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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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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