Biology subjects

Mattiangeli, V.

Publications and source records attributed to Mattiangeli, V..

13 recordsLinked to original sources

bioRxiv2026

Plague-driven selection enriched familial Mediterranean fever mutations in Armenia

The discovery that positive selection due to resistance to malarial infection maintained the prevalence of sickle cell and other disease alleles was a landmark in evolution, genetics and epidemiology. Mutations in the MEFV gene causing familial Mediterranean fever with high frequency in Eastern Mediterranean populations give the only other strong candidates for a similar process. Here we estimate a pathogenic MEFV mutation burden in Armenians with a carrier rate of ~41%: a worldwide maximum. By combining these data with regional ancient MEFV genotypes spanning more than 60 centuries, we establish that the allele frequencies of three mutations M694V, M680I, and V726A underwent recent rapid increases, indicating positive selection with an onset consistent with the first Yersinia pestis plague pandemic, ~541 CE to 767 CE or even earlier in time, echoing functional data implying resistance to this infection as the selective agent. This extends to three the number of MEFV variants for which there is evidence for strong concurrent selection at this locus in the Eastern Mediterranean, making it unlikely that this geographic peak resulted from chance alone. Although bubonic plague was extremely widespread, the restricted geography of this selection points toward the Eastern Mediterranean as a longstanding enzootic centre with continuous recycling of outbreaks.

genomics↗

bioRxiv2026

PIGSTI: a modular, reproducible pipeline for detecting species identity, pathogens, and microbes from animal palaeogenomic data

Ancient genomics has enabled discovery of diverse pathogens across various time periods, host species, and material types. However, existing palaeogenomic pipelines predominantly focus on screening data from human hosts, or do not incorporate microbial screening methodologies. We present PIGSTI (Pathogen anImal Genome Sequence ToolkIt), a bioinformatic pipeline specifically designed for both the initial screening and subsequent detection of pathogens in shotgun sequencing data from ancient animal remains. PIGSTI's integrated Snakemake workflow performs both host detection, genome mapping and pathogen identification, generating outputs suitable for population genetics and phylogenetic analyses. Testing on 952 newly sequenced and publicly available animal palaeogenomic datasets, we identified ~15 ancient zoonotic and animal pathogens with high confidence, including the first documented case of Rickettsia felis and Leptospira borgpetersenii in an ancient animal. Our results demonstrate PIGSTI's utility for screening pathogen diversity in ancient animal hosts and reconstructing historical host-pathogen relationships.

genomics↗

bioRxiv2026

Mediterranean dispersal imposed bottlenecks in Neolithic sheep and goats

The Neolithic period in western Eurasia involved major dispersal events, including the translocation of livestock into Europe. These domestic animal translocations likely featured founder effects, fundamentally reshaping their genetic landscape. One well-known example is the Mediterranean dispersal, hypothesised to involve rapid maritime translocation with small founding herds, yet the genetic consequences for the livestock themselves remain poorly understood. To investigate this, we generated 12 palaeogenomes of sheep and goat from La Draga and Cova de lAvellaner, and coanalyzed these with other Neolithic Mediterranean assemblages, including 4 additional novel genomes. We observe a significantly lower genetic diversity and higher runs of homozygosity (ROH) in Iberian sheep and goat populations compared to other ancient European and southwest Asian populations. We quantify the magnitude of the bottleneck in goats at [~]205 Ne, highlighting the severity of the founder event. We further identify species-specific demographic trajectories: goats experienced a severe and prolonged bottleneck, likely driven by regional isolation within the western Mediterranean, intensive exploitation strategies, and small initial founding herds, while sheep were likely more frequently exchanged across the region. Lastly, identity-by-descent (IBD) indicates connectivity along the Mediterranean coast compatible with a cabotage model. This suggests that seaways facilitated rapid initial dispersal but not sustained livestock transfer from southwest Asia, shaping the genetic foundation of Iberian livestock herds. SignificanceThe Neolithic transition in western Eurasia fundamentally restructured human societies, yet the genetic consequences for translocated livestock remain poorly characterized. Analyzing 16 novel palaeogenomes from Mediterranean Neolithic sheep and goats, we demonstrate that maritime dispersal imposed severe founder effects on early Iberian livestock, reducing effective population sizes to as low as [~]205 in goats. Species-specific demographic trajectories reveal that goats experienced prolonged genetic isolation within the western Mediterranean, while sheep maintained broader regional connectivity. Identity-by-descent analyses support a cabotage model of coastal dispersal, indicating that Mediterranean seaways facilitated rapid initial colonization but not sustained genetic exchange with southwest Asian source populations. These findings reveal that the earliest livestock introductions into Europe were demographically constrained events whose genetic signatures persist in the foundations of Iberian pastoral heritage.

genomics↗

bioRxiv2026

Evolutionary history and genomic vulnerability of the extinct giant deer Megaloceros giganteus

The extinct giant deer (Megaloceros giganteus) was one of the most striking megafaunal species of the Late Quaternary, distinguished by its enormous palmated antlers reaching up to 3.5 m across, the largest known among both living and extinct cervids. Despite its iconic status, little is known about its genomic history prior to extinction [~]8 thousand years ago (kya). We generated the first nuclear palaeogenomes for Megaloceros, represented by nine individuals from Germany ([~]40 kya) and Ireland ([~]11 kya), mapped to a new chromosome-level reference genome of the fallow deer (Dama dama). Phylogenomic analyses placed Megaloceros as sister to Dama (divergence [~]3.5 Ma) and revealed evidence of gene flow with ancestral Cervus lineages. Population analyses identified clear differentiation between German and Irish lineages, with higher genetic diversity in the German individuals. Two genes under strong positive selection, BNIPL and SLC10A7, are associated with apoptosis regulation and skeletal development/bone mineralisation, respectively, and may relate to the species large body and antler size. Demographic reconstructions indicate a long-term decline in effective population size, extremely low heterozygosity, little evidence of extensive runs of homozygosity, and an elevated burden of predicted deleterious alleles. Together, these results suggest that Megaloceros entered the terminal Pleistocene in a genomically fragile state, offering new insight into the biology and evolutionary legacy of one of the largest and most distinctive cervids that ever lived.

evolutionary biology↗

bioRxiv2026

Mitochondrial genomes reveal maternal lineages of Late Iron Age sheep (Ovis aries) in Denmark

Sheep husbandry played an important role in the agrarian and textile economies of Late Iron Age Denmark, yet the genetic structure of sheep populations from this period remains poorly understood. In this study, we analyse complete mitochondrial genomes from five Late Iron Age sheep recovered from four Danish archaeological sites dating to the fifth to tenth centuries AD. All sequenced sheep belong to mitochondrial haplogroup B and fall within the B1a lineage, the predominant maternal lineage in European sheep. Each individual represents a distinct haplotype, resulting in high haplotype diversity despite the limited sample size. Population differentiation between Danish ancient sheep and modern reference populations from Fennoscandia and northwest Europe is very low, indicating limited maternal genetic differentiation at the regional scale. Median-joining network analysis further shows that Danish haplotypes are distributed across the broader northern European haplogroup B lineage rather than forming a geographically distinct cluster. These results suggest that Danish sheep populations during the Late Iron Age maintained multiple maternal lineages and were embedded within wider northern European genetic networks. The observed mitochondrial diversity is consistent with sheep husbandry systems that were not restricted to narrow maternal breeding stocks during a period associated with expanding textile production. HighlightsO_LIComplete mitogenomes from Danish Late Iron Age sheep C_LIO_LIHigh maternal diversity within haplogroup B C_LIO_LIGenetic links between Late Iron Age and modern sheep C_LI

molecular biology↗

bioRxiv2025

Genetic analysis of 7,000 year old preserved goat leather from Cueva de los Murcielagos (Albunol, Spain).

Advances in ancient DNA research have expanded the range of materials from which genetic information can be recovered, enabling the analysis of atypical materials. These often preserve both host and exogenous DNA, for example due to handling or native microbes, offering a window into past diversity. Here we report one such exceptional material: a well-preserved goat leather specimen from Cueva de los Murcielagos (Albunol, Spain), associated with an Early Neolithic context. Archaeozoological analyses show clear evidence of tanning and anthropogenic modification of the skin, while radiocarbon dating confirms it to be [~]7,250-7,000 years old. We generated genome-wide data from the leather (Murcielagos1) and demonstrated that it derives from a domestic goat of European ancestry. Comparisons with modern goats show highest affinity to the Bermeya breed from northern Spain, demonstrating genetic connectivity in goat herds from the Neolithic to present day Iberia. We additionally recover fragmented DNA from the leather deriving from human and canid sources, the former likely reflecting handling/wearing of the leather and the latter indicating post-depositional disturbance. Murcielagos1 represents one of the oldest nuclear genome data from organic remains outside of high altitude, high latitude regions, and demonstrates the value of ancient DNA analysis in exceptional cases of organic preservation.

genomics↗

bioRxiv2025

Old Goats: 3,000 years of genetic connectivity of the domestic goat in Ireland

The domestic goat likely first arrived to the island of Ireland as part of the introduction of agriculture approximately 5,900 years ago, and remains a part of the islands biocultural heritage. However, due to the challenges of differentiating goat remains from that of sheep using traditional archaeozoological approaches, there are few specimens specifically identified as goat. To address this we employed genetic, proteomics, and archaeozoological techniques to assess faunal remains from the Late Bronze assemblage of Haugheys Fort (Armagh) and medieval assemblage of Carrickfergus (Antrim). We identify these specimens as goats using proteomics and genetics, and additionally determine their molecular sex. Genomic data recovered from a Haugheys Fort goat reveals a three-millenia genetic connection between herds in the Late Bronze Age, medieval period, and the indigenous Irish breed extant today, the Old Irish Goat. We additionally find varying levels of inbreeding within goats from the settlement of Carrickfergus, suggesting possible mixed use of herds within medieval Irish society. Our results demonstrate the continuing potential of combining archaeological and biomolecular techniques to clarify existing ambiguities and at the same time reveal new facets of the past.

genomics↗

bioRxiv2024

Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa

BackgroundThe Islamic influence on the Iberian Peninsula left an enduring legacy culturally and linguistically, however the demographic impact is less well understood. This study aims to explore the dynamics of gene flow and population structure in eastern Iberia from the early to late Medieval period through ancient DNA. ResultsOur comprehensive genomic analysis uncovered gene flow from various Mediterranean regions into Iberia before the Islamic period, supporting a pre-existing pan-Mediterranean homogenization phenomenon during the Roman Empire. North African ancestry is present but sporadic in late antiquity genomes but becomes consolidated during the Islamic period. We uncovered one of the earliest dated Islamic burials in Spain, which showed high levels of inbreeding. For the first time we also prove the persistence of North African ancestry in a Christian cemetery until the 17th century, in addition to evidence of slave traffick from the Maghreb. ConclusionsThis study reveals the complex interaction between political events and cultural shifts that influenced the population of eastern Iberia. It highlights the existence of a slave trade and underscores the lasting impact of historical events, such as the Expulsion of the Moriscos in 1609 CE, on the regions genetic and cultural landscape through mass population displacement and replacement.

evolutionary biology↗

bioRxiv2023

Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria

The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modelled as a mixture of sources from ancient Anatolia, Levant and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria-resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5-6 kya onwards, around the time agriculture appeared in the region. Our study provides the first characterisation of the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of aDNA studies in the region.

genomics↗

bioRxiv2022

A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics.

AO_SCPLOWBSTRACTC_SCPLOWDirekli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra species, find a novel lineage best represented by a [~]14,000 year old 2.59X genome sequenced from specimen Direkli4. This newly discovered Capra lineage is a sister clade to the Caucasian tur species (Capra cylindricornis and Capra caucasica), both now limited to the Caucasus region. We identify genomic regions introgressed in domestic goats with high affinity to Direkli4, and find that West Eurasian domestic goats in the past, but not those today, appear enriched for Direkli4-specific alleles at a genome-wide level. This forgotten "Taurasian tur" likely survived Late Pleistocene climatic change in a Taurus Mountain refugia and its genomic fate is unknown.

genomics↗

bioRxiv2022

Millennium-Old Pathogenic Mendelian Mutation Discovery for MultipleOsteochondromas from a Gaelic Medieval Graveyard.

Only a limited number of genetic diseases are diagnosable in archaeological individuals and none have had causal mutations identified in genome-wide screens. Two individuals from the Gaelic Irish Medieval burial ground of Ballyhanna, Co. Donegal, showed evidence of bone tumors consistent with the autosomal dominant condition multiple osteochondromas. Genome sequencing of the earlier individual uncovered a missense mutation in the second exon of EXT1, a specific lesion that has been identified in several modern patients. The later individual lacked this but displayed a novel frameshift mutation leading to a premature stop codon and loss of function in the same gene. These molecular confirmations of a paleopathological diagnosis within a single rural ancient context are surprisingly disjunct, given the observation of clusters of this disease in modern isolated populations and a de novo mutation rate of only 10%.

genomics↗

bioRxiv2021

Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrabad, Iran

Mummified remains have long attracted interest as a potential source of ancient DNA. However, mummification is a rare process that requires an anhydrous environment to rapidly dehydrate and preserve tissue before complete decomposition occurs. We present the whole genome sequences of a [~]1600 year old naturally mummified sheep recovered from Chehr[a]b[a]d, a salt mine in northwestern Iran. Comparative analyses of published ancient sequences revealed remarkable DNA integrity of this mummy. Hallmarks of postmortem damage, fragmentation and hydrolytic deamination, are substantially reduced, likely due to the high-salinity of this taphonomic environment. Metagenomic analyses reflect the profound influence of high salt content on decomposition; its microbial profile is predominated by halophilic archaea and bacteria, possibly contributing to the preservation of this sample. Applying population genomic analyses we find consistent clustering of this sheep with Southwest Asian modern breeds, suggesting ancestry continuity. Genotyping of a locus influencing the woolly phenotype showed the existence of an ancestral "hairy" allele in this sheep, consistent with hair fibre imaging, further elucidating Sasanian-period animal husbandry.

genomics↗

bioRxiv2017

The York Gospels: a one thousand year biological palimpsest

Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA we report a cost effective and simple-to-use biomolecular sampling technique. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1,000 year lifespan of this cherished object that remains an active participant in the life of York Minster. This biological data provides insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.

genomics↗