We typed the mtDNA of 111 medieval individuals and performed population genetic and statistical analyses, focusing on three populations that existed in the 7th–12th centuries in the Carpathian Basin. The earliest population under study is the 7th–8th century Avars from the southern part of modern Hungary (Fig. 1). The genetic results from the Avars demonstrate their predominant southern and eastern European maternal genetic composition, with some Asian elements. The local continuity of the Avar population on the southern Great Hungarian Plain to the Hungarian conquest-period cannot be rejected by haplogroup based simulation analyses (TPC, Supplementary Table S7) and was also demonstrated on PCA plots (Fig. 3a, Supplementary Fig. S1). However, sequence-based tests and shared haplotype analyses showed a low level of identical maternal lineage among the Avars and ancient Hungarians, even when including the geographically connecting southeastern group of the conquerors in the calculations (Fig. 5, Supplementary Table S10). The Avar dataset originates from a single micro regional group of the complex Avar society, who buried their dead in catacomb graves. Furthermore, anthropological results showed that this part of the Avar population represents mostly Europid, local morphological characters, and therefore it cannot be used as a proxy of the whole Avar population of the Carpathian Basin. Further regional groups should be analyzed from the late Avar period for a better estimation of the Avar-Hungarian continuity.

The Hungarian conqueror genetic dataset from the 10th century showed more explicit connections toward Central Asian ancient and modern populations, in contrast to the preceding Avars. Asian haplogroups occurred among both male and female conquerors (Supplementary Tables S1 and S3), which can be an argument for a Hungarian settlement in which both men and women took part. It reflects the physical anthropological and archaeological data, which showed that, not only an armed population stratum, but a whole population arrived in the Carpathian Basin25. However, Asian lineages in the conqueror dataset can also be an argument for the continuity of the Avars, who could have mixed and acculturated during the Hungarian conquest-period26. We would need more Avar period genetic data, especially from the late Avar period to assess this hypothesis.

In a previous study, Tömöry et al. presented mitochondrial genetic data of 26 Hungarian conquerors, who were divided into “commoners” (n = 15) and “high status” (n = 12) groups according to the excavated grave goods12. The latter group shows more heterogeneous haplogroup composition, and also some haplotypes that are rare in modern populations. We do not follow this concept in our current study, because grave goods cannot represent evidence of social status with a high level of certainty26,27, and therefore levels of richness or status cannot be categorized precisely. Furthermore, people of low social status could also have been part of the conqueror community, who most probably arrived from the east of the Carpathian Basin as well. Chronological subdivision of the studied graves is also challenging, even 14C dating is not accurate enough for dating 9th–10th centuries AD.

Most of the Asian mtDNA lineages occurred in 10th century cemeteries with small numbers of graves (7–18 graves), and identical lineages were found among cemeteries, rather than within them. This is especially interesting in light of the fact that seven analyzed cemeteries have been completely excavated (Kiskundorozsma, Balatonújlak, Harta, Makó-Igási járandó, Levice-Géňa, Szeged-Öthalom, Szentes-Derekegyháza graveyards). This phenomenon suggests that the conquerors had a mobile way of life or can be explained by the strong marriage connections of the Hungarian communities. The lack of, or small number of intra-cemetery maternal relations is striking at the sites Kiskundorozsma and Levice-Géňa (nine typed and maternally unrelated individuals in both cases), Szeged-Öthalom (eight unrelated people) and Harta. At the Harta site, fifteen women, three men and two children were excavated. We found only one pair of females with identical HVS-I sequences (a common rCRS H type), but in other cases the maternal kinship relation among the 16 typed individuals could be excluded by HVS-I analyses. Many academic archaeologists explain that the small conqueror graveyards were small family graveyards, and use the grave goods of the assumed generations in these graveyards as chronological horizons28. The example of Harta raises the possibility that family relations were not the sole rule of burial order. Mobile groups of people could use these cemeteries for a short period of time. These observations are relevant for the relative chronological and socio-archaeological assumptions about the 10th century Carpathian Basin. Nevertheless, other classic 10th-century graveyards, such as Balatonújlak, contained more signs of possible maternal relations within the cemetery (Supplementary Table S3). The unequal geographic distribution of the samples did not allow us to make further conclusions on the internal (geography or chronology based) genetic structure of the presented 10th-century population of the Carpathian Basin.

We found genetic similarities of the conquerors with the Late Bronze Age population of the Baraba region, situated between the rivers Ob and Irtis17, and with Bronze Age and Iron Age populations that lived in Central Asia15 and south Siberia14,16. Comparing the conqueror mtDNA dataset to a large modern-day population dataset, we also found comprehensive genetic affinities towards modern populations of Central Asia and Central Russia. The parallels of these Asian haplogroups are found in modern ethnic groups speaking both Ugric and Turkic languages. The historically and linguistically assumed homeland of the ancient Hungarians was in the Central Ural region, which is an easily accessible part of the mountain range. Finno-Ugric-speaking groups might have settled on both sides of the Urals during the early Medieval period29. Archeological records, for example, from central-eastern Uralic site Uelgi, indicate archaeological cultural mixture of northern Ugric and eastern steppic Turkic elements. These eastern components show cultural connections toward the region of the Emba River in today’s western Kazakhstan and toward the Srostki culture30, which indicates that the ancient Hungarian population could already have been reached in the Central Ural region by several cultural and genetic influences. Newly revised archaeological connections of the Central Urals and the Carpathian Basin suggest a quick migration from the forest steppe to the Carpathian Basin31, and during these events, the genetic make-up of the conquerors retained some Central Asian signatures.

Modern-day Hungarians were very similar to their surrounding Central European populations from the maternal genetic point of view, as demonstrated by previous mtDNA studies12,19. In our analyses, the Hungarian speaking Szekler, Ghimes, and Csango minorities in today’s Romania showed differing genetic connections from each other. Whereas the Szekler population was consistent with the Central and Eastern European maternal genetic diversity, the haplogroup and haplotype composition of the Csangos was more related to Near Eastern populations (Supplementary Fig. S4, Table S9). These results correspond to the fact that the Csangos, in the Romanian Ghimes region, are a genetically isolated population20, living separately from both Romanians and Szeklers.

The maternal gene pool of Csangos, Szeklers and “average” Hungarians can be descended from 10th–12th century ancient Hungarians, and the differences in their haplogroup composition from the conquerors can be explained by genetic drift (Supplementary Table S7). It is an interesting phenomenon that some Asian haplogroups (A, B, C, G2a) that occured in the conquerors also occurred among Szeklers. This could suggest a sizeable legacy of the conquerors or it may mean that these Asian influences reached Romania in other time periods. Of the 76 detected conqueror haplotypes, 21 had matches in the modern Szekler and Hungarian populations (11.2–15.4% of all lineage types), but none were Asian (Supplementary Table S11). Fourteen conqueror lineages had matches in the Csango dataset, which represents a greater proportion (22.6%) of the total number of Csango lineage types, one of which belonged to the Asian C haplogroup. We would need more medieval samples from Romania and a reconsidered sampling of the current population in the Carpathian Basin in order to better estimate the genetic relations among past and present populations.

The 10th century population of the Carpathian Basin had regionally different, but mostly heterogeneous physical anthropological and linguistic natures, which could be a consequence of the varied ethnic and linguistic composition of the conquerors. On the one hand, this parallels with the genetic diversity of the conquerors, and that the tribe alliance of the Hungarians was a culturally and linguistically mixed community in the steppe2. On the other hand, it could also be a consequence of the mixture of several populations, which had experienced the conquest-period in the Carpathian Basin and the geopolitical environment of the new homeland. The mixed nature of the newly founded Hungarian State was documented in the early 11th century, and described as a basic characteristic of a successful medieval state11. The samples from the 10th–12th century contact zone dataset from the fringes of the Hungarian territory originate from different geographic regions. They represent a mixed dataset within medieval Europe, which showed haplogroup-level connections to the conquerors and ancient Asia (Fig. 3B), but on the sequence level they had affinities with medieval Poles, Lombards, and Avars. Their subsisted maternal genetic signature was found today in Southern Europe and the Near East (Figs S2 and S7). Written sources document the diverse acculturation speed of local populations in the Carpathian Basin. For example, the population of the Čakajovce settlement slowly adopted items of Hungarian traditions to their culture32. This process could last 100–150 years, until burials with poor costume elements and jewels appeared, and Christian cemeteries became used. A new mixed culture began to form in the mid-10th century, which disseminated in the whole territory of the Hungarian Principality regardless of ethnicity.

The results presented here provide a picture of the maternal gene pool of three medieval populations in the Carpathian Basin. Research should continue with the analysis of whole mitochondrial genomes for more exact haplogroup definitions, and Y chromosomal genetic diversity of these populations, in order to define the paternal genetic components of these populations, along with possible sex differences in migration and dispersal patterns. Furthermore, genome-wide sequencing of these samples and analyses of the comparatively ancient (early medieval) Eastern European, Central and North Asian data, which are currently still lacking, might reveal further signs of origin and admixture of the populations discussed here. Moreover, this may shed light on a complex population genetic structure of the first millennium BC of West, North, and Central Eurasia.