Biology subjects

Hajdu, T.

Publications and source records attributed to Hajdu, T..

10 recordsLinked to original sources

bioRxiv2025

Unveiling the complexity of post-Roman polity formation using ancient DNA

The transformation of the Roman world (4th-9th centuries CE) culminating in the dissolution of the Western Roman Empire in the 5th century marked a fundamental transition in European history. "Barbarian" groups and Roman provincial societies merged into enduring political frameworks in some places but not in others. Key questions persist regarding the regionally specific nature of this transformation. Here, we present one of the most densely sampled early medieval datasets to date, enabling the reconstruction of a post-Roman polity at an unprecedented micro-regional resolution. Our integrated genetic and archaeological analysis of two Roman-period (n=68) and five post-Roman (n=246) sites from the Little Hungarian Plain, a former Roman frontier region, reveals a significant increase in Northern European genetic ancestry, likely reflecting a large-scale population movement into the region. Moreover, while all post-Roman sites, dated to the time of the Langobard Kingdom, share similar genetic profiles, burial practices, and material culture, they display distinct patterns of social organization, especially regarding the role that biological relatedness played in each community. Our results suggest that distinct social hierarchies might have existed between sites, and their intensive connectivity probably formed the basis for regional-level organisation within the post-Roman polity. Our study provides a framework for investigating how new polities take shape after the collapse of major political systems. Applied more broadly, this approach can deepen our understanding of societal transformation across early medieval Europe and beyond, offering a richer and more nuanced view of the human past than ever before.

evolutionary biology↗

bioRxiv2025

Murder in cold blood? Forensic and bioarchaeological identification of the skeletal remains of Bela, Duke of Macso (c. 1245-1272)

In 1915, the remains of a male were discovered in a 13th-century monastery on Margaret Island, Budapest. Historical context suggested that the remains may belong to Duke Bela of Macso (c. 1245-1272), grandson of King Bela IV of Hungary (House of Arpad) and son of Duke Rostislav (Rurik dynasty). We applied a complex approach to identify the individual and reconstruct the circumstances of his death. Radiocarbon dating, when adjusted for freshwater reservoir effects linked to a high-protein diet, placed the burial in the mid-13th century. Skeletal features corresponded to a young adult male. Stable isotope and dental calculus analyses indicated a high-status diet rich in animal proteins and C3 cereals. Ancient DNA confirmed descent from King Bela III (Arpad dynasty) and Y-chromosomal affiliation with the Rurikid lineage. Forensic evidence revealed 26 perimortem injuries, suggesting a coordinated, premeditated assassination involving at least three assailants. The pattern of injuries indicates both planning and intense emotional involvement. Our findings provide the first genetic identification of a medieval royal, and resolve a century-old archaeological question, and illustrate the power of integrating multidisciplinary methods to confirm historical hypotheses and reconstruct violent deaths from the past with unprecedented detail. TeaserWith unprecedented details, this study shows the impact of integrating multidisciplinary methods to confirm historical hypotheses and reconstruct violent deaths from the past.

genetics↗

bioRxiv2025

Podocalyxin and ciliary neurotrophic factor receptor are novel components of the surfaceome of chondrogenic cells

BackgroundOsteoarthritis is a degenerative joint disease characterized by progressive loss of articular cartilage and limited capacity for intrinsic repair. A major barrier to developing effective regenerative strategies is the incomplete understanding of the molecular mechanisms regulating chondrogenesis and cartilage maintenance. Cell surface proteins are key mediators of extracellular communication, adhesion, and signaling, yet the chondrogenic surfaceome remains incompletely mapped, with prior studies focusing primarily on mature or cytokine-activated chondrocytes. The aim of this study was to provide a temporal profile of the surfaceome during in vitro chondrogenic differentiation and to identify novel membrane proteins with potential roles in cartilage biology. MethodsWe applied a sialoglycoprotein-targeted glycocapture strategy to selectively enrich plasma membrane proteins from chick embryonic limb bud-derived micromass cultures undergoing chondrogenesis. Enriched samples underwent high-resolution shotgun proteomic analysis, and differentially expressed candidates were validated by western blotting, immunocytochemistry, and transient gene silencing. Functional effects on extracellular matrix gene regulation were assessed by quantitative RT-PCR and matrix histochemistry. ResultsThis approach generated the first temporal surfaceome map of chondrogenic progenitors. Among identified candidates, two proteins not previously linked to chondrogenesis, podocalyxin (PODXL) and ciliary neurotrophic factor receptor (CNTFR), were detected at the plasma membrane and confirmed at the protein and transcript levels. Both proteins exhibited time-dependent downregulation during differentiation. Targeted knockdown revealed differential regulation of the fibrocartilage marker COL1A1 expression, indicating non-redundant roles in cell-matrix signaling and survival pathways. Single-cell transcriptomic meta-analysis confirmed expression of both proteins in discrete human articular chondrocyte subpopulations. ConclusionsThis study expands the molecular framework of chondrogenesis, identifying PODXL and CNTFR as novel, temporally regulated surfaceome components with distinct roles in extracellular matrix signaling. These findings complement prior proteomic analyses of cytokine-activated mature articular chondrocytes and suggest new candidates for developmental cartilage biomarkers and therapeutic targets for osteoarthritis. Our results provide a resource for future cross-species surfaceome studies and highlight key pathways for further investigation into cartilage lineage specification and matrix adaptation. Plain English SummaryOsteoarthritis is the most common joint disease worldwide, causing pain, stiffness, and reduced mobility as the smooth cartilage that covers the ends of bones gradually breaks down. Cartilage has a very limited ability to heal itself, and there are currently no treatments that can stop or reverse the disease. Scientists are working on new ways to repair or replace damaged cartilage, but to do this effectively, they need to understand the molecular "language" that cartilage-forming cells use to develop and maintain healthy tissue. In this study, we examined the set of proteins that are present on the surface of cartilage-forming cells, known as the "surfaceome." These surface proteins play important roles in how cells connect to their surroundings, receive signals, and work together to build the cartilage matrix. Using a method to selectively capture and analyze these proteins, we discovered two that had never been linked to cartilage development: podocalyxin and ciliary neurotrophic factor receptor. We found that these two proteins may have opposite effects on cartilage quality. Because they can be detected on the outside of cells, they could be developed into markers for early osteoarthritis detection or as targets for new therapies. Our findings open the door to new strategies for diagnosing and treating joint disease by focusing on cell-surface communication.

cell biology↗

bioRxiv2025

Ancient DNA reveals diverse community organizations in the 5th millennium BCE Carpathian Basin

Little is known about the genetic connection system and community organization of Late Neolithic and Early Copper Age populations of the Carpathian Basin. Here, we present a comprehensive genetic investigation of these populations, leveraging whole genome data from 125 individuals. Using population genetics, kinship analyses and the study of networks of identity-by-descent haplotype segment sharing, we elucidate the social and genetic dynamics of these communities between 4800-3900 calibrated years BCE. Despite changes in settlement patterns, burial practices, and material culture, we document a high degree of genetic continuity. While one set of individuals from a large community cemetery is genetically diverse, another site is more homogenous and closed, with numerous consanguineous relationships and evidence of patrilineality and patrilocality. In this work, we document important differences in kinship systems in contemporaneous Early Copper Age communities using similar material culture and living only about 100 km apart.

genomics↗

bioRxiv2024

The Genetic Origin of the Indo-Europeans

The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a "Caucasus-Lower Volga" (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga. Bidirectional gene flow across the CLV cline created admixed intermediate populations in both the north Caucasus, such as the Maikop people, and on the steppe, such as those at the site of Remontnoye north of the Manych depression. CLV people also helped form two major riverine clines by admixing with distinct groups of European hunter-gatherers. A "Volga Cline" was formed as Lower Volga people mixed with upriver populations that had more Eastern hunter-gatherer (EHG) ancestry, creating genetically hyper-variable populations as at Khvalynsk in the Middle Volga. A "Dnipro Cline" was formed as CLV people bearing both Caucasus Neolithic and Lower Volga ancestry moved west and acquired Ukraine Neolithic hunter-gatherer (UNHG) ancestry to establish the population of the Serednii Stih culture from which the direct ancestors of the Yamnaya themselves were formed around 4000BCE. This population grew rapidly after 3750-3350BCE, precipitating the expansion of people of the Yamnaya culture who totally displaced previous groups on the Volga and further east, while admixing with more sedentary groups in the west. CLV cline people with Lower Volga ancestry contributed four fifths of the ancestry of the Yamnaya, but also, entering Anatolia from the east, contributed at least a tenth of the ancestry of Bronze Age Central Anatolians, where the Hittite language, related to the Indo-European languages spread by the Yamnaya, was spoken. We thus propose that the final unity of the speakers of the "Proto-Indo-Anatolian" ancestral language of both Anatolian and Indo-European languages can be traced to CLV cline people sometime between 4400-4000 BCE. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/589597v1_ufig1.gif" ALT="Figure 1"> View larger version (91K): org.highwire.dtl.DTLVardef@127de98org.highwire.dtl.DTLVardef@87010aorg.highwire.dtl.DTLVardef@1554627org.highwire.dtl.DTLVardef@170dd63_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSummary Figure:C_FLOATNO The origin of Indo-Anatolian and Indo-European languages. Genetic reconstruction of the ancestry of Pontic-Caspian steppe and West Asian populations points to the North Caucasus-Lower Volga area as the homeland of Indo-Anatolian languages and to the Serednii Stih archaeological culture of the Dnipro-Don area as the homeland of Indo-European languages. The Caucasus-Lower Volga people had diverse distal roots, estimated using the qpAdm software on the left barplot, as Caucasus hunter-gatherer (purple), Central Asian (red), Eastern hunter-gatherer (pink), and West Asian Neolithic (green). Caucasus-Lower Volga expansions, estimated using qpAdm on the right barplot as disseminated Caucasus Neolithic (blue)-Lower Volga Eneolithic (orange) proximal ancestries, mixing with the inhabitants of the North Pontic region (yellow), Volga region (yellow), and West Asia (green). C_FIG

genetics↗

bioRxiv2023

Improved detection of methylation in ancient DNA

Reconstructing premortem DNA methylation levels in ancient DNA (aDNA) has led to breakthrough studies such as the prediction of anatomical features of the Denisovan, as well as the castration status of ancient horses. These studies relied on computationally inferring methylation levels from damage signals in naturally deaminated cytosines. Because of statistical constraints, this inference requires high-coverage sequencing, and is thus not only expensive but also restricted to samples with exceptional DNA preservation. Instead, a method to directly measure methylation levels in aDNA, as exists in modern DNA samples, would open the door to a more thorough and cost effective ability to study ancient DNA methylation. We have tested two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. We find that both methods preserve sufficient DNA yields to allow for methylation measurement. Bisulfite treatment, combined with a single stranded library preparation, shows the least reduction in DNA yields compared to no methylation treatment, as well as the least biases during methylation conversion. In addition, we show that applying bisulfite treatment to [~]0.4-fold coverage sample provides a methylation signal that is comparable to, or even better, than the computationally inferred one. We thus present a method to directly measure methylation in ancient DNA that is cost effective and can be used on a wide variety of ancient samples.

genomics↗

bioRxiv2022

Investigating community formation through dense spatial and temporal sampling of 5-6th century cemeteries in Pannonia

As the collapse of the Western Roman Empire accelerated during the 4th and 5th centuries, arriving "barbarian" groups began to establish new communities in the border provinces of the declining (and eventually former) empire. This was a time of significant cultural and political change throughout not only these border regions but Europe as a whole.1,2 To better understand post-Roman community formation in one of these key frontier zones after the collapse of the Hunnic movement, we generated new paleogenomic data for a set of 38 burials from a time series of three 5th century cemeteries3-5 at Lake Balaton, Hungary. We utilized a comprehensive sampling approach to characterize these cemeteries along with data from 38 additional burials from a previously published mid-6th century site6 and analyzed them alongside data from over 550 penecontemporaneous individuals7-19. The range of genetic diversity in all four of these local burial communities is extensive and wider ranging than penecontemporaneous Europeans sequenced to date. Despite many commonalities in burial representation and demography, we find that there were substantial differences in genetic ancestry between the sites. We detect evidence of northern European gene flow into the Lake Balaton region. Additionally, we observe a statistically significant association between dress artefacts and genetic ancestry among 5th century genetically female burials. Our analysis shows that the formation of early Medieval communities was a multifarious process even at a local level, consisting of genetically heterogeneous groups.

genetics↗

bioRxiv2021

An integrative skeletal and paleogenomic analysis of prehistoric stature variation suggests relatively reduced health for early European farmers

Human culture, biology, and health were shaped dramatically by the onset of agriculture ~12,000 years before present (BP). Subsistence shifts from hunting and gathering to agriculture are hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a simultaneous decline in physiological health as inferred from paleopathological analyses and stature reconstructions of skeletal remains. A key component of the health decline inference is that relatively shorter statures observed for early farmers may (at least partly) reflect higher childhood disease burdens and poorer nutrition. However, while such stresses can indeed result in growth stunting, height is also highly heritable, and substantial inter-individual variation in the height genetic component within a population is typical. Moreover, extensive migration and gene flow were characteristics of multiple agricultural transitions worldwide. Here, we consider both osteological and ancient DNA data from the same prehistoric individuals to comprehensively study the trajectory of human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared predicted genetic contributions to height from paleogenomic data and achieved adult osteological height estimated from long bone measurements on a per-individual basis for n=160 ancient Europeans from sites spanning the Upper Paleolithic to the Iron Age (~38,000-2,400 BP). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of -4.47 cm relative to individuals from the Upper Paleolithic and Mesolithic (P=0.016). The average osteological vs. expected stature then increased relative to the Neolithic over the Copper (+2.67 cm, P=0.052), Bronze (+3.33 cm, P=0.032), and Iron Ages (+3.95 cm, P=0.094). These results were partly attenuated when we accounted for genome-wide genetic ancestry variation in our sample (which we note is partly duplicative with the individual polygenic score information). For example, in this secondary analysis Neolithic individuals were -3.48 cm shorter than expected on average relative to individuals from the Upper Paleolithic and Mesolithic (P=0.056). We also incorporated observations of paleopathological indicators of non-specific stress that can persist from childhood to adulthood in skeletal remains (linear enamel hypoplasia, cribra orbitalia, and porotic hyperostosis) into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.

genomics↗

bioRxiv2020

A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth

Ancient DNA sampling methods--although optimized for efficient DNA extraction--are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but standard destructive sampling methods often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and 9 corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.

evolutionary biology↗

bioRxiv2019

Human Auditory Ossicles as an Alternative Optimal Source of Ancient DNA

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provide optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of valuable morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluated the efficacy of ossicles as an alternative source of ancient DNA. We demonstrate that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quality, quantity, or authenticity across a range of preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that, when available, they should be selected over the cochlea to reduce damage to skeletal integrity. These results identify a second optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

genomics↗