Biology subjects

Kabral, H.

Publications and source records attributed to Kabral, H..

7 recordsLinked to original sources

bioRxiv2026

Ancient whole genomes reveal regional selection during adaptation to Neolithic lifestyle in Western Eurasia

The introduction of agriculture in Western Eurasia during the Mesolithic-Neolithic transition reshaped human lifestyle, demography and pathogen exposure. Yet, the associated selective pressures remain incompletely resolved because previous ancient DNA studies relied on targeted SNP panels and yielded non-overlapping results. Here, using high-coverage whole-genome data from 152 ancient individuals, including 12 newly sequenced genomes from the Iron Gates, we show that adaptation during this transition was geographically structured and involved selection of both Early Farmer and Hunter-Gatherer alleles. By combining scans of population differentiation, extended haplotype homozygosity, and adaptive admixture, we identify candidate loci under selection in ancestral and admixed populations. Extending the analysis beyond SNPs, we also detect differential copy-number variants, ancestry-associated shifts in transposable-element abundance, and an early Neolithic hepatitis B infection. Functional analyses including effects on gene expression suggested selection on immune, metabolic, reproductive, sensory, and behavioural processes. Taken together, our results reveal a broader and more regionally variable adaptive landscape than previously appreciated.

evolutionary biology↗

bioRxiv2026

Co-occurrence of Yersinia pestis and other zoonoses during European prehistory

The infection of humans by the causal agent of Plague, Yersinia pestis, has been attested as far back as 5,500 BP. Although the specific patho-mechanism and ultimate origin of the disease caused by these prehistoric genomes remains unclear, the bacterium spread through Europe, likely during the Late Neolithic to Bronze Age (LNBA). In this study, we analysed 9 genomic samples originating from 8 different human individuals dating to around 4950 cal BP from the site of Grotta della Spinosa, Tuscany, Italy. Metagenomic screening of these samples reveals one individual (GSP013) to be co-infected by Yersinia pestis, Erysipelothrix rhusiopathiae, and Hepatitis B virus (HBV). At least three further individuals from the site were infected with HBV, indicating its wider presence within the community. The phylogenetic placement of Y. pestis in GSP013 shows that this strain is closely related to the earliest LNBA Caucasus genomes of the bacterium, basal to later European diversity. This represents the earliest evidence of Y. pestis in the Italian peninsula (and Southern Europe more widely) to date, predating previously discovered genomes by at least 200 years. Furthermore, we retrieved 60 newly reported ancient genomes of Erysipelothrix rhusiopathiae and Erysipelothrix tonsillarum from animals and humans, dating back from 8,300 BP to 100 BP. Of these new genomes, 15 of which stem from individuals known to be infected by Y. pestis. This contributes to our understanding of Y. pestis transmission in prehistoric Europe and possible reservoirs, and offers insights into disease dynamics in communities during the 3rd millennium BCE.

evolutionary biology↗

bioRxiv2026

Lets Tweap again: Economic and SNP retrieval optimisation for target enrichment of ancient DNA

Advancements in ancient DNA (aDNA) research have enabled the recovery of individual human genomes through target enrichment approaches. Despite the decreasing cost of next-generation sequencing, enrichment methods targeting single-nucleotide polymorphisms (SNPs) compiled in RNA/DNA hybrid panels remain costly and require further authentic optimisations. Here, we present the Tweap (Twist cheap) protocol as a cost-effective alternative to the commercialised Twist protocol for target enrichment via in-solution hybridisation of ancient human DNA by replacing the streptavidin-coated superparamagnetic beads for binding the hybridised targeted DNA. We evaluated the protocol on 14 double-stranded DNA libraries from ancient human individuals originating from a hot and humid climate zone known to accelerate DNA degradation. The selected individuals reflected similar preservation levels and a broad range of endogenous human DNA content (0.79 - 41.69 %). We optimised and simplified both the Twist and Tweap protocols for target enrichment, particularly for libraries with ultra-low library complexity, making it reproducible in any life sciences laboratory. The modified Tweap protocol not only reduced overall reagent costs and consumption, contributing to more climate-conscious research, but also recovered up to 7% more unique SNPs when applying multi-pooling of libraries from the same individual. Our findings demonstrate that the Tweap protocol is a viable, efficient, and scalable alternative for SNP capture in ancient DNA (aDNA) studies, supporting broader accessibility and sustainability in ancient DNA research.

molecular biology↗

bioRxiv2025

Ancient genomes from the siege and destruction of Middle Bronze Age Roca Vecchia (Apulia, Italy) shed light on Aegean contacts and conflicts

BackgroundRoca Vecchia, an iconic Bronze Age stronghold in Apulia, Southern Italy, was completely destroyed during a siege between the end of the 15th century BCE and the beginning of the 14th century BCE. During the siege, seven of the local people hid within the stronghold walls. Two others, who could have been as well attackers as defenders, were found under the ruins of the main gate. The material culture found at Roca Vecchia and associated with the period of the siege includes Minoan-type pottery produced from local clay, imported Aegean pottery and an Aegean-type dagger, pointing to an established relationship between the site and the Minoan civilization. Therefore, the site offers an unprecedented opportunity to characterise the genetic components of the population inhabiting an indigenous settlement with increasing contacts with the Aegean world, and to shed light on the demic or cultural modes of the Minoan presence in the central Mediterranean. ResultsWith our work, we sampled six out of nine available unburied Middle Bronze Age individuals, contemporary with the siege and destruction of the site, and obtained genome-wide information for two individuals. When compared with available Minoan, Apulian and broadly Mediterranean genomes, the individuals showed a characteristic Bronze/Iron Age Italian peninsula genetic signature, with limited contribution from Minoans. ConclusionsWe conclude that the local population of Roca Vecchia, at the moment of the siege, was predominantly autochthonous, with a minoritarian Minoan component. A Minoan genetic signal is indeed likely present in one out of two analysed individuals who were certainly part of the dwellers of Roca Vecchia. This confirms previous hypotheses supposing that a nucleus of "foreigners" coming from the Minoan world was living in the site and mixed with locals. Archaeological data suggest that the Roca Vecchia Aegean population component probably increased in the following centuries.

genetics↗

bioRxiv2025

Paratyphoid Fever and Relapsing Fever in 1812 Napoleon's Devastated Army

During Napoleons retreat from Russia in 18121, countless soldiers of the French army succumbed to infectious diseases, but the responsible pathogen or pathogens remain debated2-5. We recovered and sequenced ancient DNA from the teeth of 13 soldiers who, based on historical records, likely died from infectious diseases, aiming to identify the pathogens responsible for their deaths6. Our results confirmed the presence of Salmonella enterica subsp enterica belonging to the lineage Para C, the causative agent of paratyphoid fever7 ; and Borrelia recurrentis, responsible for relapsing fever transmitted by body lice8. We were not able to detect Rickettsia prowazekii (the agent of typhus) and Bartonella quintana (the cause of trench fever), which had previously been associated with this deadly event, based on PCR results and historical symptom descriptions3. The presence of these previously unsuspected pathogens in these soldiers reveals that they could have contributed to the devastation of Napoleons Grande Armee during its disastrous retreat in 1812. HighlightsO_LIGenetic evidence of S. Paratyphi C and B. recurrentis in Napoleonic soldiers C_LIO_LIPhylogeny-driven authentication workflow for ultra-low-coverage pathogen aDNA C_LIO_LIHistorical descriptions of Napoleons army illness match paratyphoid fever symptoms C_LIO_LIMultiple infections likely contributed to the collapse of Napoleons 1812 campaign C_LI

microbiology↗

bioRxiv2025

Probing the zooarchaeological record across time and space for ancient pathogens

Zoonoses are among the greatest threats to human health, with many zoonotic pathogens believed to have emerged during prehistory. Palaeomicrobiological investigations of the zooarchaeological record hold potential to uncover the reservoirs, host ranges, and host adaptations of zoonotic pathogens but face challenges in identifying promising specimens and pathogen DNA preservation. We performed palaeopathological and genetic examinations of 346 skeletal elements from domesticated and wild animals collected from 34 Eurasian sites dating across the last six millennia. We identified 68 signatures of ancient (opportunistic) pathogens, including the important zoonotic pathogen Salmonella enterica, and found support that palaeopathological lesions provide guidance for specimen selection. For two pathogen species, Erysipelothrix rhusiopathiae and Streptococcus lutetiensis, we confirmed their ancient authenticity using phylogenetics, showcasing an approach to explore the relationship between ancient low-coverage genomes and their modern-day relatives. Our work presents a pathway to understanding prehistoric zoonotic diseases by integrating zooarchaeological, palaeopathological, and genetic data.

microbiology↗

bioRxiv2024

2500 Years of Human Betaherpesvirus 6A and 6B Evolution Revealed by Ancient DNA

Human betaherpesviruses 6A and 6B are double-stranded DNA viruses, specialised in infecting humans and are best known as the main causative pathogens of the common childhood infection "sixth disease". Despite only being discovered in the 1980s, these viruses are speculated to have a much longer and more complex history within the human population than available modern data make clear. The viruses are carried by large fractions of the human population and can integrate into the human genome, leading to a wide range of clinical manifestations of varied severity. Here, we present the first nine full and two partial ancient genomes of HHV-6A and 6B, dating as far back as the Italian Iron Age (ca. 1100-600 BCE). We demonstrate that large fractions of the current HHV-6 diversity were already well established in the human population by the 14th century CE. Our data suggests that HHV-6B integrated into the human genome at the latest before the 1st-6th century CE, with two integrated clades being populated by ancient DNA genomes in our phylogeny, which further supports that they originated from likely much older ancient founder events. Additionally, we show that all known inherited chromosomally integrated (ici-)HHV-6A clades were already represented in European historical populations, confirming that ici-HHV-6A no longer integrates into the human germline within populations of European ancestry and likely endogenized in early human history. Finally, our results demonstrate the unique suitability of archaeological remains and ancient DNA for the study of the evolution of integrated viruses in human populations.

evolutionary biology↗