Biology subjects

Aneli, S.

Publications and source records attributed to Aneli, S..

8 recordsLinked to original sources

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↗

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↗

bioRxiv2023

Ancestral genetic components are consistently associated with the complex trait landscape in European biobanks

The genetic structure in Europe was mostly shaped by admixture between the Western Hunter-Gatherer, Anatolian Neolithic and Steppes Yamnaya ancestral components. Such structure is regarded as a confounder in GWAS and follow-up studies, and gold-standard methods exist to correct for it. However, it is still poorly understood to which extent these ancestral components contribute to complex trait variation in present-day Europe. In this work we harness the UK Biobank to address this question. By extensive demographic simulations and incorporating previous results obtained using the Estonian Biobank, we carefully evaluate the significance and scope of our findings. Heart rate, platelet count, monocyte percentage and many other traits show stratification similar to height and pigmentation traits, likely targets of selection and divergence across ancestral groups. The consistency of our results across biobanks indicates that these ancestry-specific genetic predispositions act as a source of variability and as potential confounders in Europe as a whole.

genomics↗

bioRxiv2023

Recombulator-X: a fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

Background and ObjectiveGenetic markers (especially short tandem repeats or STRs) located on the X chromosome are a valuable resource to solve complex kinship cases in forensic genetics in addition or alternatively to autosomal STRs. Groups of tightly linked markers are combined into haplotypes, thus increasing the discriminating power of tests. However, this approach requires precise knowledge of the recombination rates between adjacent markers. Recombination rates vary across the human genome and cannot be automatically derived from linkage physical maps. The International Society of Forensic Genetics recommends that recombination rate estimation on the X chromosome is performed from pedigree genetic data while taking into account the confounding effect of mutations. However, the only existing implementations that satisfy these requirements have several drawbacks: they were never publicly released, they are very slow and/or need cluster-level hardware and strong computational expertise to use. In order to address these key concerns, we developed Recombulator-X, a new open-source Python tool. MethodsThe most challenging issue, namely the running time, was addressed with dynamic programming techniques to greatly reduce the computational complexity of the algorithm, coupled with JIT compilation to further increase performance. We also extended the statistical framework from STR to any polymorphic marker. ResultsCompared to the previous methods, Recombulator-X reduces the estimation times from weeks or months to less than one hour for typical datasets. Moreover, the estimation process, including preprocessing, has been streamlined and packaged into a simple command-line tool that can be run on a normal PC. Where previous approaches were limited to small panels of STR markers (up to 15), our tool can handle greater numbers (up to 100) of mixed STR and non-STR markers. ConclusionsIn the genetic forensic community, state-of-the-art estimation methods for X chromosome recombination rates have seen limited usage due to the technical hurdles posed by previous implementations. Recombulator-X makes the process much simpler, faster and accessible to researchers without a computational background, hopefully spurring increased adoption of best practices. Moreover, it extends the estimation framework to larger panels of genetic markers (not only STRs), allowing analyses of sequencing-based data.

bioinformatics↗

bioRxiv2022

Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy

Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithic transition and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidence points to demic and cultural influences between Southern Italians and the Balkans, starting with the initial Palaeolithic occupation until historical and modern times. To shed light on the dynamics of these contacts, we analysed a genome-wide SNP dataset of more than 700 individuals from the South Mediterranean area (102 from Southern Italy), combined with ancient DNA from neighbouring areas. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with the presence of a Bronze Age component ultimately originating from the Caucasus and characterised by high frequencies of Iranian and Anatolian Neolithic ancestries. Furthermore, to reveal possible signals of natural selection, we looked for extremely differentiated allele frequencies among Northern and Southern Italy, uncovering putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits, such as ALDH2, NID1 and CBLB.

genomics↗

bioRxiv2021

The genetic origin of Daunians and the Pan-Mediterranean southern Italian Iron Age context

The geographical location and shape of Apulia, a narrow land stretching out in the sea at the South of Italy, made this region a Mediterranean crossroads connecting Western Europe and the Balkans. Such movements culminated at the beginning of the Iron Age with the Iapygian civilization which consisted of three cultures: Peucetians, Messapians and Daunians. Among them, the Daunians left a peculiar cultural heritage, with one-of-a-kind stelae and pottery, but, despite the extensive archaeological literature, their origin has been lost to time. In order to shed light on this and to provide a genetic picture of Iron Age Southern Italy, we collected and sequenced human remains from three archaeological sites geographically located in Northern Apulia (the area historically inhabited by Daunians) and radiocarbon dated between 1157 and 275 calBCE. We find that Iron Age Apulian samples are still distant from the genetic variability of modern-day Apulians, they show a remarkable genetic heterogeneity, even though a few kilometers and centuries separate them, and they are well inserted into the Iron Age Pan-Mediterranean genetic landscape. Our study provides for the first time a window on the genetic make-up of pre-imperial Southern Italy, whose increasing connectivity within the Mediterranean landscape, would have contributed to laying the foundation for modern genetic variability. In this light, the genetic profile of Daunians may be compatible with an autochthonous origin, with plausible contributions from the Balkan peninsula.

genetics↗

bioRxiv2021

Genetics and material culture support repeated expansions into Paleolithic Eurasia from a population hub out of Africa

The population dynamics that followed the out of Africa expansion (OoA) and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macro populations have long been debated. Shedding light on these events may, in turn, provide clues to better understand cultural evolution in Eurasia between 50kya and 35kya. Here we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which UstIshim, Bacho Kiro and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 kya, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 kya, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones while moving through Siberia (Yana, Malta).

evolutionary biology↗

bioRxiv2018

Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

European populations display low genetic diversity as the result of long term blending of the small number of ancient founding ancestries. However it is still unclear how the combination of ancient ancestries related to early European foragers, Neolithic farmers and Bronze Age nomadic pastoralists can fully explain genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the overall continental diversity, but to date have been systematically understudied. Here we characterised the ancestry profiles of modern-day Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe and the rest of the world. Italian genomes captured several ancient signatures, including a non-steppe related substantial ancestry contribution ultimately from the Caucasus. Differences in ancestry composition as the result of migration and admixture generated in Italy the largest degree of population structure detected so far in the continent and shaped the amount of Neanderthal DNA present in modern-day populations.\n\nOne sentence summaryAncient and historical admixture events shaped the genetic structure of modern-day Italians, the ancestry profile of Southern European populations and the continental distribution of Neanderthal legacy.

genomics↗