ORIGINAL ARTICLE On the path to extinction: Inbreeding and admixture in a declining grey wolf population Daniel Gómez-Sánchez 1 | Iñigo Olalde 1 | Natalia Sastre 2,3 | Conrad Enseñat 4 | Rafael Carrasco 5 | Tomas Marques-Bonet 1,6,7 | Carles Lalueza-Fox 1 | Jennifer A. Leonard 8 | Carles Vilà 8 | Oscar Ramírez 1,9 1 Ciencies Experimetals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra – CSIC), Barcelona, Spain 2 Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Servei Veterinari de Genètica Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain 3 Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California 4 Parc Zoològic de Barcelona, Barcelona, Spain 5 Departamento de Biologia Animal, Biologia Vegetal y Ecología, Universidad de Jaén (UJA), Jaen, Spain 6 Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain 7 Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain 8 Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD- CSIC), Seville, Spain 9 Vetgenomics S.L., Bellaterra, Spain Correspondence Carles Vilà, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain. Email: carles.vila@ebd.csic.es and Oscar Ramírez, Ciencies Experimetals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra – CSIC), Barcelona, Spain. Email: oscar.ramirez@vetgenomics.com Present address Daniel Gómez-Sánchez, Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Wien, Austria. Funding information Fundació Barcelona Zoo and Ajuntament de Barcelona Abstract Allee effects reduce the viability of small populations in many different ways, which act synergistically to lead populations towards extinction vortexes. The Sierra Mor- ena wolf population, isolated in the south of the Iberian Peninsula and composed of just one or few packs for decades, represents a good example of how diverse threats act additively in very small populations. We sequenced the genome of one of the last wolves identified (and road‐killed) in Sierra Morena and that of another wolf in the Iberian Wolf Captive Breeding Program and compared them with other wolf and dog genomes from around the world (including two previously published genome sequences from northern Iberian wolves). The results showed relatively low overall genetic diversity in Iberian wolves, but diverse population histories including past introgression of dog genes. The Sierra Morena wolf had an extraordinarily high level of inbreeding and long runs of homozygosity, resulting from the long isolation. In addition, about one‐third of the genome was of dog origin. Despite the introgres- sion of dog genes, heterozygosity remained low because of continued inbreeding after several hybridization events. The results thus illustrate the case of a small and isolated wolf population where the low population density may have favoured hybridization and introgression of dog alleles, but continued inbreeding may have resulted in large chromosomal fragments of wolf origin completely disappearing from the population, and being replaced by chromosomal fragments of dog origin. The latest population surveys suggest that this population may have gone extinct. KEYWORDS Allee effect, Canis lupus, conservation, hybridization, inbreeding, whole-genome sequence Received: 27 March 2018 | Revised: 13 July 2018 | Accepted: 16 July 2018 DOI: 10.1111/mec.14824 Molecular Ecology. 2018;27:3599–3612. wileyonlinelibrary.com/journal/mec © 2018 John Wiley & Sons Ltd | 3599