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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RBINS Staff Publications 2025
EVALUATION OF DIFFERENT TAXONOMIC LEVELS AS SURROGATES OF ANT DIVERSITY IN GREEN AREAS IN AN URBANIZED ENVIRONMENT E. B. A. KOCH1, T. S. MELO2,3,4, A. R. S. ANDRADE2,3, M. LEPONCE5 & J. H. C. DELABIE2,4 1Programa de Pós-graduação em Ecologia e Evolução, Universidade Estadual de Feira de Santana (UEFS), CEP: 44.036-900 - Feira de Santana, Bahia, Brazil, e-mail: elmoborges@gmail.com; 2Programa de Pós-graduação em Ecologia, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil; 3Centro de Ecologia e Conservação Animal, Universidade Católica do Salvador (UCSal), Salvador, Bahia, Brazil; 4Laboratório de Mirmecologia, Convênio Universidade Estadual de Santa Cruz (UESC)/Comissão Executiva do Plano da Lavoura Cacaueira (CEPLAC), Ilhéus, Bahia, Brazil; 5Biodiversity Monitoring & Assessment, Royal Belgian Institute of Natural Sciences (RBINS), Bruxelas, Belgium. In cities located in environments of high biological importance, urbanization leads to changes in biotic diversity, while monitoring these changes can be difficult. Studies have pointed to the use of metrics that replace species as an alternative. Surrogate models are easily determined measures of biodiversity that correlate strongly with species richness and with what you want to investigate, being useful for detecting or monitoring environmental changes. The use of higher taxonomic levels has been applied to groups of megadiverse organisms, such as arthropods, since difficulties in identifying species are predictable. The aim of this study was to evaluate the practicality of using taxonomic diversity of ants as a surrogate of green area coverage in an urban environment. Four levels of "surrogate resolutions" (subfamily, genus, indicator taxa, and intermediate resolution) were assessed to the taxonomic diversity of ants across three levels of urban green areas (Small = 0 to 35%
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RBINS Staff Publications 2023
