Biology subjects

Gelabert, P.

Publications and source records attributed to Gelabert, P..

15 recordsLinked to original sources

bioRxiv2026

Genomic impact of the second plague pandemic on three human populations

The second plague pandemic (early 14th-early 19th centuries), which was caused by Yersinia pestis, had a profound demographic, socio-economic and cultural impact across Eurasia and North Africa. Many regions in Europe and the Middle East are estimated to have lost 40-60% of their human populations, with some areas suffering even higher mortality. Whether exposure to Y. pestis drove strong positive selection on protective genetic variants in the human genome, and how it shaped migration patterns, remains debated, despite several recent studies based on ancient DNA. Here, we analyse a markedly larger, higher coverage, and geographically diverse dataset based on shotgun sequencing of genomes from 529 ancient individuals to a mean depth 8.8x dating to either before or after the arrival of the pandemic at three sites in northern Europe: Trondheim (Norway), Lund (Sweden) and Vilnius (Lithuania). Genome-wide scans for signatures of selection provide no evidence for strong positive selection acting on specific genetic variants driven by Y. pestis exposure: we neither replicate selection signatures reported by previous studies nor identify new genome-wide significant candidates. However, for all three sites, we observe evidence for a reduction in long-range immigration, indicated by a drop in the diversity of ancestry that followed the arrival of Y. pestis and broadly coincided with the end of the Viking Age, Christianisation and the onset of the Little Ice Age. Our results shed important light on the demographic impact of major sociohistorical changes that occurred during the late Medieval period in Scandinavia and the Baltic region and link Christianisation to increased diversity in ancestry before the pandemic.

genomics↗

bioRxiv2025

Genetic insights into Iron Age Saka culture: Ancient DNA analysis of the Boz-Barmak burial ground, Kyrgyzstan

The nomadic cultures of the Iron Age played an important role in shaping the genetic and cultural landscape of Eurasian populations. Yet despite its key geographical location, the Central Eurasian region remains underrepresented in ancient DNA studies of humans. We address this gap through genomic analysis of 12 individuals from the Boz-Barmak burial site in Kyrgyzstan associated with Saka pastoralists (4th-2nd centuries BCE), 9 of which yielded low-coverage genomes. Genetic clustering analysis placed these individuals within the genetic variation of ancient and modern Central Eurasian and Siberian populations. We found no evidence of first-degree relatives in a kinship analysis, however a network of second- and third-degree relationships seems to be present. Notably, all male individuals share the same Y-chromosomal haplotype, common in present-day Kyrgyz and Tajik groups, while mitochondrial DNA showed comparably high diversity, with distinct haplogroups observed across the analysed individuals. These findings are in line with archaeological and ethnographic evidence of patrilocality in Early Iron Age Saka, where male lineages remained stable across generations, while female mobility contributed to genetic diversity. Our study complements our understanding of the interplay between kinship, social organization and population history in nomadic cultures.

genomics↗

bioRxiv2025

Genetic admixture between East and West European Gravettian-associated populations in Western Europe before the Last Glacial Maximum

Modern humans first settled in Europe at least 45,000 years ago. However, limited genomic data from individuals dating between 45,000 and 20,000 years ago still restricts our understanding of population dynamics and admixture during the Upper Palaeolithic. Before the Last Glacial Maximum (LGM, 26.5-19 cal kya), Gravettian culture-associated populations were widespread and genetically diverse, comprising at least two distinct genetic groups, referred to as the Fournol and V[e]stonice clusters. We present genome-wide data from three Gravettian-associated individuals: two from cave sites in the Franco-Cantabrian region (Chufin and Isturitz) and one from Italy (Ostuni1b). These data reveal previously undetected gene flow linking the ancestry of 34,000-year-old individuals from Sungir (Russia) to Gravettian individuals from Western Europe, challenging the prevailing model of population continuity from the Aurignacian to the Solutrean. As osseous remains are scarce for this time period, DNA from sediments deposited by ancient humans opens a new possibility to obtain genomic data. We thus examine sedimentary DNA from Solutrean Layer 122 at El Miron Cave (Cantabria, [~]22,000 cal BP), recovering approximately 16,000 human SNPs, among the highest yields reported from a Palaeolithic context. Generating these data required over 1.15 billion sequencing reads, illustrating both the potential of sediment DNA for autosomal analysis and the technical challenges of the approach.

genomics↗

bioRxiv2024

Bioarchaeological Perspectives on Late Antiquity in Dalmatia: Paleogenetic, Dietary, and Population Studies of the Hvar Radosevic burial site

Late Antiquity Dalmatia was a time and place of political unrest in the Roman Empire that influenced the lives of the people living in that region. The Late Antique burial site of Hvar - Rado[s]evi[c], spanning the 3rd to 5th centuries, is located on the Croatian Dalmatian island of Hvar. Given the time frame and its location on a busy marine trade route, study of this burial site offers us a glimpse into the lives of the Late Antique population living on this island. It comprises 33 individuals, with 17 buried within a confined grave tomb, and the remaining individuals buried in separate locations in the tombs proximity. Our objective was to provide new perspectives on the lives of people on the island during those times by studying ancestry, population structure, possible differences within the buried population, dietary habits, and general health. Analysis of the ancestral origins of the individuals buried at Hvar - Rado[s]evi[c] revealed a diverse population reflective of the eras genetic variability. The identification of genetic outliers suggests affiliations with distinct regions of the Roman Empire, possibly linked to trade routes associated with the Late Antique port in ancient Hvar. Stable isotope ratio analysis ({delta}{superscript 1}3C and {delta}{superscript 1}N) indicated a diet mainly consisting of C3 plants, with minimal consumption of marine foods. High childhood mortality rates, physiological stress markers, and dental diseases suggest a low quality of life in the population. Assessment of kinship and dietary patterns revealed no discernible distinctions between individuals buried within the tomb and those buried outside, indicative of an absence of differential burial practices based on social status and familial ties.

genomics↗

bioRxiv2024

Screening great ape museum specimens for DNA viruses

Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined the presence of multiple viruses within this dataset from historical specimens and obtained several near-complete viral genomes. In particular, we report high-coverage (>18-fold) hepatitis B virus genomes from one gorilla and two chimpanzee individuals, which are phylogenetically placed within clades infecting the respective host species.

genomics↗

bioRxiv2024

A complete mitochondrial genome of a Roman-era Plasmodium falciparum

Malaria has historically been one of the leading infection-related causes of death in human populations. To this day, it continues to pose a significant public health threat in African countries, particularly among children. Humans are affected by five Plasmodium species, with Plasmodium falciparum being the most lethal. The study of pathogenic DNA from ancient human remains has been vital in understanding the origin, evolution, and virulence of human-infecting pathogens. However, there have been no complete pre-20th century mitochondrial DNA (mtDNA) or genomic sequences of Plasmodium falciparum reported to date. This gap in knowledge makes it difficult to understand the genetic dynamics of this pathogen in the past. The difficulty in identifying ancient malaria cases through bioarchaeology and the infrequent presence of Plasmodium DNA in ancient bones contribute to these limitations. Here, we present the first complete mtDNA genome of P. falciparum recovered from an archaeological skeleton (a 2nd century CE Roman individual from Italy). The study of the 43-fold mtDNA genome supports the hypothesis of an Indian origin for P. falciparum in Europe and provides evidence for the genetic continuity of this lineage over the past 2,000 years. Additionally, our research highlights that extensive sampling may be necessary for malaria screening to gain insights into the evolution of this vector-borne disease from archaeological samples.

genomics↗

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↗

bioRxiv2023

Maximizing Efficiency in SedaDNA Analysis: A Novel Extract Pooling Approach

In recent years, the field of ancient DNA (aDNA) has taken a new direction toward studying human population dynamics through sedimentary DNA (sedaDNA), enabling the study of past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing method. Our approach involves combining multiple extracts, allowing users to parallelize laboratory procedures early in the sample preparation pipeline while effectively screening for the presence of aDNA. Pooled samples that exhibit aDNA signals can then undergo detailed analysis, while empty pools are discarded. We have successfully applied our extract pooling method to various sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.

genomics↗

bioRxiv2023

Social and genetic diversity in first farmers of central Europe

The Linearbandkeramik (LBK) Neolithic communities were the first to spread farming across large parts of central Europe, settling fertile regions from Ukraine to France during the second half of the 6th millennium BCE. The LBK had a high degree of material culture uniformity, albeit with regional differences in settlement patterns, subsistence, and mortuary practices. To date, ancient DNA data from LBK individuals have been generated for a limited number of locations and often in small sample sizes, making it challenging to study variation within and across sites. We report genome-wide data for 178 LBK individuals, from the Alfold Linearbankeramik Culture (ALPC) eastern LBK site of Polgar-Ferenci-hat in Hungary, the western LBK site of Nitra in Slovakia, and the enclosed western LBK settlement and massacre site of Schletz in Austria, as well as 42 LBK individuals from 18 other sites. We also report genome-wide data for 28 Early Neolithic Koros and Star[c]evo individuals from 13 sites, viewed as the predecessors of the LBK. We observe a higher percentage of western hunter-gatherer (WHG) admixture among individuals in the eastern LBK than in the far more widely distributed western LBK, showing that these two archaeologically distinct cultures also had different genetic trajectories. Most WHG-farmer mixture occurred just before the dawn of the LBK culture and there is no evidence that the WHG ancestry came systematically more from males or females. However, we do find strong genetic evidence for patrilocality among the LBK, extending previous findings based on isotopic analysis, with more genetic structure across sites on the male than on the female line, and a higher rate of within-site relatives for males. At Schletz we detect almost no first-degree relatives despite reporting data from almost every skeleton present at the site, showing that this massacre involved people from a large population, not a small community.

genetics↗

bioRxiv2023

A minimally-invasive method for ancient DNA sampling of Prehistoric bone and antler tools and hunting weapons

Internal and external bony tissues from diverse mammalian taxa are one of the primary animal raw materials exploited for technical and symbolic purposes by Eurasian Upper Palaeolithic hunter-gatherers. Identifying the source species used for osseous raw material is critical to gain insights into these populations behaviour, technology, and subsistence. The study of osseous tools has advanced in the last few years by combining archaeological and biomolecular methods. Ancient genomics opens many new analytical opportunities. Ancient DNA (aDNA) can provide a wealth of information about the animal sources of these objects. Unfortunately, aDNA analyses often involve destructive sampling. Here, we develop and apply a minimally-invasive aDNA sampling method for an assemblage of 42 prehistoric hunting weapons and tools from various Eurasian archaeological sites. We evaluated the impact of our approach on the specimens visually, microscopically and through Micro-CT scans. The surface impacts are marginal, ranging from 0.3-0.4 mm. Using a custom-made DNA capture kit for 54 mammalian species, we obtained sufficient aDNA to identify the taxa of 33% of the objects. For one of the tools, we recovered enough endogenous aDNA to infer the genetic affinities of the individual. Our results also demonstrate that ancient antler, one of the primary raw materials used during a large part of prehistory, is a reliable source of aDNA. Our minimally-invasive aDNA sampling method is therefore effective while preserving osseous objects for potential further analyses: morphometric, technical, genetic, radiometric and more.

genomics↗

bioRxiv2021

Diverse northern Asian and Jomon-related genetic structure discovered among socially complex Three Kingdoms period Gaya region Koreans

The genetic history of prehistoric and protohistoric Korean populations is not well understood due to the lack of ancient Korean genomes. Here, we report the first paleogenomic data from Korea; eight shotgun-sequenced genomes (0.7x[~]6.1x coverage) from two archeological sites in Gimhae: Yuha-ri shell mound and Daesung-dong tumuli, the most important funerary complex of the Gaya confederacy. All eight individuals are from the Korean Three Kingdoms period (4th-7th century CE), during which there is archaeological evidence of extensive trade connections with both northern (modern-day China) and eastern (modern-day Japan) kingdoms. All genomes are best modeled as an admixture between a northern-Chinese Iron Age genetic source and a Japanese-Jomon-related ancestry. The proportion of Jomon-related ancestry suggests the presence of two genetic groups within the population. The observed substructure indicates diversity among the Gaya population that is not related to either social status or sex. Teaser1,700-year-old genomes reveal the genetic diversity of ancient Koreans in the Gimhae region.

evolutionary biology↗

bioRxiv2021

TKGWV2: An ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data

Estimation of genetically related individuals is playing an increasingly important role in the ancient DNA field. In recent years, the numbers of sequenced individuals from single sites have been increasing, reflecting a growing interest in understanding the familial and social organisation of ancient populations. Although a few different methods have been specifically developed for ancient DNA, namely to tackle issues such as low-coverage homozygous data, they require a 0.1 - 1x minimum average genomic coverage per analysed pair of individuals between. Here we present an updated version of a method that enables estimates of 1st and 2nd-degrees of relatedness with as little as 0.026x average coverage, or around 1.3 million aligned reads per sample - 4 times less data than 0.1x. By using simulated data to estimate false positive error rates, we further show that a threshold even as low as 0.012x, or around 600,000 reads, will always show 1st-degree relationships as related. Lastly, by applying this method to published data, we are able to identify previously undocumented relationships using individuals previously excluded from kinship analysis due to their very low coverage. This methodological improvement has the potential to enable relatedness estimation on ancient whole genome shotgun data during routine low-coverage screening, and therefore improve project management when decisions need to be made on which individuals are to be further sequenced.

bioinformatics↗

bioRxiv2021

Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

Archaeological sediments have been shown to preserve ancient DNA, but so far have not yielded genome-scale information of the magnitude of skeletal remains. We retrieved and analysed human and mammalian low-coverage nuclear and high-coverage mitochondrial genomes from Upper Palaeolithic sediments from Satsurblia cave, western Georgia, dated to 25,000 years ago. First, a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe. Second, a wolf genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage that diverged from the ancestors of modern wolves and dogs before these diversified. Third, a bison genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the late Pleistocene genetic histories of these three species, and demonstrate that sediment DNA can be used not only for species identification, but also be a source of genome-wide ancestry information and genetic history. HighlightsO_LIWe demonstrate for the first time that genome sequencing from sediments is comparable to that of skeletal remains C_LIO_LIA single Pleistocene sediment sample from the Caucasus yielded three low-coverage mammalian ancient genomes C_LIO_LIWe show that sediment ancient DNA can reveal important aspects of the human and faunal past C_LIO_LIEvidence of an uncharacterized human lineage from the Caucasus before the Last Glacial Maximum C_LIO_LI[~]0.01-fold coverage wolf and bison genomes are both basal to present-day diversity, suggesting reshaping of population structure in both species C_LI

developmental biology↗

bioRxiv2019

Plasmodium vivax Malaria viewed through the lens of an eradicated European strain

The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonisation of the Americas. In addition, we found that some known variants for resistance to anti-malarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.

genetics↗

bioRxiv2017

Recent Regulatory Changes Shaped the Human Facial and Vocal Anatomy

SummaryRegulatory changes are broadly accepted as key drivers of phenotypic divergence. However, identifying regulatory changes that underlie human-specific traits has proven very challenging. Here, we use 63 DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting the face and vocal tract went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-affecting genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.View Full Text

evolutionary biology↗