Abstract We analyzed 399 shotgun genomes from the Royal Basilica of Székesfehérvár, representing the elite of the Medieval Hungarian Kingdom. Our results reveal that the Carpathian Basin population underwent a marked homogenization during the Middle Ages, driven largely by admixture with eastern immigrant groups, especially the conquering Hungarians, resulting in a genomic landscape distinct from that of the surrounding European populations. The European ancestry component also shifted: the Avar-period Balkan element disappeared, while northern and northwestern European ancestry increased, likely reflecting changing political connections. We identified a previously unrecognized Conquest-period stratum at the site, including two individuals closely related to the Árpád dynasty. No large, continuous kinship networks were detected, indicating a dynamic and continuously renewed elite. At the population level, the strongest affinities were observed with the Conq_Asia_Core group and its ancestor, the Karayakupovo horizon, as well as with medieval populations from neighboring regions (present-day Croatia, Serbia, Slovakia, Poland, and Montenegro), reflecting the diverse sources of the medieval Hungarians.

Shotgun sequencing of >400 genomes from the ossuary of the Royal Basilica of Székesfehérvár identified three additional skeletal remains carrying the Árpád Dynasty's Y chromosome haplogroup R-ARP, raising the total known R-ARP+ individuals from four to seven. Kinship and IBD analyses placed these individuals within the dynasty alongside Béla, Duke of Macsó (†1272)-a Rurikid prince and great-great-grandson of King Béla III- and a fetus from a tomb adjacent to Béla III. One of these is King Béla II "the Blind" (1131-1141); a second is a likely second-degree relative of St. Ladislaus (probably an uncle, identity unresolved); the third, buried outside the original Basilica walls, is related to the Árpáds only by Y-haplogroup. The authenticity of Béla, Duke of Macsó's remains was genetically confirmed. IBD also linked Árpáds to conquering Hungarians, Vikings, and the Aba, Báthory, and Corvinus families.

The nomadic Sarmatians dominated the Pontic Steppe from the 3rd century BCE and the Great Hungarian Plain from 50 CE until the Huns' 4th-century expansion. In this study, we present a large-scale genetic analysis of 156 genomes from 1st- to 5th-century Hungary and the Carpathian foothills. Our findings reveal minor East Asian ancestry in the Carpathian Basin (CB) Sarmatians, distinguishing them from other regional populations. Using F4 statistics, qpAdm, and identity-by-descent (IBD) analysis, we show that CB Sarmatians descended from Steppe Sarmatians originating in the Ural and Kazakhstan regions, with Romanian Sarmatians serving as a possible genetic bridge between the two groups. We also identify two previously unknown migration waves during the Sarmatian era and a notable continuity of the Sarmatian population into the Hunnic period despite a smaller influx of Asian-origin individuals. These results shed new light on Sarmatian migrations and the genetic history of a key population neighboring the Roman Empire.

Background/Objectives: Ancient DNA (aDNA) research workflows heavily depend on efficient aDNA extraction and NGS library preparation. In this study, we compared some of the commonly used laboratory protocols and compared the source of the bone material for sufficient and reliable results. Methods: We executed a three-phase study. First, we analyzed about 2000 previously processed archaic bone samples and conducted a comparative analysis. The second phase involved a controlled experiment of five ancient individuals, with internal control, to further investigate the efficiency of some of the methods. In the third phase, we made a comparison between the efficiency of two enzymes used for library preparation. Results: Samples made from Pars petrosa resulted in the highest yield of endogenous DNA and longer fragment sizes compared to tooth or skeletal samples. DNA extraction made by MinElute columns preserved slightly longer fragments than the handmade silica suspension. NGS libraries indexed using AccuPrime Pfx produced slightly more consistent insert sizes compared to GoTaq G2. Samples prepared with GoTaq G2 contained slightly more unique molecules. The duplication rates showed no significant impact from enzyme choice. Conclusions: Pars petrosa remains the most reliable source of aDNA, with the extraction method using MinElute columns. While AccuPrime Pfx ensures precise NGS library preparation, a more economical choice of the GoTaq G2 enzyme is a viable alternative for degraded archaic samples.

The Aba family played a pivotal role in Medieval Hungary, dominating vast territories and producing influential figures. We conducted an archaeogenetic study on remains from the necropolis in Abasár, the political center of the Aba clan, to identify family members and explore their genetic origins. Using Whole Genome Sequencing (WGS) data from 19 individuals and radiocarbon dating, we identified 6 Aba family members with close kinship ties. Four males carried identical N1a1a1a1a4∼ haplogroups, and our phylogenetic analysis traced this royal paternal lineage back to Mongolia, indicating migration to the Carpathian Basin with the conquering Hungarians. Genome analysis, including ADMIXTURE, Principal Component Analysis (PCA), and qpAdm, revealed East Eurasian genetic patterns, aligning with our phylogenetic findings. Identity by Descent (IBD) analysis confirmed family kinship and revealed connections to prominent Hungarian noble families like the Árpáds, Báthorys, and Corvinus, as well as to the first-generation immigrant elite of the Hungarian conquest.

Female burials equipped with weapons, a topic of interest among scholars and the general public, remain rare occurrences in archaeological records. The interpretation of such cases requires an interdisciplinary approach and a comprehensive evaluation of the available evidence, particularly regarding the sex and potential lifestyle of the deceased. Consequently, data on specific populations, regions, and time periods remain scarce. For instance, no such case has been reported before concerning the 10th century CE of the Carpathian Basin, known as the Hungarian Conquest period. Our study focuses on an interdisciplinary investigation of a previously known burial, grave No. 63 from the 10th-century-CE cemetery of Sárrétudvari-Hízóföld (eastern Hungary), which represents a unique case with grave goods including jewelry typically associated with females and archery equipment traditionally linked to males. Through archeological, anthropological, and archaeogenetic analyses, we aim to determine if this case represents the first-known female burial with weapon from the 10th-century-CE Carpathian Basin. Despite the poor bone preservation, a factor limiting data recording and evaluation, all analyses consistently indicate that the skeletal remains belonged to a female individual. The burial customs, including weapon equipment composition show analogies with male counterparts in the series. In addition, the pattern of pathological and supposed activity-related changes observed on the bones may have resulted from regular physical activity during her lifetime. In summary, our findings support the identification of this case as the first known female burial with weapon from the 10th-century-CE Carpathian Basin.

The prediction of externally visible traits (eye, hair and skin colours) from DNA can provide valuable information for both contemporary and ancient human populations. The validated HIrisPlex-S method is the primary tool in forensics for phenotyping modern samples. The HIrisPlex-S multiplex PCR assay can handle trace DNA from modern samples, but the analysis of degraded, low coverage ancient DNA (aDNA) presents additional challenges. Genotype imputation has recently proven successful in effectively filling in missing information in aDNA sequences. To assess the feasibility of this approach, we evaluated how key factors, such as genome coverage, minor allele frequency, extent of post mortem damage, and the population origin of the test individual influence the efficiency of imputing HIrisPlex-S markers and predicting phenotypes. We used high coverage sequence data from ancient remains for the evaluation. Our results demonstrate that even with genome coverages as low as 0.1-0.5x, the proposed workflow is capable of predicting phenotypes from degraded ancient (or forensic) WGS data with good accuracy. To aid the archaeogenetics community, we have developed a user-friendly, easily deployable imputation-based framework that includes the new bioinformatics tools and the pre-made reference data sets required for the whole analysis.

Középkori uralkodóink sírjai a történelem viharaiban elvesztek, maradványaik ismeretlen helyen, azonosítatlanul nyugszanak. Máig egyedül III. Béla maradványai kerültek elő, valamint szent királyaink ereklyéi maradtak meg az utókornak, melyek eredetiségét azonban sokan kétségbe vonják. Munkánk során a legtöbb királyunk temetkezési helyéül szolgált székesfehérvári királyi bazilika területén feltárt maradványok archeogenetikai vizsgálatát végezzük el, és azonosítjuk uralkodóink csontvázait. Emellett a Szent László-herma koponyaereklyéjét is megvizsgáltuk, hogy valódiságát igazoljuk. Míg a székesfehérvári vizsgálatokból csak részeredményeket közlünk, lévén a munka még nem fejeződött be, addig a Herma vizsgálata lezajlott, bemutatjuk, hogy eredetisége igazolást nyert, valóban Szent László koponyáját rejti. Mi több, azt is ismertetjük, hogyan járult hozzá Szent László genomvizsgálata az Árpád-házi maradványok személyazonosításához, és kimutatjuk a honfoglalók genetikai örökségét a Szent Király örökítőanyagában.

The Báthory family was one of the most powerful noble families in the medieval Hungarian Kingdom. Their influence peaked during the Ottoman occupation of Hungary, when the only partially autonomous region of the country was Transylvania, under Turkish protectorate. Several members of the family became Princes of Transylvania, and one of them, István Báthory, was also the elected King of Poland. We hereby present the first genetic data about this extinct family. Archaeological excavations in Pericei, a settlement now part of Romania, revealed the former family chapel of the Báthory family. Through this work, two Báthory family members were successfully identified among the 13 skeletons found at the site. The presence of Y chromosome haplogroup R-S498 fits the historical account describing the family's German (Swabian) origins. Their genomic composition also indicates a family of Germanic origin that intermixed with medieval Hungarians.

A régészeti leletekből kinyerhető archaikus DNS vizsgálata fényt deríthet egyének, populációk eredetére és rokoni kapcsolataira. Korábbi munkánk során elsősorban a honfoglalás kori szállási temetők genetikai kapcsolatait derítettük fel régészeti genetikai módszerekkel. A karosi és kenézlői temető együttesek nagy felbontású teljes mitogenom analízise azt mutatta, hogy a honfoglalók anyai ágú vonalai visszavezethetők az eurázsiai sztyeppe távoli részeire: harmaduk Közép-Belső Ázsia területéről származott, kétharmaduk pedig a bronzkori pontusi-kaszpi sztyeppe Poltavka-Potakovka-Szrubnaja kultúráira vezethető vissza. Felvetődött a kérdés, hogy ezek az adatok milyen mértékben vonatkoztathatók a teljes honfoglaló populációra? Hogy ezt a kérdést megválaszoljuk, vizsgálatainkat kiterjesztettük a 10. századi nagyobb sírszámú falusi temetőkre, melyek a honfoglalás kori köznépet rejthetik. A kiválasztott 6 falusi temető mindegyikéből 20-30 egyén anyai vonalait vizsgáltuk. A mintaválasztást elsősorban régészeti és antropológiai adatok alapján végeztük. Mivel a temetők többsége átnyúlik az Árpád-korba és korábbi antropológiai vizsgálatok több temetőben lehetséges népességcserét jeleztek, ezért a korai és a későbbi sírok összehasonlításával a népességcsere kérdésére is választ remélhetünk. A projekt jelen állása szerint csaknem az összes szekvencia adat elkészült és most folyik az adatok filogenetikai és populációgenetikai kiértékelése, ezért az előzetes eredményeket tudjuk bemutatni.

The Xiongnu Empire was the first integrated political formation of Eastern Steppe nomads, whose history is known from the contemporaneous Chinese written sources and the archaeological findings of their burials. Here we present a complex multidisciplinary study of a tomb from the Xiongnu cemetery of Belkhin Am. The archaeological features characterized the grave as an elite Xiongnu burial. By radiocarbon analysis the tomb could be dated to the middle of the Xiongnu era, between the 1st century BCE and 1st century CE. The phylogenetic connections of the human remains found in the grave were in concordance with its Inner East Asian location.

A honfoglaló magyarok nomád csoportjai meghatározó szerepet játszottak a magyar őstörténetben, de genetikai adatok csak a bevándorló elit rétegből állnak rendelkezésre. A X-XI. századi Kárpát-medencei maradványok nagy része a köznéphez tartozik, akiknek származása és a bevándorló elithez való viszonya széles körben vitatott. A mitogenom-szekvenciákat 202 egyedből nyertük ki újgenerációs szekvenálás és hibridizációs dúsítás kombinációjával. A filogenetikai vizsgálatokhoz Median-Joining Network-elemzést használtunk. A köznépi populációt 87 ősi eurázsiai populációval hasonlítottuk össze szekvenciaalapú (Fst) és haplocsoport-alapú populációgenetikai módszerekkel. A köznép haplocsoport-összetétele markánsan eltér az elitétől, és az elittel ellentétben a köznép európai populációkkal csoportosult. Emellett a megfigyelhető alhaplocsoport-megoszlás az elit és a köznép közötti keveredést jelzi. A X-XI. századi köznép többsége nagy valószínűséggel a Kárpát-medence ősi helyi lakosságát képviseli, amely keveredett a keleti eredetű bevándorló csoportokkal (akik között voltak honfoglaló magyarok is).

A 9. században nomád magyar törzsek csoportjai érkeztek a Kárpát-medencébe. Ez az esemény alapvető fontosságú Magyarország történelmében, azonban a 10-11. századi magyarság etnikai eredete máig tisztázatlan. A temetkezési jellemzők és régészeti mellékletek alapján egy elit társadalmi réteg megkülönböztethető a honfoglalás kori nagyobb, köznépi rétegtől, de e két csoport genetikai rokonságáról keveset tudunk. Az eddigi genetikai vizsgálatok leginkább az elit réteg vizsgálatára koncentráltak, ezért tanulmányunkban a köznépi réteg filogeográfiai eredetének vizsgálatát, valamint e két csoport genetikai összetételének összehasonlítását tűztük ki célul. 202 maradvány teljes mitokondriális genomszekvenciáját határoztuk meg, amelyek többsége a 10-11. századi Kárpát-medence köznépi rétegéhez tartozott. A populációgenetikai vizsgálataink jelentős különbségeket tártak fel a két magyar csoport között, és a köznépi populációt archaikus európai populációkkal csoportosították, ez pedig arra utal, hogy a köznépi réteg helyben élő populációk leszármazottja lehet. Az elit és a köznépi rétegek megosztott alhaplocsoportjai azonban a két csoport közötti keveredésre utalnak.

Summary Huns, Avars and conquering Hungarians were Migration Period nomadic groups which arrived in three successive waves in the Carpathian Basin between the 5 th and 9 th centuries. Based on historical data each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations has been debated. In this study we have sequenced 9 Hun, 143 Avar and 113 Hungarian conquest period samples, and identified three core populations, representing immigrants from each period, with no recent European ancestry. Our results suggest that this “immigrant core” of both Huns and Avars originated in present day Mongolia, and their origin can be traced back to Xiongnus. On the other hand, the “immigrant core” of the conquering Hungarians derived from an earlier admixture of Mansis, early Sarmatians and descendants of late Xiongnus. In addition, we detected shared Hun-related ancestry in numerous Avar and Hungarian conquest period genetic outliers indicating a genetic link between these successive nomadic groups. Aside from the immigrant core groups we identified that the majority of the individuals from each period were local residents, harboring “native European” ancestry.

We introduce a novel population genetic approach suitable to model the origin and relationships of populations, using new computation methods analyzing Hg frequency distributions. Hgs were selected into groups which show correlated frequencies in subsets of populations, based on the assumption that correlations were established in ancient separation, migration and admixture processes. Populations are defined with this universal Hg database, then using unsupervised artificial intelligence, central vectors (CVs) are determined from local condensations of the Hg-distribution vectors in the multidimensional point system. Populations are clustered according to their proximity to CVs. We show that CVs can be regarded as approximations of ancient populations and real populations can be modeled as weighted linear combinations of the CVs using a new linear combination algorithm based on a gradient search for the weights. The efficacy of the method is demonstrated by comparing Copper Age populations of the Carpathian Basin to Middle Age ones and modern Hungarians. Our analysis reveals significant population continuity since the Middle Ages, and the presence of a substrate component since the Copper Age.

Középkori uralkodóink sírjai a történelem viharaiban elvesztek, maradványaik ismeretlen helyen, azonosítatlanul nyugszanak. Máig egyedül III. Béla maradványai kerültek elő, valamint szent királyaink ereklyéi maradtak meg az utókornak, melyek eredetiségét azonban sokan kétségbe vonják. Munkánk során a legtöbb királyunk temetkezési helyéül szolgált székesfehérvári királyi bazilika területén feltárt maradványok archeogenetikai vizsgálatát végezzük el, és azonosítjuk uralkodóink csontvázait. Emellett a Szent László-herma koponyaereklyéjét is megvizsgáltuk, hogy valódiságát igazoljuk. Míg a székesfehérvári vizsgálatokból csak részeredményeket közlünk, lévén a munka még nem fejeződött be, addig a herma vizsgálata lezajlott, bemutatjuk, hogy eredetisége igazolást nyert, valóban Szent László koponyáját rejti. Mi több, azt is ismertetjük, hogyan járult hozzá Szent László genomvizsgálata az Árpád-házi maradványok személyazonosításához, és kimutatjuk a honfoglalók genetikai örökségét a Szent Király örökítőanyagában.

The house of Arp ad ruled Hungary for more than four centuries,establishing dynastical relationships with numerous European nobleand ruling houses, and giving many Catholic saints and blesseds to the Catholic Church. They were one of the significant dynasties of Medieval Europe （Krist o and Makk, 1996）. The knight-king Saint Ladislaus I （c.1040-1095, reign:1077-1095） is one of the most outstanding kings of this dynasty. In addition to the hand relic （the Holy Right） of King Saint Stephanus I （c. 975-1038, reign:1000/1001-1038）, the skull relic in the Saint Ladislaus’ Herma（Fig. 1A-1C） preserved in the Cathedral of Gy or, is one of the most important relics for Hungarians （Klaniczai, 2000）.

Huns, Avars, and conquering Hungarians were migration- period nomadic tribal confederations that arrived in three successive waves in the Carpathian Basin between the 5th and 9th centuries. Based on the historical data, each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations have been debated. Recently, hundreds of ancient genomes were analyzed from Central Asia, Mongolia, and China, from which we aimed to identify putative source populations for the above-mentioned groups. In this study, we have sequenced 9 Hun, 143 Avar, and 113 Hungarian conquest period samples and identified three core populations, representing immigrants from each period with no recent European ancestry. Our results reveal that this "immigrant core'' of both Huns and Avars likely originated in present day Mongolia, and their origin can be traced back to Xiongnus (Asian Huns), as suggested by several historians. On the other hand, the "immigrant core'' of the conquering Hungarians derived from an earlier admixture of Mansis, early Sarmatians, and descendants of late Xiongnus. We have also shown that a common "proto-Ugric'' gene pool appeared in the Bronze Age from the admixture of Mezhovskaya and Nganasan people, supporting genetic and linguistic data. In addition, we detected shared Hun-related ancestry in numerous Avar and Hungarian conquest period genetic outliers, indicating a genetic link between these successive nomadic groups. Aside from the immigrant core groups, we identified that the majority of the individuals from each period were local residents harboring "native European'' ancestry.

The Hunyadi family is one of the most influential families in the history of Central Europe in the 14th–16th centuries. The family’s prestige was established by Johannes Hunyadi, a Turk-beater who rose to the position of governor of the Kingdom of Hungary. His second son, Matthias Hunyadi, became the elected ruler of the Kingdom of Hungary in 1458. The Hunyadi family had unknown origin. Moreover, Matthias failed to found a dynasty because of lacking a legitimate heir and his illegitimate son Johannes Corvinus was unable to obtain the crown. His grandson, Christophorus Corvinus, died in childhood, thus the direct male line of the family ended.In the framework of on interdisciplinary research, we have determined the whole genome sequences of Johannes Corvinus and Christophorus Corvinus by next-generation sequencing technology. Both of them carried the Y-chromosome haplogroup is E1b1b1a1b1a6a1c ∼, which is widespread in Eurasia. The father-son relationship was verified using the classical STR method and whole genome data. Christophorus Corvinus belongs to the rare, sporadically occurring T2c1+146 mitochondrial haplogroup, most frequent around the Mediterranean, while his father belongs to the T2b mitochondrial haplogroup, widespread in Eurasia, both are consistent with the known origin of the mothers. Archaeogenomic analysis indicated that the Corvinus had an ancient European genome composition.Based on the reported genetic data, it will be possible to identify all the other Hunyadi family member, whose only known grave site is known, but who are resting assorted with several other skeletons.

According to the written historical sources, the Gepids were a Germanic tribe that settled in the Carpathian Basin during the Migration Period. They were allies of the Huns, and an independent Gepid Kingdom arose after the collapse of the Hun Empire. In this period, the Carpathian Basin was characterized by so-called row-grave cemeteries. Due to the scarcity of historical and archaeological data, we have a poor knowledge of the origin and composition of these barbarian populations, and this is still a subject of debate. To better understand the genetic legacy of migration period societies, we obtained 46 full mitogenome sequences from three Gepid cemeteries located in Transylvania, Romania. The studied samples represent the Classical Gepidic period and illustrate the genetic make-up of this group from the late 5th and early 6th centuries AD, which is characterized by cultural markers associated with the Gepid culture in Transylvania. The genetic structure of the Gepid people is explored for the first time, providing new insights into the genetic makeup of this archaic group. The retrieved genetic data showed mainly the presence of Northwestern European mitochondrial ancient lineages in the Gepid group and all population genetic analyses reiterated the same genetic structure, showing that early ancient mitogenomes from Europe were the major contributors to the Gepid maternal genetic pool.