Ancient DNA indicates 3,000 years of genetic continuity in the Northern Iranian Plateau, from the Copper Age to the Sassanid Empire

Abstract

In this study, we present new ancient DNA data from prehistoric and historic populations of the Iranian Plateau. By analysing 50 samples from nine archaeological sites across Iran, we report 23 newly sequenced mitogenomes and 13 nuclear genomes, spanning 4700 BCE to 1300 CE. We integrate an extensive reference sample set of previously published ancient DNA datasets from Western and South-Central Asia, enhancing our understanding of genetic continuity and diversity within ancient Iranian populations. A new Early Chalcolithic sample, predating all other Chalcolithic genomes from Iran, demonstrates mostly Early Neolithic Iranian genetic ancestry. This finding reflects long-term cultural and biological continuity in and around the Zagros area, alongside evidence of some western genetic influence. Our sample selection prioritizes northern Iran, with a particular focus on the Achaemenid, Parthian, and Sassanid periods (355 BCE-460 CE). The genetic profiles of historical samples from this region position them as intermediates on an east-west genetic cline across the Persian Plateau. They also exhibit strong connections to local and South-Central Asian Bronze Age populations, underscoring enduring genetic connections across these regions. Diachronic analyses of uniparental lineages on the Iranian Plateau further highlight population stability from prehistoric to modern times.

Keywords: Achaemenid; Ancient DNA; Genetic ancestry; Iran; Parthian; Persian Plateau; Sassanid.

Fig. 1

Map of the Iranian Plateau and its surroundings. Present-day Iran is highlighted, with the archaeological sites mentioned in the text. Filled circles represent new samples, empty circles mark sites from which ancient DNA data has been published in previous studies^,–,. For further sites that were processed but not analysed, refer to Supplementary Table S1.

Fig. 2

Summary of the uniparental data. (A) Distribution of the ancient Iranian mtDNA haplogroups; asterisks denote the samples analysed in this study. (B) PCA plot based on mtDNA haplogroup frequencies in modern Iranian and selected ancient Iranian groups. Using the frequencies of 36 haplogroups in modern and ancient Iranian populations, the first two principal components (PCs) capture 22.1% of the total variance (see Supplementary Table S6 for details). To maintain consistency and prevent sampling bias, we selected only those ancient groups that had more than 10 individuals or could be merged geographically and temporally, such as our historical samples. (C) Distribution of the ancient Iranian Y-chromosomal haplogroups (details in Supplementary Table S7).

Fig. 3

Eurasian PCA and supervised ADMIXTURE focusing on the genetic variation of Western Asia and its adjacent territories. (A) Grey dots represent modern reference populations, with some labelled in blue. Three-letter codes and detailed information on the ancient and modern populations used in the PCA plot are provided in Supplementary Table S9. A detailed view of the PCA is available in Supplementary Figure S11.2. (B) Supervised ADMIXTURE analyses of the most relevant samples and groups with Iranian EN Ganj Dareh, Anatolian Neolithic (ANF), Onge (AHG), WSHG and Botai (ANE-related), Shamanka Eneolithic (ANA), China LN, and Iron Gates HG (Balkan HG) as fixed sources. For more details and references, see Supplementary Table S10. Individual values and standard errors per component were used for the group-based representation, as described in Methods. Results of the full ADMIXTURE run are presented in Supplementary Figure S11.3.

Fig. 4

Two-dimensional scatterplots of seven f4-statistics. The four panels represent scatterplots of different f4 model combinations. f4 estimates and corresponding Z-scores are provided in Supplementary Table S11. Non-significant Z-scores are indicated with red error bars. Blue lines represent regression analyses (Weighted Least Squares (WLS) linear regression) and blue stars denote groups that deviate significantly from the regression, based on the model fit and the variability captured by the weighted standard deviation. Data produced using different laboratory methods from the same sample is indicated with a single symbol.