title: Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.
abstract: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction.
  
  
  
  We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species.
  
  
  
  The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.
authors.affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.
authors.forename: Federico
authors.initials: F
authors.lastname: Abascal
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
authors.forename: André
authors.initials: A
authors.lastname: Corvelo
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.|Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Cruz
authors.affiliation: Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: José L
authors.initials: JL
authors.lastname: Villanueva-Cañas
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Vlasova
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Marina
authors.initials: M
authors.lastname: Marcet-Houben
authors.affiliation: Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain.
authors.forename: Begoña
authors.initials: B
authors.lastname: Martínez-Cruz
authors.affiliation: Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, 8000, Aarhus, Denmark.
authors.forename: Jade Yu
authors.initials: JY
authors.lastname: Cheng
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Pablo
authors.initials: P
authors.lastname: Prieto
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain.
authors.forename: Víctor
authors.initials: V
authors.lastname: Quesada
authors.affiliation: Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003, Barcelona, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Quilez
authors.affiliation: Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
authors.forename: Gang
authors.initials: G
authors.lastname: Li
authors.affiliation: Servei de Cultius Cel.lulars (SCC, SCAC), Universitat Autònoma de Barcelona, Barcelona, Spain.
authors.forename: Francisca
authors.initials: F
authors.lastname: García
authors.affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.
authors.forename: Miriam
authors.initials: M
authors.lastname: Rubio-Camarillo
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
authors.forename: Leonor
authors.initials: L
authors.lastname: Frias
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
authors.forename: Paolo
authors.initials: P
authors.lastname: Ribeca
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Salvador
authors.initials: S
authors.lastname: Capella-Gutiérrez
authors.affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.|National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.
authors.forename: José M
authors.initials: JM
authors.lastname: Rodríguez
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Câmara
authors.affiliation: Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Ernesto
authors.initials: E
authors.lastname: Lowy
authors.affiliation: Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Luca
authors.initials: L
authors.lastname: Cozzuto
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Ionas
authors.initials: I
authors.lastname: Erb
authors.affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Tress
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Jose L
authors.initials: JL
authors.lastname: Rodriguez-Ales
authors.affiliation: Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Jorge
authors.initials: J
authors.lastname: Ruiz-Orera
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Ferran
authors.initials: F
authors.lastname: Reverter
authors.affiliation: Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain.
authors.forename: Mireia
authors.initials: M
authors.lastname: Casas-Marce
authors.affiliation: Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain.
authors.forename: Laura
authors.initials: L
authors.lastname: Soriano
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain.
authors.forename: Javier R
authors.initials: JR
authors.lastname: Arango
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
authors.forename: Sophia
authors.initials: S
authors.lastname: Derdak
authors.affiliation: Department of Environmental Biology, Center for Biological Research (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
authors.forename: Beatriz
authors.initials: B
authors.lastname: Galán
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
authors.forename: Julie
authors.initials: J
authors.lastname: Blanc
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.affiliation: Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003, Barcelona, Spain.
authors.forename: Belen
authors.initials: B
authors.lastname: Lorente-Galdos
authors.affiliation: Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Andrés-Nieto
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: López-Otín
authors.affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.|National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
authors.forename: Ivo
authors.initials: I
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authors.affiliation: Department of Environmental Biology, Center for Biological Research (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
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authors.initials: JL
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authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.|Computational Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.affiliation: Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
authors.forename: William J
authors.initials: WJ
authors.lastname: Murphy
authors.affiliation: Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain.|Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain.
authors.forename: Aurora
authors.initials: A
authors.lastname: Ruiz-Herrera
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.|Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003, Barcelona, Spain.|Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
authors.forename: Tomas
authors.initials: T
authors.lastname: Marques-Bonet
authors.affiliation: Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Guglielmo
authors.initials: G
authors.lastname: Roma
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Cedric
authors.initials: C
authors.lastname: Notredame
authors.affiliation: Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, 8000, Aarhus, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Mailund
authors.affiliation: Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.|Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
authors.forename: M Mar
authors.initials: MM
authors.lastname: Albà
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.|Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Tyler
authors.initials: T
authors.lastname: Alioto
authors.affiliation: Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain. godoy@ebd.csic.es.
authors.forename: José A
authors.identifier: 0000-0001-7502-9471
authors.initials: JA
authors.lastname: Godoy
mesh_terms: D000818:Animals; D056727:Endangered Species; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D046008:Lynx / Q000235:genetics*; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA
keywords: Conservation genomics; Genetic diversity; Genetic drift; Inbreeding; Lynx