Maternal Lineages from 10-11th Century Commoner Cemeteries of the Carpathian Basin.

Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10-11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the immigrant elite have been widely debated. Mitogenome sequences were obtained from 202 individuals with next generation sequencing combined with hybridization capture. Median joining networks were used for phylogenetic analysis. The commoner population was compared to 87 ancient Eurasian populations with sequence-based (Fst) and haplogroup-based population genetic methods. The haplogroup composition of the commoner population markedly differs from that of the elite, and, in contrast to the elite, commoners cluster with European populations. Alongside this, detectable sub-haplogroup sharing indicates admixture between the elite and the commoners. The majority of the 10-11th century commoners most likely represent local populations of the Carpathian Basin, which admixed with the eastern immigrant groups (which included conquering Hungarians).

1. Introduction

Hungarian history was profoundly determined by the conquering Hungarians (succinctly, the Conquerors), who arrived at the Carpathian Basin from the Eastern European steppe at the end of the 9th century AD as an alliance of seven tribes. The leaders of the alliance (Álmos and his son Árpád) founded a steppe state upon the ashes of the Avar Khaganate [1,2], and their descendants later established the Hungarian Kingdom. The archaeological legacy of the Conquerors is well defined, especially in the small 10th century cemeteries of the military leader strata whose grave finds included precious metal jewels and costume ornaments as well as decorated horse riding- and weapon-related grave goods [3]. Most of the larger cemeteries attributed to the common people are dated somewhat later, to the 10–12th centuries. People in these so-called village cemeteries were buried with simpler jewels and grave goods, with the sporadic appearance of weapons or harness accessories. There is a general agreement that elite graves with typical grave goods represent first- or second-generation immigrant Conquerors, but the affiliations of people in the village cemeteries are far less clear. For 50 years, they were identified with the Bijelo Brdo culture of the local Slavic people, until their relation to the Conquerors was recognized in 1962 [4] (see Appendix A for details), but to what extent they can be identified with the immigrants as opposed to the previous local population is not yet clear. The answer to this question considerably determines the historical interpretation of the conquest and subsequent events in the Carpathian Basin, and genetic data may contribute to clarifying this issue.

Hitherto, most genetic studies were focused on the elite graves, as these promised an answer for the origin of the immigrant groups. In [5], 76 individuals were selected from 23 cemeteries mainly representing the 10th century elite, and 23% of the maternal lineages identified from hypervariable region (HVR) sequences were east Eurasian and 77% were west Eurasian. Another study, [6], aimed at characterizing the population of entire group of elite cemeteries, sequencing 102 mitogenomes (30% of which had Central–Inner Asian maternal ancestry, while most of the remaining lineages originated from western Eurasia). Y-chromosome studies [7] found that male lineages had similar phylogeographic compositions to female ones. Thus, all studies had congruent results, inferring that the Conqueror elite population originated from an admixture of Asian and European groups on the Pontic steppe.

This raises the question of whether the commoners were genetically similar to the elite, and, if so, could they be one and the same population, or did the poorer strata have a different origin? This question was addressed in the first HVR-based study [8], in which 27 selected graves from 15 cemeteries were grouped according to the type of grave goods present, and the population with “classical” grave goods were found to contain a higher proportion of east Eurasian haplogroups (Hgs) than the group with poor archaeological remains. However, this conclusion was based on a small sample size and a low resolution HVR study, and a systematic characterization of the commoner population with a representative dataset has not been performed yet.

We set out to implement a comprehensive study in this matter, and to this end, we selected eight cemeteries archaeologically evaluated as belonging to the 10–11th century commoners, from which we obtained 202 whole mitogenome sequences. Phylogenetic analysis was performed to illuminate the origin of each maternal sub-Hg of the studied remains. We compared the mitochondrial haplogroup compositions of the commoner and elite populations to find out their genetic relationship and applied different population genetic methods to elucidate the relationship of the commoners with other ancient Eurasian populations. For this reason, we also built a comprehensive database of ancient Eurasian populations, which included all available published mitogenome data.

2. Materials and Methods

2.1. Archeological Background

In contrast to the small 10th century cemeteries with characteristic grave goods [9] representing the conquering Hungarian elite (ConqE), archaeologists classify large 10–11th century cemeteries containing poor grave goods with the sporadic appearance of ConqE findings (see Appendix A for details) as belonging to Hungarian commoners (ConqC). We collected petrous bones (or where these were unavailable, teeth) from 229 human remains from 10 archeological sites (Figure 1) associated with Hungarian commoners.

Figure 1

The locations of the graveyards of the Hungarian commoners (ConqC) under study. Sample size is indicated next to cemetery names; two numbers in Magyarhomorog and Szegvár indicate that two nearby cemeteries were sampled. The map was generated using QGIS 3.12.0 [10].

We made an effort to carry out representative sampling. Thus, graves were selected from each section of the cemeteries (including males and females from burials both with and without grave goods and all anthropological types). The number of collected, processed and analyzed samples from each cemetery is summarized in Table 1.

Table 1

Summary of the studied sample size from each cemetery. The mitogenome sequence was obtained after hybridization capture or whole genome sequencing (WGS) as indicated. Samples represent 10–11th century commoners except 14 samples from Magyarhomorog and 20 samples from Vörs-Papkert B. As indicated, we also co-analyzed 13 previously published mitogenomes with new data from this study.

Archaeological Site	Dating (Century CE) Type of Cemetery	No. of Graves	Collected Samples in This Study	Obtained Mitogenomes in This Study (Capture or WGS)	Previously Published Mitogenomes	No. of Samples Analyzed
Sárrétudvari-Hízóföld	10th commoner	262	32	31 (capture)	8	39
Püspökladány-Eperjesvölgy	10–12th commoner	637	36	31 (capture)		31
Ibrány-Esbóhalom	10–11th commoner	269	32	26 (capture)		26
Homokmégy-Székes	10–11th commoner	206	36	34 (capture)		34
Magyarhomorog-Kónyadomb (10–11th century commoner)	10–11th commoner	523	27	25 (capture)	1	26
Magyarhomorog-Kónyadomb (10th century elite)	10th elite	17	14	14 (capture)		14
Vörs-Papkert B	8–9th	716	Avar period: 9	8 (capture)		8
	9–10th		Carolingian period: 11	11 (capture)		11
	10–11th commoner		Conquest period: 10	9 (capture)		9
Nagytarcsa-Homokbánya	10–11th commoner	21	4	4 (WGS)		4
Szegvár-Oromdűlő	10–11th commoner	372	7	4 (WGS)	2	6
Szegvár-Szőlőkalja	10th commoner	62	11	5 (WGS)		5
Orosháza-Görbicstanya	10th commoner	3			1	1
Szabadkígyós-Pálliget	10th commoner	17			1	1

The largest 10th century commoner cemetery with 262 graves was excavated in Sárrétudvari-Hízóföld [11] (Appendix A.2.6), with a high proportion of graves containing archery equipment and stirrups. We recovered 31 mitogenomes from this site, and a further 8 sequences were added from our previous study [6,12].

Another large commoner cemetery with 637 graves is located in the nearby Püspökladány-Eperjesvölgy [11] (Appendix A.2.5). This cemetery contains a “pagan” and a “Christian” section. Both sections of the graveyard were sampled and we obtained 31 mitogenomes.

The Ibrány-Esbóhalom commoner cemetery with 269 graves also stretches into the Christian era [13] (Appendix A.2.2). We analyzed 32 remains from this site, resulting in the obtainment of 26 mitogenomes.

We studied 36 remains from the Homokmégy-Székes cemetery excavated at the Duna-Tisza Interfluve [14] with 206 graves, which was referred to by the archaeologist as a “typical cemetery of conquest period commoners” (Appendix A.2.1), and obtained 34 mitogenomes.

Among the studied cemeteries, Magyarhomorog-Kónyadomb [15] (Appendix A.2.3) is an exceptional case, as archaeologically it can be divided into two sections: a small section with 17 individuals was used by the 10th century Conqueror elite, while the larger section with 523 graves of 10–11th century commoners raises the question of potential continuity. We sequenced 14 samples from the elite section and 25 samples from the commoner section.

From the Transdanubia region, we included the Vörs-Papkert-B cemetery [16] (Appendix A.2.9), the 716 excavated burials of which are mostly from the late Avar and Carolingian periods. However, 33 people can be dated to the time of the Hungarian conquest. The uninterrupted usage of this graveyard raises the possibility that it might represent the same population in the subsequent periods; thus, we sampled graves from each period as indicated in Table 1.

Finally, we complemented our sample set with a few individuals from the Nagytarcsa-Homokbánya (Appendix A.2.4), Szegvár-Oromdűlő (Appendix A.2.7) and Szegvár-Szőlőkalja (Appendix A.2.8) commoner cemeteries, as listed in Table 1. All of the 13 samples came from poor burials or from graves devoid of archaeological grave goods. For a detailed description of the sites and archaeological findings, see Table S1.

2.2. Library Preparation, Sequencing and Hg Assignment

All pre-PCR laboratory procedures leading to next generation sequencing (NGS) were conducted in the common ancient DNA laboratory of the Department of Archaeogenetics of the Institute of Hungarian Research and Department of Genetics, University of Szeged, Hungary. Details concerning the ancient DNA purification, library preparation, hybridization capture, sequencing and sequence analysis method are given in [12]. We used the double stranded library protocol of [17] with double indexing [18]. All libraries were made from partial uracil-DNA glycosylase (UDG)-treated DNA extracts [19]. We estimated the endogenous human DNA content of each library with low coverage shotgun sequencing (Table S2a). Then, the mitogenomes from samples with similar proportions of human DNA content were pooled and enriched together according to [20]. Captured and amplified libraries were purified on MinElute columns. Quantity and quality measurements were performed with the Qubit fluorometric quantification system and the TapeStation automated electrophoresis system (Agilent). A further 13 mitogenome sequences were obtained from whole genome sequencing, as indicated in Table 1 and Table S2.

The adapters of paired-end reads were trimmed with the Cutadapt software [21] in paired end mode. Read quality was assessed with FastQC [22]. Sequences shorter than 25 nucleotides were removed from this dataset. The resulting analysis-ready reads were mapped to the GRCh37.75 human genome reference sequence that also contains the mtDNA revised Cambridge Reference Sequence (rCRS, NC_012920.1) [23] using the Burrows Wheeler Aligner (BWA) v0.7.9 software [24] with the BWA mem algorithm in paired mode and default parameters. Samtools v1.1 [25] was used for sorting and indexing binary alignment map (BAM) files. PCR duplicates were removed using Picard Tools v 1.113 [26]. Ancient DNA damage patterns were assessed using MapDamage 2.0 [27] and read quality scores were modified with the rescale option to account for post-mortem damage. Mitochondrial genome contamination was estimated using the Schmutzi algorithm [28] (Table S2b). Mitochondrial haplogroup (Hg) determination was performed using HaploGrep v2.1.25 [29] (Table S3a). The biological sex of the individuals was identified according to [30] based on the X/Y ratio of the reads obtained from shotgun sequencing.

The raw nucleotide sequence data of the 202 samples were deposited to the European Nucleotide Archive (http://www.ebi.ac.uk/ena) under the accession number: PRJEB40566.

2.3. Assembling an Ancient Eurasian Mitogenome Database

For the phylogenetic and population genetic analyses, we built a database containing 4191 published ancient Eurasian mitogenomes (Table S4). Sequences were downloaded from the NCBI and the European Nucleotide Archive databases. Where it was necessary, mitogenome sequences were sorted out from whole genomes. This database was then augmented with the 202 new mitogenomes from this study. We ordered the published samples into 88 populations based on time range, archaeological site and context, as well as the classification of the published genome data. In cases when populations were under-represented due to a low sample size, we grouped samples from related cultures like Alans and Saltovo-Mayaki, Medieval samples from Italy, Germany and England, Iberian Chalcolithic and Bronze Age samples, Chalcolithic samples from Iran and Turan, early and late Sarmatians, etc. (Table S4).

2.4. Phylogenetic and Population Genetic Study

A sub-set of the published sequences was of poor quality. We excluded sequences with >5% missing data from the phylogenetic and Fst analysis and used 3844 fasta files of ancient sequences and 11,682 fasta files of modern sequences for building median joining (MJ) networks, as described in [6]. The phylo-geographic origins of the samples were assessed from the geographic origin of the nearest Hgs. We distinguished four regions: east Eurasia, west Eurasia, Eurasia and Caucasus–Middle East (Figure S1).

For population genetic analysis, we merged all 169 ConqC data to a single population (Tables S3c and S4), excluding members of the elite Magyarhomorog cemetery as well as Avar and Caroling samples from the Vörs-Papkert cemetery (excluded samples are color labeled in Table S2b). These were supplemented with 13 commoner mitogenomes published previously [6], as listed in Table 1. The merged ConqC population was compared to the 88 ancient Eurasian groups from the newly assembled mitogenome database, including the previously published military elite strata of the Conquerors [6,12,31], which was supplemented with the Magyarhomorog elite graveyard data from the present study (Table 1, Tables S3c and S4).

Three independent methods were applied to measure the genetic distances of ConqC from other ancient populations. In the first analysis, we reduced the Hg assignments of all samples to major Hgs, which decreased population data to 34 dimensions, which is sufficient to display the main correlations. Then, major Hg frequencies were calculated and principal component analysis (PCA) was conducted, employing the function “prcomp” in R 3.6.3. [32]. We also compared the major Hg frequencies of the ConqC and ConqE groups separately.

In a second approach, a traditional sequence-based method was implemented, calculating pair-wise population differentiation values (Fst) with Arlequin 3.5.2.2 [33] from whole mtDNA genomes, as described in [6]. Multi-dimensional scaling (MDS) was applied on the matrix of linearized Slatkin Fst values [34], and the values were visualized in the two-dimensional space using the cmdscale function implemented in R 3.6.3 [32].

In a third approach, shared haplogroup distance (SHD) values were measured between the populations according to our previous study [6], which calculates the frequency of identical terminal sub-Hgs (the deepest determined Hg level) between populations, as these testify shared ancestry or past admixture.

3. Results

3.1. Sequencing Results and Assigned Haplogroups

We collected a total of 229 samples from the listed sites, but could not obtain DNA from 13 samples. Another 10 samples were excluded from the analysis due to low mitogenome sequence coverage and 3 further samples were excluded due to high contamination values. Using the NGS method combined with target enrichment, we acquired 189 ancient mitogenome sequences, and a further 13 were obtained from whole genome sequencing; thus, we report 202 new mitogenomes in this paper (Table S3a). We obtained 4.2-3068x mitogenome coverage, and the average coverage was 231x. Schmutzi estimated negligible contamination for most of the 202 samples. Seven samples were indicated to carry significant (15–21%) contamination; nonetheless, Schmutzi could determine the endogenous sequence unambiguously for these samples due to high coverage, enabling a correct Hg assignment. For details of the sequencing data, see Table S2. On the grounds of haplogroup determination by HaploGrep 2.0, the 202 samples belong to 154 sub-Hgs and 187 different haplotypes (Table S3a).

3.2. Kinship Analysis

We examined a possible kinship relation between and within cemeteries. We detected 10 pairs of identical mitochondrial haplotypes within cemeteries and 4 pairs between cemeteries (Table S3b), which indicate a potential direct maternal relationship of these individuals, but this of course is not inherent evidence of close family relations.

3.3. Phylogenetic Analysis

As some of the mitochondrial sub-clades may have specific geographical distribution [35,36], we elucidated the phylogenetic relations of each mitogenome sequence using M–J networks, as shown in Figure S1. The closest sequence matches pointed at a well-defined geographical region in most cases, which is indicated next to the phylogenetic trees and is summarized on Figure 2.

Figure 2

The phylogeographic origin of the ConqC maternal lineages from different cemeteries. Data are summarized from Figure S1 and from a previous study [6]. West Eurasian haplogroups (Hgs) are marked with pink, east Eurasian Hgs are marked with yellow, Eurasian Hgs are marked with green and Caucasus–Middle East Hgs are marked with brown. (A) Distribution of the merged data of 182 Hungarian commoner samples from all cemeteries. (B–G) The phylogeographic distribution of the maternal lineages from individual cemeteries: (B) Homokmégy-Székes (n = 34); (C) Püspökladány-Eperjesvölgy (n = 31); (D) Sárrétudvari-Hízóföld (n = 39); (E) Ibrány-Esbóhalom (n = 26); (F) Magyarhomorog-Kónyadomb (n = 26, with samples taken just from the commoner part); (G) Vörs-Papkert-B (n = 28, including all samples from this cemetery).

Phylogenetic trees revealed that, out of the 182 commoner maternal lineages, 23 were unequivocally derived from east Eurasia and 107 were derived from west Eurasia, while 52 are widespread throughout Eurasia. Out of the western Eurasian lineages, 11 have a primarily Caucasus–Middle East distribution (Figure 2A).

3.4. Haplogroup Composition of Individual Cemeteries

The 34 investigated samples from Homokmégy-Székes belonged to 30 Hgs (Table S3a). As for the lineages, 47.1% were of European origin and 14.7% were of east Eurasian origin, while 38.2% showed general Eurasian distribution (Figure 2B).

From the Püspökladány-Eperjesvölgy cemetery, 31 remains were analyzed. The maternal lineages were classified into 28 Hgs (Table S3a), and they showed 54.8% west Eurasian ancestry, 19.4% east Eurasian ancestry and 12.9% Eurasian ancestry, while 12.9% had a Caucasus–Middle East affinity (Figure 2C).

The newly reported mitogenomes of 31 individuals from Sárrétudvari-Hízóföld belonged to 26 Hgs (Table S3a). In a previous study, the mitochondrial lineage of eight individuals from this cemetery were obtained [6]. Merging these data, 59% of the lineages had west Eurasian ancestry, 10.3% had east Eurasian ancestry, 28.2% had Eurasian ancestry and 2.6% had Caucasian–Middle Eastern maternal ancestry (Figure 2D).

The Ibrány-Esbóhalom cemetery was represented by 26 samples falling to 26 different Hgs (Table S3a). 46.2% of the maternal lineages originated from Europe, 7.7% originated from east Eurasia and 19.2% originated from the Caucasus–Middle East region, while 26.9% of the lineages had a Eurasian distribution (Figure 2E).

We sequenced 14 mitogenomes out of the 17 remains from the elite part of Magyarhomorog-Kónyadomb, and their Hg composition was very similar to those of previously studied elite cemeteries [6]; 35.7% of the lineages were of east Eurasian origin, 42.9% were of European origin and 21.4% were of Eurasian origin (Table S1). The high frequency of N1a1a1a1a and T1a1, as well as the occurence of N1a1a1a1 and D4 in this small cemetery, finds its best parallels in the Karos and Kenézlő elite graveyards [4], supporting the archaeological evaluation; thus, we included these data in the elite dataset (Table S3c).

From the 11–12th century commoner part of Magyarhomorog, we sequenced 25 samples which belonged to 22 mitochondrial Hgs (Table S3a), supplemented with one published sample from this site [6]. From the 26 samples, 61.5% had a west Eurasian origin, 34.6% had an Eurasian origin and 3.8% had a Caucasus–Middle East affinity (Figure 2F); thus, genetic data also corroborated the hypothesis that the large graveyard represents a separable commoner population.

The cemetery of Vörs-Papkert is another special case, as it was used for centuries by successive populations of Avars, Carolingians and Conquerors populations. Evaluating the entire 28 sample set from this cemetery together (Figure 2G) showed a very similar overall picture to that of other commoner cemeteries, with 25 Hgs, 67.9% of which had a west Eurasian origin, 7.1% had an east Eurasian origin, 21.4% had an Eurasian origin and 3.6% had a Caucasus–Middle East affinity. Hg H dominated this graveyard, as 16 out of the 28 remains belonged to Hg H irrespective of historical period. A single D4e4 Hg was detected among the studied ConqC and a single A16 was detected among the Avar period samples as weak signs of Asian impact (Table S1). By all means, for the population genetic analysis, we removed Avar and Carolingian samples from this dataset.

The six ConqC graveyards with a meaningful sample size showed a rather similar overall picture, with an average of 12.6% east Eurasian Hgs almost confined to C and D, which allowed us to infer a similar overall east Eurasian impact throughout cis-Danubia.

We also investigated a few individuals from other commoner cemeteries, namely four samples from Nagytarcsa-Homokbánya, four samples from Szegvár-Oromdűlő and five samples from Szegvár-Szőlőkalja, resulting in two east Eurasian lineages besides the European ones (Table S3a).

We acknowledge that the average of 30 samples per site may poorly represent the individual cemeteries, but the total number of 182 commoner remains (Table S3c) can be regarded as considerably representative for population genetic analysis.

3.5. Population Genetic Analysis

First, we compared the major Hg distribution of the conqueror period elite and commoner populations (Figure 3). The heterogeneity of the major Hg distribution of ConqE is comparable to that of ConqC (22 and 19 main Hgs, respectively); however, the Hg compositions of the two groups show considerable differences. The ratio of east Eurasian major-Hgs in the commoners is 7.69%, contrary to the 19.64% of the elite. The elite contains a broad spectrum of east Eurasian Hgs (A, B, C, D, F, G and Y), while only C and D occur with notable frequency in the commoners, with a single appearance of B.

Figure 3

Comparison of the major Hg distributions from ancient Hungarian populations. The major Hg distribution of commoner samples (n = 182) from this study is distinct from that of Conqueror elite samples (n = 112) taken from previous studies [6,12,31], including elite data from Magyarhomorog in the present study. Brackets mark east Eurasian Hgs.

West Eurasian Hgs of ConqC and ConqE also show notable differences: Hgs HV, I, M, R, U1, U8 and W occur with moderate frequencies in commoners, while these are completely absent from the elite population. Three Hgs (N, T1 and X), typically widespread both in east and west Eurasia, show much higher ratio in the elite than in commoners: N’s ratios are 11.61% in the elite population and 3.85% in the commoner population; T1’s ratios are 11.61% in the elite population and 2.75% in the commoner population; and X’s ratios are 4.46% in the elite population and 0.55% in the commoner population. The opposite is true for Hgs H and T2; among commoners, H is the most prevalent Hg with a 33.52% frequency, while in the elite group, its proportion is significantly lower (19.64%); T2 has a 6.59% proportion in the commoner population and a 1.79% proportion in the elite population.

As the Hg composition of the studied commoner samples markedly differs from that of the elite, we measured ConqC’s genetic distances from ConqE as well as its distances from 87 published ancient Eurasian populations (Table S5). PCA obtained from the major Hg frequencies of 88 populations (Figure 4) highlights the distance between ConqE and ConqC. The ConqC clustered in the eastern side of the European aggregation, with the closest genetic affinity to Baltic Bronze Age populations, Baltic Iron Age populations, Baltic Medieval populations, Bell Baker Germany and Great Britain Bronze Age populations, and is not far away from the Steppe Early-Middle Bronze Age (Steppe EMBA) population, though these relative distances need to be interpreted with care, as our population dataset certainly incompletely represents the past genetic variability. In contrast, the Conqueror Elite is located between ancient European and Asian populations and its closest clusters are the Sarmatian Iron Age population, the Tien Shan Iron Age population, the Karasuk late Bronze Age population and the two groups suggested to be in connection with the Conquerors [31]: the Cis-Ural Medieval population and the Uyelgi Trans-Ural Medieval population.

Figure 4

The principal component analysis (PCA) plot of the major mtDNA haplogroup distribution (distinguishing Hgs A, B, C, D, F, G, H, HV, I, J, K, L, M, N, N1a, N1b, R, T, T1, T2, U, U1, U2, U3, U4, U5, U6, U7, U8, V, W, X, Y and Z) of 88 Eurasian populations. The abbreviations of the population names are given in Table S4b. Color shadings denote geographic regions as indicated. ConqC and ConqE are highlighted with arrowheads. PC1 separates European populations to the left and Asian populations to the right side. PC2 separates Anatolian–Caucasus groups to the bottom and hunter–gatherers to the top.

In order to further reveal the genetic relationships of ConqC with other ancient groups, we drew an MDS plot (Figure 5) from linearized Slatkin Fst values (Table S5a). Fst distances confirmed that ConqC is nearest to ancient European and Near Eastern populations; in the Pairwise Fst matrix, the closest groups are the European Medieval (0.0098), Anatolia Bronze Age (0.00991), Iceland Medieval (0.01433), pre-Roman (Umbri) Iron Age from Italy (0.01691) and Roman Antiquity (0.01701) groups, followed by other European Bronze Age, Neolithic and Chalcolithic groups. Accordingly these are located close on the MDS plot. On the other hand, Fst data show that ConqC significantly differs from ConqE (p < 0.00000); in other words, the probability that the two populations are identical is below 1/100,000.

Figure 5

A multi-dimensional scaling (MDS) plot from the linearized Slatkin Fst values from Table S5a. Abbreviations of the population names are given in Table S4b. European populations are sequestered to the left and Asian populations are sequestered to the bottom right. Color shading denotes geographic regions as indicated. ConqC and ConqE are highlighted with arrowheads.

The novel SHD population genetic method gave similar results, but also revealed new information (Table S5b). ConqE has the smallest SHD distance from ConqC, followed by European populations from the Neolithic to the Medieval periods. It is also notable that the SHD and Fst distances of Steppe EMBA populations are comparable to those of European groups. European Scythian and Scytho–Siberian populations have noteworthy SHD distances as well, indicating that ConqC significantly shared sub-Hgs with these Eurasian steppe populations.

4. Discussion

In this paper, an attempt was made to provide a genetic description of the common people of the Carpathian Basin who lived in the 10–11th centuries during the period of the Hungarian conquest. Of the 202 obtained mitogenomes, 169 belonged to commoners, while 14 samples from the Magyarhomorog cemetery were revealed to represent a small elite graveyard, not related to the adjacent commoner remains. The elite has been shown to comprise around 30% of the east Eurasian Hgs, including characteristic ones like N1a1a1a1a [6] (Table S3c).

The overall Hg composition of the commoner population proved to be significantly different from that of the elite with respect to both east and West Eurasian Hgs, indicating that these two groups likely had different origins. Population genetic analysis definitely clustered ConqC primarily with European and Near Eastern populations, separating them from the elite, suggesting that people with local European origin dominated the ConqC population.

The presence of a non-negligible proportion of east Eurasian Hgs in the ConqC population is a clear sign of admixture with eastern immigrants, presumably with Avars and/or Conquerors. This effect distinguishes ConqC from contemporary European populations, as well as from modern Hungarians, in whom east Eurasian Hgs are negligible. Thus, despite their significant differences, ConqC might have admixed with ConqE to some extent.

This admixture is clearly validated by the SHD method, as ConqC had the smallest SHD distance from ConqE (Table S5b), meaning that out of the studied ancient populations, ConqE shared the highest proportion of identical Hgs with ConqC, best explained by admixture. As the SHD value perfectly represents the common gene pool, the SHD distance of 0.85 indicates a 14% common gene pool between ConqE and ConqC. Out of the 18 shared Hgs, 4 had an east Eurasian origin (Table S3c), so these were very likely transferred from the elite to the commoners. It is especially telling that the most frequent ConqE Hgs (N1a1a1a1, its derivative N1a1a1a1a and T1a1) were present in numerous commoner cemeteries. The east Eurasian N1a1a1a1 ConqE marker most likely originated from the Afanasievo or Sintashta–Tagar cultures [37,38], while, despite its general Eurasian range, a Mongolian Chemurchek–Uyuk–Deer stone–khirigsuur [39] origin of T1a1 in ConqE is very plausible (Table S3c). The close SHD distance of ConqE to Steppe EMBA and Steppe MLBA populations (Table S5b) implies that the Steppe EMBA affinity of ConqC, observed in Figure 4, can also be a consequence of ConqE admixture.

The phylogeographic origin of shared Hgs also signals a possible reciprocal gene flow from ConqC to ConqE, as some of their shared Hgs (H7, K1c1, T2b and V7a) were absent from east Eurasia but had been present in the Carpathian Basin from the Neolithic–Bronze Age, as shown in Table S3c. As a consequence, the 14% common gene pool between ConqE and ConqC cannot be interpreted as a headcount proportion of immigrants and local people. Furthermore, both could have acquired common elements from other unknown populations.

The contemporary local population is descended from previous peoples of the Carpathian Basin, and it has indeed been shown that a large number of people survived to the 10th century from the previous Avar period [40,41]. The Avars also brought along a package of east Eurasian Hgs, and a significant fraction of east Eurasian Hgs which are found in ConqC and are not shared with ConqE (such as B5b4, C4a1b, C5b1a, D4b1, D4e4, D4l2, D4m2a and D5a3a1, as shown in Table S3c). These Hgs are potential candidates for Avar heritage.

5. Conclusions

For more accurate conclusions, future investigations are necessary, including high-resolution genome analysis of commoner and elite cemeteries. Additionally, genome data from the pre-Avar, Avar and later Árpádian populations would provide a more complete picture about the exact contribution of subsequent nomadic migrations to the demographic history of the Carpathian Basin.