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Genome Biol. 2016 Dec 14;17(1):251.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

Author information

1
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.
2
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
3
Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain.
4
Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
5
Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
6
Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.
7
Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, 8000, Aarhus, Denmark.
8
Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain.
9
Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003, Barcelona, Spain.
10
Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
11
Servei de Cultius Cel.lulars (SCC, SCAC), Universitat Autònoma de Barcelona, Barcelona, Spain.
12
National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.
13
Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.
14
Department of Environmental Biology, Center for Biological Research (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
15
Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain.
16
Computational Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
17
Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain.
18
Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
19
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.

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSIONS:

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.

KEYWORDS:

Conservation genomics; Genetic diversity; Genetic drift; Inbreeding; Lynx

PMID:
27964752
PMCID:
PMC5155386
DOI:
10.1186/s13059-016-1090-1
[Indexed for MEDLINE]
Free PMC Article

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