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.

CE3C Centre for Ecology Evolution and Environmental Changes and 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

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 Ecological and Evolutionary Synthesis Department of Biosciences University of Oslo PO BOX 1066 Blinderm 0316 Oslo Norway

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

Department of Biology University of Antwerp Universiteitsplein 1 2610 Wilrijk Antwerp Belgium

Department of Biosciences University of Milan Milan Italy

Department of Ecology and Genetics Uppsala University Norbyvägen 18D 75246 Uppsala Sweden

Estación Biológica de Doñana CSIC Calle Americo Vespucio 26 41092 Sevillle Spain

Estación Biológica de Doñana CSIC Calle Americo Vespucio 26 41092 Sevillle Spain; CIBER de Epidemiología y Salud Pública Spain

Evolutionary and 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

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

InBios Conservation Genetics Lab University of Liege Chemin de la Vallée 4 4000 Liege Belgium

Institute of Zoology University of Cologne Zülpicherstrasse 47b D 50674 Cologne Germany

Leibniz Institute for Zoo and Wildlife Research Koenigin Luise Str 6 8 14195 Berlin Germany

LOEWE Centre for Translational Biodiversity Genomics Senckenberg Biodiversity and Climate Research Centre Georg Voigt Str 14 16 60325 Frankfurt Main Germany

Marine and Freshwater Research Institute Fornubúðir 5 220 Hanafjörður Iceland

Naturalis Biodiversity Center Darwinweg 2 2333 CR Leiden The Netherlands; Wellcome Sanger Institute Tree of Life Wellcome Genome Campus Hinxton CB10 1SA UK

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

Primate Genetics Laborator German Primate Center Kellnerweg 4 37077 Göttingen Germany

The Rockefeller University 1230 York Ave New York NY 10065 USA

The Rockefeller University 1230 York Ave New York NY 10065 USA; Hunter College City University of New York NY USA

Universita degli Studi di Milano Via Celoria 26 20133 Milan Italy

University of Florence Department of Biology Via Madonna del Piano 6 Sesto Fiorentino 50019 Italy

University of Goettingen Institute for Microbiology and Genetics Department of Applied Bioinformatics Goettingen Center for Molecular Biosciences Goldschmidtstr 1 37077 Goettingen Germany

University of Göttingen Department of Animal Evolution and Biodiversity Untere Karspüle 2 37073 Göttingen Germany

University of Lausanne Department of Ecology and Evolution Le Biophore UNIL Sorge 1015 Lausanne Switzerland; Swiss Institute of Bioinformatics 1015 Lausanne Switzerland

References provided by Crossref.org

Dealing With the Complexity of Effective Population Size in Conservation Practice

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics