The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.

BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal

Center for Evolutionary Hologenomics the Globe Institute University of Copenhagen Copenhagen Denmark

Center for Wildlife Genetics Senckenberg Research Institute and Natural History Museum Frankfurt Gelnhausen Germany

Charles University Department of Zoology Faculty of Science Prague 2 Czech Republic

CIBIO InBIO University of Porto Vairão Portugal

Department of Biological Chemical and Pharmaceutical Sciences and Technology University of Palermo Palermo Italy

Department of Biology University of Copenhagen Copenhagen Denmark

Department of Ecology Institute of Functional Biology and Ecology Faculty of Biology University of Warsaw Biological and Chemical Research Centre Warszawa Poland

Department of Zoology Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia

Ecology and Genetics Research Unit University of Oulu Finland

Faculty of Forestry Technical University Zvolen Slovakia

Faculty of Tropical AgriSciences Czech University of Life Sciences Prague Czech Republic

FIZV Via Marco Aurelio 2 Roma Italy

Forest Ecology Unit Research and Innovation Centre Fondazione Edmund Mach San Michele all'Adige Italy

Konrad Lorenz Institute of Ethology University of Veterinary Medicine Vienna Austria

Laboratory of Ancient DNA Department of Cultural Heritage University of Bologna Bologna Italy

Museo dell'Ecologia di Cesena Cesena Italy

Museum of Zoology P Doderlein SIMUA University of Palermo Palermo Italy

National Center for Wildlife Al Imam Faisal Ibn Turki Ibn Abdullah Ulaishah Saudi Arabia

Natural Resources Institute Finland Rovaniemi Finland

Nature Research Centre Vilnius Lithuania

NTNU University Museum Norwegian University of Science and Technology Trondheim Norway

Palaeogenomics Group Department of Veterinary Sciences Ludwig Maximilian University Munich Germany

School of Biological and Behavioural Sciences Queen Mary University of London London UK

Section for Evolutionary Genomics the Globe Institute University of Copenhagen Copenhagen Denmark

Società Amatori Cirneco dell'Etna Modica Italy

Swedish University of Agricultural Sciences Grimsö Wildlife Research Station Department of Ecology Riddarhyttan Sweden

Università di Roma La Sapienza Department Biology and Biotechnologies Charles Darwin Roma Italy

University Museum Norwegian University of Science and Technology Trondheim Norway

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