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Evaluating imputation accuracy for ancient low-coverage domestic cat genomes
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Recent studies on animal domesticates (e.g., dogs, cattle, donkeys) have shown that imputing ancient low-coverage genomes can achieve high accuracy, enabling finer-scale population genomic analyses based on haplotypes. However, these studies underscore the lack of a standard imputation strategy, as species-specific factors—such as genetic architecture, introgression from wild relatives, and reference panel composition—critically influence accuracy. Despite being one of humanity’s closest companions, the domestic cat (Felis catus) remains underrepresented in genomic research, leaving many aspects of its evolutionary history unresolved. Ancient and modern genomic datasets for both wild and domestic cats are sparse, with population allele frequencies often inferred from single or few individuals, resulting in potential biases. Addressing these biases requires haplotype-based approaches and thus a tailored imputation pipeline. Imputing cat genomes poses several challenges, including the absence of a high-density genetic map essential for phasing the reference panel. Additionally, only three high-coverage genomes of Felis lybica lybica, the domestic cat’s wild ancestor, are currently available. Including more genomes of wild relatives as well as ancient high-coverage genomes in reference panels has proven to enhance imputation accuracy. To enrich the reference panel, we thus generated novel modern and ancient high-quality genomes (>10X) of both wild and domestic cats. By constructing a fine-scale genetic map and testing various imputation filtering pipelines, we aim to establish a gold standard for cat imputation, enabling robust haplotype-based analyses. This will provide unprecedented insights into the domestication, adaptation, and evolutionary history of domestic cats.
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The Genomic make-up of ancient wild and domestic cats from the Levant and North Africa
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The domestic cat (Felis catus) descends from the North African and Near Eastern wildcat subspecies Felis lybica lybica. Its close association with humans facilitated its global spread, making it one of the most successful mammal species. Recent archaeogenomic and zooarchaeological studies indicate that domestic cats were introduced to Europe within the last 2,000 years, much later than previously assumed. However, the scarcity of genomic data from the Near and Middle East and North Africa leaves key questions unresolved, particularly regarding the origins of domestic cats and the contributions of the two proposed centres of domestication, the Neolithic Levant and Pharaonic Egypt. To fill this gap of knowledge, we generated 60 low-coverage (0.1- to 0.6-fold) genomes from cat remains from North Africa, the Near and Middle East, and the Iberian and Italian peninsulas dated from the 7th millennium BCE to the 15th century CE, along with 23 low- to high-coverage (0.4- to 15-fold) genomes of present-day and museum wildcats from the Levant and central and northern Africa. Our findings suggest that North Africa was the original centre of cat domestication. As domestic cats spread to the Levant and the Middle East, they most likely acquired Levantine genetic ancestry through admixture with local F. l. lybica populations. This work lay the foundations for further disentangling the origins of domestic cats and tracing their expansion across Southwest Asia.
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Paleogenomic insights into the dispersal of domestic cats into Europe and selection patterns over time
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Zooarchaeological and genetic evidence from the last two decades demonstrated that domestic cats originated from the North African and Near Eastern wildcat, Felis lybica lybica. The commensal relationship between humans and cats started about 11 thousand years ago in the Neolithic Levant. Recent paleogenomic evidence showed that cats were introduced to Europe several millennia later, in the Roman era. Yet, archaeozoological and ancient mitochondrial DNA data from northwest Europe suggest that domestic cats were already present in this region in the 1st millennium BCE, in Iron Age settlements. Until now, only three cats from Europe dated to this period have been analysed at the nuclear level, thus leaving uncertainty on the times and circumstances of the human mediated dispersal of domestic cats into Europe. To address that, we analysed the DNA of 30 cat remains dated from the Bronze Age to the Roman era from northern and western Europe. We built double-stranded genomic libraries and generated low-coverage genome-wide data via shotgun sequencing. The temporal transect of genomic variation that we reconstructed made it possible to refine the timing of the introduction of the domestic cat to Europe. In addition, to investigate patterns of selection in the history of cat domestication, we show here the preliminary results of the analysis of cat phenotypic variants across time and place, with a particular focus on the sex-linked orange coat colour.
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RAPTORS AS A RESOURCE: NEW INSIGHTS INTO MIDDLE AND UPPER PALEOLITHIC BIRD USE AT WALOU CAVE (BELGIUM) BY NEANDERTHALS AND MODERN HUMANS
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Expanding dietary and ecological insights of archaeofauna at Aqaba Castle, Jordan, using non-exchangeable hydrogen isotope ratio (δ²H) analysis
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Non-exchangeable hydrogen isotope ratios (δ²H) are an underused proxy for studying past human-animal relationships, offering insights into diets, water intake, and ecological ranges. This study examines 218 bone collagen samples for δ¹³C, δ¹⁵N, and δ²H values of wild and domestic terrestrial species, and marine fishes from Ottoman-period Aqaba Castle, Jordan (16th–19th century CE). In this hyperarid region, high δ¹⁵N values reflect the elevated δ¹⁵N baseline of plants, causing overlaps in taxa with varying trophic levels. δ²H helps mitigate this by acting as an additional trophic level indicator. Domesticated herbivores mostly possess δ²H values close to that of predicted local rainfall, while hypercarnivorous cats (Felis catus) exhibit the highest δ²H values, averaging +42.4‰ above herbivores. Fish also show high δ²H values, correlated with trophic level (r = 0.84, R² = 0.70) and estimated body size (r = 0.61, R² = 0.37). Cattle and chickens, have the lowest δ²H values of all terrestrial species, likely due to their significant water requirements and the consumption of ²H-depleted aquifer water. Mapping wild gazelle (Gazella sp.) and chukar (Alectoris chukar) δ²H values on rainwater δ²H isoscapes indicates limited home ranges in the surrounding hyperarid highlands, in line with their expected behaviours. We assess the utility of δ2H for determining fish consumption using Bayesian dietary models for cats and hyenas (Hyaena hyaena), revealing higher fish consumption by cats when δ²H is included alongside δ¹³C and δ¹⁵N. This study highlights the value for δ²H values to enhance interpretations of animal diets and behaviours in archaeological contexts.
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Genomic and isotopic insights into cat dispersal and diet from Viking to medieval northern Germany
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Bioarchaeological studies of ancient wild and domestic animals provide critical insights into animal translocation and human-animal relationships over time. Domestic cats (Felis catus), in particular, have a long history of association with humans as companions and pest controllers. This makes them valuable bio-proxies for reconstructing human movements via sea and land routes, as well as dietary shifts in the anthropogenic niche. In this study, we performed genomic and stable isotope analyses on over 90 cat remains from two major trade hubs in northern Germany: the Viking settlement of Haithabu (AD 800 - 1050) and its medieval successor, the town of Schleswig (AD 1050 - 1250). Ancient DNA analysis showed no clear geographical pattern in mitochondrial DNA ancestries from the two sites, all of which belong to clade IV of F. s. lybica and are assigned to haplogroups A, C, and D. This likely reflects the widespread dispersal of domestic cats in Europe starting from the Roman era. Nuclear DNA analysis revealed limited gene flow from European wildcats, consistent with previous findings on ancient domestic cats from other regions in Europe. Stable carbon (δ13C µ = -19.1 ± 0.7‰) and nitrogen (δ15N µ = 10.5 ± 1.1‰) isotope ratio analysis of cats from both sites indicates that most cats had mixed diets involving some marine foods supplied by or scavenged from humans. This multidisciplinary approach enables a comprehensive reconstruction of human-mediated cat dispersals and their dietary patterns during pivotal socio-economic transformation.
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A river with a story: development of a specific methodology to study the ancient Senne river in Brussels
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In July 2015 a rescue excavation took place to recover the remains of a previously unknown ancient branch of the Senne river on the site of Tour & Taxis in Brussels (Belgium). Such a large-scale excavation of a river branch required the development of a specific approach, where the close collaboration of archaeologists and many natural science specialists showed to be a crucial factor. Multiple logistic and scientific challenges were met to accurately document and correlate the river and the traces of human activities during the salvation operation. In order to cope with these challenges a protocol was elaborated focussing on the realisation and geoarchaeological study of multiple sedimentary profiles across the river bed, the excavation of the archaeological features and structures related to the river management, and an extensive sampling campaign for the natural science specialists (geoarchaeologists, archaeozoölogists and archaeobotanists). This resulted in a large and varied dataset, permitting to document the evolution of the river bed and the impact of the management activities, but also to reconstruct the surrounding landscape (De Cupere et al., 2017). In the spring of 2019, the remains of the medieval harbour in the historical center of Brussels were discovered during construction works. This instigated the largest rescue excavation in Brussels where the stakes were high: documenting the evolution of the river, understanding the impact of the embankments, but also documenting the progressing urbanisation and its impact on the river in a very limited amount of time (Ghesquière et al., 2024). Armed with the experiences of the previous salvation operation, a large-scale operation was conducted, following an adapted protocol. The present contribution intends to discuss how the experiences of the two large-scale rescue operations forged our research framework for tackling comparable contexts in the future.
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Echoes in the sediment: reconstructing the Senne through molluscs and caddisflies
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The Senne River has shaped the landscape and development of Brussels for centuries. However, its course and environmental conditions have been continuously altered by human interventions. This study compares freshwater mollusc and caddisfly (Trichoptera) remains from two archaeological sites, one Gallo-Roman (1st-3rd century AD) and one medieval (10th-16th century AD), to reconstruct changes in river flow, sedimentation, and water quality over time. At the Gallo-Roman site, a previously unknown river meander of the Senne river was uncovered, initially characterized by fast-flowing water, as indicated by coarse sand and gravel deposits. Over time, sedimentation patterns show a shift to finer materials, such as silt and organic muds, suggesting a transition to slower-moving or stagnant water before the meander was ultimately cut off. The site is located within a rural environment. In contrast, the medieval site, located within the historic centre of Brussels, represents a heavily modified urban river environment. Mollusc remains indicate predominantly slow-moving water, with occasional stagnant conditions. The discovery of caddisfly larvae cases, including the confirmed presence of Brachycentrus subnubilus, suggests that despite extensive waste dumping, parts of the medieval Senne still maintained sufficient water quality for oxygen-dependent species. By combining data from these two sites, this study attempts to document the Senne’s hydrology, sedimentation, and aquatic ecosystems in a rural and urban environment. The findings describe the river’s natural environment alongside increasing human impact, from early riverbank modifications in Gallo-Roman times to the canalization and pollution of the medieval period.
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Lost in the river: animals and daily life of medieval Brussels
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Within the historic centre of Brussels, excavations over a huge area have revealed the well-preserved remains of a medieval harbour along the Senne River. This watercourse, essential to the city’s origins and development, saw continuous occupation from the 10th to 16th centuries. The riverbanks were gradually reinforced in the 12th century, and by the 14th–15th centuries, the Senne was canalised, as indicated by a stone quay wall and boat dock. These transformations reflect the river’s critical role in shaping the city's economy and infrastructure. A diverse range of artifacts, including fish traps, pottery, metal objects and leather goods, have been unearthed, alongside an extensive collection of animal remains, providing crucial insights into medieval diet, economy, and waste disposal practices. The faunal assemblage, primarily from the 14th–15th century channelled riverbed, consists largely of consumption refuse, with clear evidence of butchery marks on bones. Remains of domestic livestock such as cattle, sheep, and pigs, together with poultry (geese and chicken) and a variety of fish species from both marine and freshwater environments, indicate not only a diversified food supply, but also the activities of butchers operating nearby. In addition to these dietary remains, the excavation uncovered whole carcasses of dogs, cats, and horses, discarded into the river, as well as small bones, likely originating from human excrements. Evidence of artisanal activities, such as horn, bone, and antler processing, suggests that craft industries were also located near the river. These findings highlight the Senne River’s dual role as both a resource and a repository, illustrating medieval Brussels’ complex human-environment interactions. The study of these animal remains offers valuable data on urban food consumption, and waste disposal in the medieval period. Despite centuries of transformation, the river remains a key witness to the city’s past.
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De la mer à la terre : aperçu chronologique des mollusques marins dans les fouilles archéologiques en Belgique
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Les coquillages marins apparaissent régulièrement dans les fouilles archéologiques en Flandre, à Bruxelles et en Wallonie. Il s’agit principalement de moules (Mytilus edulis) et d’huîtres (Ostrea edulis), mais d’autres espèces, bien que plus rares, sont également présentes. Ces vestiges sont fréquemment mentionnés dans les rapports et publications archéozoologiques, souvent en tant que simples compléments aux restes de mammifères, oiseaux et poissons, mais ils reçoivent rarement une attention spécifique. Pourtant, leur présence offre des pistes de réflexions intéressantes concernant les échanges économiques, les habitudes alimentaires, ou encore le statut social des consommateurs. Cette présentation propose un survol chronologique des découvertes de coquillages marins dans les contextes archéologiques belges. En replaçant ces données dans leur contexte culturel et géographique, nous tenterons de mieux comprendre la place de ces produits marins dans les sociétés passées au cours du temps.
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