2010). PubMed

Günther T. et al.. Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques. Proc. Natl. Acad. Sci. USA 112, 11917–11922 (2015). PubMed PMC

Lampa S., Dahlö M., Olason P. I., Hagberg J. & Spjuth O. Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data. GigaScience 2, 9 (2013). PubMed PMC

Juras A. et al.. Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA. Forensic Sci. Int. Genet. doi: 10.1016/j.fsigen.2016.10.008. PubMed DOI

Anderson S. et al.. Sequence and organization of the human mitochondrial genome. Nature 290, 457–465 (1981). PubMed

Andrews R. M. et al.. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23, 147 (1999). PubMed

Li H. & Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinforma. Oxf. Engl. 25, 1754–1760 (2009). PubMed PMC

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).

Andrews S. A. Quality control tool for high throughput sequence data (2012).

Merriman B. & Rothberg J. M., Ion Torrent R&D Team. Progress in ion torrent semiconductor chip based sequencing. Electrophoresis 33, 3397–3417 (2012). PubMed

Jónsson H., Ginolhac A., Schubert M., Johnson P. L. F. & Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinforma. Oxf. Engl. 29, 1682–1684 (2013). PubMed PMC

Robinson J. T. et al.. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011). PubMed PMC

Korneliussen T. S., Albrechtsen A. & Nielsen R. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 15, 356 (2014). PubMed PMC

Vianello D. et al.. HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment. Hum. Mutat. 34, 1189–1194 (2013). PubMed

van Oven M. & Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat. 30, E386–E394 (2009). PubMed

Skoglund P., Stora J., Götherström A. & Jakobsson M. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J. Archaeol. Sci. 40, 4477–4482 (2013).

Hunter J. D. Matplotlib: A 2D Graphics Environment. Comput. Sci. Eng. 9, 90–95 (2007).

Nei M. & Li W. H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76, 5269–73 (1979). PubMed PMC

Excoffier L. & Lischer H. E. L. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564–567 (2010). PubMed

Excoffier L., Smouse P. E. & Quattro J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479–491 (1992). PubMed PMC

Pedregosa F. et al.. Scikit-learn: Machine Learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).

QGIS Development Team. QGIS Geographic Information System. Open Source Geospatial Foundation Project http://www.qgis.org (2015).

Brandt G. et al.. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity. Science 342, 257–261 (2013). PubMed PMC

Lazaridis I. et al.. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014). PubMed PMC

Gamba C. et al.. Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun. 5, 5257 (2014). PubMed PMC

Haak W. et al.. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015). PubMed PMC

Zhang F. et al.. Prehistorical East–west admixture of maternal lineages in a 2,500-year-old population in Xinjiang. Am J Phys Anthr. 142, (2010). PubMed

Ricaut F.-X. et al.. Comparison between morphological and genetic data to estimate biological relationship: The case of the Egyin Gol necropolis (Mongolia). Am. J. Phys. Anthropol. 143, 355–364 (2010). PubMed

Keyser-Tracqui C., Crubézy E. & Ludes B. Nuclear and Mitochondrial DNA Analysis of a 2,000-Year-Old Necropolis in the Egyin Gol Valley of Mongolia. Am. J. Hum. Genet. 73, 247–260 (2003). PubMed PMC

Keyser-Tracqui C., Crubézy E., Pamzsav H., Varga T. & Ludes B. Population origins in Mongolia: Genetic structure analysis of ancient and modern DNA. Am. J. Phys. Anthropol. 131, 272–281 (2006). PubMed

Fu Q. et al.. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015). PubMed PMC

Bollongino R. et al.. 2000 Years of Parallel Societies in Stone Age Central Europe. Science 342, 479–481 (2013). PubMed

Sánchez-Quinto F. et al.. Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers. Curr. Biol. 22, 1494–1499 (2012). PubMed

Allentoft M. E. et al.. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015). PubMed

Posth C. et al.. Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe. Curr. Biol. 26, 827–833 (2016). PubMed

Mallory J. P. & Adams D. Q. Encyclopedia of Indo-European Culture, Fitzroy Dearborn Publishers (eds Mallory J. P. & Adams D. Q.) (London – Chicago 1997).

Malmström H. et al.. Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process. Phil Trans R Soc B 370, 20130373 (2015). PubMed PMC

Kılınç G. M. et al.. The Demographic Development of the First Farmers in Anatolia. Curr. Biol. doi: 10.1016/j.cub.2016.07.057 (2016). PubMed DOI PMC

Dönmez S. In Knowledge Production From the Black Sea to the Euphrates. Studies Presented in Honour of Önder Bilgi. 129–146 (Bilgin Kültür Sanat Yayınları: Ankara, 2011).

Wilde S. et al.. Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y. Proc Natl Acad Sci 111, (2014). PubMed PMC

Nikitin A. G., Sokhatsky M. P., Kovaliukh M. M. & Videiko M. Y. Comprehensive site chronology and ancient mitochondrial DNA analysis from verteba cave—a trypillian culture site of eneolithic Ukraine. Interdiscip. Archaeol. 1, 9–18 (2010).

Sinor D. The Cambridge history of early inner Asia (ed. Sinor D.) 99 and 111 (Cambridge University Press, 1990).

Lalueza-Fox C. et al.. Unravelling migrations in the steppe: mitochondrial DNA sequences from ancient Central Asians. Proc Biol Sci 271, 941–947 (2004). PubMed PMC

Mooder K. P., Schurr T. G., Bamforth F. J., Bazaliiski V. I. & Savel’ev N. A. Population affinities of Neolithic Siberians: a snapshot from prehistoric Lake Baikal. Am. J. Phys. Anthropol. 129, 349–361 (2006). PubMed

Keyser C. et al.. Ancient DNA provides new insights into the history of south Siberian Kurgan people. Hum. Genet. 126, 395–410 (2009). PubMed

Molodin V. I. et al.. Human migrations in the southern region of the West Siberian Plain during the Bronze Age: Archaeological, palaeogenetic and anthropological data, In Population Dynamics in Prehistory and Early History (eds Kaiser E., Burger J. & Schier W.) 90–111 (2012).

Derenko M. et al.. Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe. PloS One 7, e32179 (2012). PubMed PMC

Wang H. et al.. Genetic data suggests that the Jinggouzi people are associated with the Donghu, an ancient nomadic group of North China. Hum. Biol. 84, 365–378 (2012). PubMed

Loogväli E. L. et al.. Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. Mol. Biol. Evol. 21, 2012–21 (2004). PubMed

Murzin V. Y. Skifskaya arkhaika Severnogo Prichernomor’a (ed. Murzin V. Y.) (1984).

Raevsky D. S. Mir Skifskoj Kultury (ed. Raevsky D. S.) (2006).

Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations