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Great Scythia was the ancient Greek name for the area stretching from the northern Black Sea coast to the Middle Don. Using high-quality genomic data generated from 131 ancient individuals from Great Scythia and neighboring regions of the Bronze Age and the Iron Age, we established the genetic structure of the Scythians, revealing their diverse origin with major European Bronze Age ancestral components, and genetic traces of migration and invasions. We uncovered relationships between Scythians, including elite Scythians. Substantial endogamy in the Scythian clan was found. We examined Scythians’ phenotypes and medical-genetic background and found a harmful gene mutation causing fructose intolerance. This ancient “Scythian” mutation has spread throughout West Eurasia and has become the most prevalent genetic cause of fructose intolerance in contemporary European populations.
In addition, a notable diversity in Y chromosome haplogroups was revealed among the studied Scythian groups of different regions and chronological periods (table S32). The predominant Y chromosome lineages among IA male individuals in the Middle Don samples are represented by two distinct subclades of haplogroup R1a (R-Y2631 and R-Y2) (see Supplementary Note 7 and table S33). The lineages of haplogroups G2a (G-S9409), J2a1 (J-Y26650 and J-FT72594), N1a (N-Z1934), and Q1b (Q-L940) were other parental lineages present among our tested Scythians, all of them found in different regions of the Great Scythia territory (table S3).