How genomics can help biodiversity conservation
Trends in Genetics, vol. 39, pp. 545–559
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
Authors 100
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Senckenberg Biodiversity and Climate Research Centre · LOEWE Centre for Translational Biodiversity Genomics
Affiliation as printed
LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
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Affiliation as printed
CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
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Affiliation as printed
The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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Naturalis Biodiversity Center · Wellcome Sanger Institute
Affiliation as printed
Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands
Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
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University of Oslo · University of Agder · Norwegian Institute for Water Research
Affiliation as printed
NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway
Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway
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Affiliation as printed
University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
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Affiliation as printed
Universita degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
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Universidade do Porto · Centro de Investigação em Biodiversidade e Recursos Genéticos
Affiliation as printed
CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal
Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
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Affiliation as printed
Department of Biosciences, University of Milan, Milan, Italy
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Affiliation as printed
Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
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Affiliation as printed
Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
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Affiliation as printed
Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
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Affiliation as printed
InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
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University of Oslo · University of Agder
Affiliation as printed
Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway
Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
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Affiliation as printed
The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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University of Groningen · Center for Coastal Studies
Affiliation as printed
Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands
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Marine and Freshwater Research Institute
Affiliation as printed
Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
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Consejo Superior de Investigaciones Científicas · Estación Biológica de Doñana · Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública
Affiliation as printed
Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
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Affiliation as printed
Department of Biosciences, University of Milan, Milan, Italy
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Affiliation as printed
Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
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City University of New York · Hunter College · Rockefeller University
Affiliation as printed
The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
Hunter College, City University of New York, NY, USA
The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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Campus-Institut Data Science (CIDAS) · University of Göttingen
Affiliation as printed
University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
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Affiliation as printed
Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
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University of Copenhagen · Kunming Institute of Zoology · Chinese Academy of Sciences · State Key Laboratory of Genetic Resources and Evolution · Zhejiang University
Affiliation as printed
Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
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Affiliation as printed
The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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Senckenberg Biodiversity and Climate Research Centre · LOEWE Centre for Translational Biodiversity Genomics
Affiliation as printed
LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
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Affiliation as printed
University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
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SIB Swiss Institute of Bioinformatics · University of Lausanne
Affiliation as printed
University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland
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Berlin Center for Genomics in Biodiversity Research · Leibniz Institute for Zoo and Wildlife Research
Affiliation as printed
Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany
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Jacob Höglund corresponding
Affiliation as printed
Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden. Electronic address: jacob.hoglund@ebc.uu.se
Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden
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Affiliation as printed
CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
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SIB Swiss Institute of Bioinformatics · University of Lausanne
Affiliation as printed
Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland
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Estación Biológica de Doñana · Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública
Affiliation as printed
CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
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Affiliation as printed
InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
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Laboratoire de Biométrie et Biologie Evolutive
Affiliation as printed
LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (43 Bld du 11 Novembre 1918 69622 VILLEURBANNE CEDEX - France)
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Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · Ressources génomique-info
Affiliation as printed
URGI - Unité de Recherche Génomique Info (INRAE, Centre de recherche de Versailles, bat.18 Route de Saint Cyr 78000 Versailles - France)
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Affiliation as printed
Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
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Affiliation as printed
Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
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SIB Swiss Institute of Bioinformatics · University of Lausanne
Affiliation as printed
Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
UNIL-Sorge, 1015 Lausanne, Switzerland
University of Lausanne, Department of Ecology and Evolution, Le Biophore,
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