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How genomics can help biodiversity conservation
Open accessAbstract
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.
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“High-quality reference genome assemblies are increasingly recognized as an important foundation of conservation genomics84–91.”
From Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics (2024) · cites this paper as [87]
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Self-citation
Metadata
- Authors
- Theissinger, K., Fernandes, C., Formenti, G., Bista, I., Berg, P. R., Bleidorn, C., Bombarely, A., Crottini, A., Gallo, G. R., Godoy, J. A., Jentoft, S., Malukiewicz, J., Mouton, A., Oomen, R. A., Paez, S., Palsbøll, P. J., Pampoulie, C., Ruiz-López, M. J., Secomandi, S., Svardal, H., Theofanopoulou, C., de Vries, J., Waldvogel, A.-M., Zhang, G., Jarvis, E. D., Bálint, M., Ciofi, C., Waterhouse, R. M., Mazzoni, C. J., Höglund, J., Aghayan, S. A., Alioto, T. S., Almudi, I., Alvarez, N., Alves, P. C., Amorim do Rosario, I. R., Antunes, A., Arribas, P., Baldrian, P., Bertorelle, G., Böhne, A., Bonisoli-Alquati, A., Boštjančić, L. L., Boussau, B., Breton, C. M., Buzan, E., Campos, P. F., Carreras, C., Castro, L. F. C., Chueca, L. J., Čiampor, F., Conti, E., Cook-Deegan, R., Croll, D., Cunha, M. V., Delsuc, F., Dennis, A. B., Dimitrov, D., Faria, R., Favre, A., Fedrigo, O. D., Fernández, R., Ficetola, G. F., Flot, J.-F., Gabaldón, T., Agius, D. R., Giani, A. M., Gilbert, M. T. P., Grebenc, T., Guschanski, K., Guyot, R., Hausdorf, B., Hawlitschek, O., Heintzman, P. D., Heinze, B., Hiller, M., Husemann, M., Iannucci, A., Irisarri, I., Jakobsen, K. S., Klinga, P., Kloch, A., Kratochwil, C. F., Kusche, H., Layton, K. K. S., Leonard, J. A., Lerat, E., Liti, G., Manousaki, T., Marques-Bonet, T., Matos-Maraví, P., Matschiner, M., Maumus, F., Mc Cartney, A. M., Meiri, S., Melo-Ferreira, J., Mengual, X., Monaghan, M. T., Montagna, M., Mysłajek, R. W., Neiber, M. T., Nicolas, V., Novo, M., Ozretić, P., Palero, F., Pârvulescu, L., Pascual, M., Paulo, O. S., Pavlek, M., Pegueroles, C., Pellissier, L., Pesole, G., Primmer, C. R., Riesgo, A., Rüber, L., Rubolini, D., Salvi, D., Seehausen, O., Seidel, M., Studer, B., Theodoridis, S., Thines, M., Urban, L., Vasemägi, A., Vella, A., Vella, N., Vernes, S. C., Vernesi, C., Vieites, D. R., Wheat, C. W., Wörheide, G., Wurm, Y., & Zammit, G.
- Affiliations
- Senckenberg Biodiversity and Climate Research Centre (DE)
- University of Lisbon (PT)
- Rockefeller University (US)
- Naturalis Biodiversity Center (NL)
- University of Oslo (NO)
- University of Göttingen (DE)
- University of Milan (IT)
- Universidade do Porto (PT)
- Estación Biológica de Doñana (ES)
- German Primate Center (DE)
- University of Liège (BE)
- University of Groningen (NL)
- Marine and Freshwater Research Institute (IS)
- University of Antwerp (BE)
- City University of New York (US)
- University of Cologne (DE)
- University of Copenhagen (DK)
- SIB Swiss Institute of Bioinformatics (CH)
- Berlin Center for Genomics in Biodiversity Research (DE)
- Uppsala University (SE)
- Laboratoire de Biométrie et Biologie Evolutive (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Corresponding author
- Höglund, Jacob
- ORCID
- Theissinger, Kathrin
- Fernandes, Carlos
- Formenti, Giulio
- Bista, Iliana
- Berg, Paul R.
- Bleidorn, Christoph
- Bombarely, Aureliano
- Crottini, Angelica
- Gallo, Guido R.
- Godoy, José A.
- Jentoft, Sissel
- Malukiewicz, Joanna
- Mouton, Alice
- Oomen, Rebekah A.
- Paez, Sadye
- Palsbøll, Per J.
- Pampoulie, Christophe
- Secomandi, Simona
- Svardal, Hannes
- Theofanopoulou, Constantina
- Waldvogel, Ann-Marie
- Zhang, Guojie
- Jarvis, Erich D.
- Bálint, Miklós
- Waterhouse, Robert M.
- Mazzoni, Camila J.
- Höglund, Jacob
- Aghayan, Sargis A.
- Alioto, Tyler S.
- Alves, Paulo C.
- Antunes, Agostinho
- Arribas, Paula
- Bertorelle, Giorgio
- Böhne, Astrid
- Boštjančić, Ljudevit L.
- Boussau, Bastien
- Breton, Catherine M.
- Campos, Paula F.
- Carreras, Carlos
- Castro, L. FIlipe C.
- Chueca, Luis J.
- Čiampor, Fedor
- Conti, Elena
- Cook-Deegan, Robert
- Croll, Daniel
- Cunha, Mónica V.
- Delsuc, Frédéric
- Dennis, Alice B.
- Dimitrov, Dimitar
- Faria, Rui
- Favre, Adrien
- Fedrigo, Olivier D.
- Fernández, Rosa
- Ficetola, Gentile Francesco
- Flot, Jean-François
- Gabaldón, Toni
- Agius, Dolores R.
- Giani, Alice M.
- Gilbert, M. Thomas P.
- Grebenc, Tine
- Guschanski, Katerina
- Guyot, Romain
- Hausdorf, Bernhard
- Hawlitschek, Oliver
- Heintzman, Peter D.
- Heinze, Berthold
- Hiller, Michael
- Husemann, Martin
- Iannucci, Alessio
- Irisarri, Iker
- Jakobsen, Kjetill S.
- Klinga, Peter
- Kloch, Agnieszka
- Kratochwil, Claudius F.
- Kusche, Henrik
- Layton, Kara K.S.
- Leonard, Jennifer A.
- Lerat, Emmanuelle
- Liti, Gianni
- Manousaki, Tereza
- Matschiner, Michael
- Maumus, Florian
- Meiri, Shai
- Mengual, Ximo
- Monaghan, Michael T.
- Montagna, Matteo
- Mysłajek, Robert W.
- Neiber, Marco T.
- Nicolas, Violaine
- Novo, Marta
- Ozretić, Petar
- Palero, Ferran
- Pârvulescu, Lucian
- Pascual, Marta
- Paulo, Octávio S.
- Pavlek, Martina
- Pegueroles, Cinta
- Pellissier, Loïc
- Pesole, Graziano
- Primmer, Craig R.
- Riesgo, Ana
- Rüber, Lukas
- Rubolini, Diego
- Salvi, Daniele
- Seidel, Matthias
- Studer, Bruno
- Theodoridis, Spyros
- Thines, Marco
- Urban, Lara
- Vasemägi, Anti
- Vella, Adriana
- Vella, Noel
- Vernes, Sonja C.
- Vernesi, Cristiano
- Vieites, David R.
- Wheat, Christopher W.
- Wörheide, Gert
- Wurm, Yannick
- Zammit, Gabrielle
- Venue
- Trends in Genetics
- Publisher
- Elsevier BV
- Published
- 2023-07
- Volume
- 39
- Issue
- 7
- Pages
- 545-559
- ISSN
- 0168-9525 (ISSN-L)
- OpenAlex
- W4321019193
- Cited by
- 401
- References
- 150
- Citations by year
- 2026: 117 · 2025: 132 · 2024: 120 · 2023: 32
- FWCI
- 10.68
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Trends in Genetics (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- Edinburgh Research Explorer (University of Edinburgh) (publishedVersion, cc-by)
- Repository of the University of Namur (publishedVersion, cc-by)
- Epsilon Open Archive (Sveriges lantbruksuniversitet biblioteket (Swedish University of Agricultural Sciences)) (acceptedVersion, other-oa)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion, cc-by-nc-nd)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by)
- OAR@UM (University of Malta) (submittedVersion, other-oa)
- KTH Publication Database DiVA (KTH Royal Institute of Technology) (submittedVersion, other-oa)
- HAL (submittedVersion, cc-by)
- Agritrop (Cirad) (submittedVersion, cc-by)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
- DiRROS repository (University of Maribor) (submittedVersion, cc-by-nc-nd)
- Florence Research (University of Florence) (submittedVersion, other-oa)
- Institutional Repository of the Ruđer Bošković Institute (Ruđer Bošković Institute) (submittedVersion, cc-by)
- CINECA IRIS Institutional Research Information System (Fondazione Edmund Mach) (submittedVersion, cc-by)
- ORBi (University of Liège) (submittedVersion, other-oa)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion, cc-by)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, other-oa)
- St Andrews Research Repository (St Andrews Research Repository) (submittedVersion, cc-by)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion, cc-by)
- Archivio Istituzionale della Ricerca - Università degli Studi dell Aquila (submittedVersion, cc-by)
- Repository of Digital Objects for Teaching Research and Culture (University of Valencia) (submittedVersion, cc-by-nc)
- SERVAL (Université de Lausanne) (submittedVersion, cc-by)
- ReIn UW (University of Warsaw) (submittedVersion, cc-by-nc-nd)
- Aberdeen University Research Archive (Aberdeen University) (submittedVersion)
- Bern Open Repository and Information System (University of Bern) (submittedVersion, cc-by)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
- Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) (submittedVersion, other-oa)
- Florence Research (University of Florence) (submittedVersion)
- Informationszentrum Lebenswissenschaften (ZB MED) (submittedVersion, cc-by)
- Institutional Research Information System University of Ferrara (University of Ferrara) (submittedVersion, cc-by)
- IRIS (submittedVersion, cc-by)
- NORA - Norwegian Open Research Archives (submittedVersion, cc-by)
- NORA - Norwegian Open Research Archives (submittedVersion, other-oa)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion, cc-by)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, cc-by)
- Institutional Research Information System University of Ferrara (University of Ferrara) (submittedVersion, cc-by-nc-nd)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion, cc-by)
- ETH Zürich Research Collection
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/T015683/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- conservation genomics, biodiversity conservation, reference genome, biodiversity assessment, species restoration, genomic resources, tree of life
- MeSH terms
- Conservation of Natural Resources, Genome, Genomics, Biodiversity
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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