The DOI matches its Crossref record; 151 of the 151 references it cites were found in a registry or an index.
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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Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03451-0 · Cited by 3,097
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Deiner, K., Bik, H. M., Mächler, E., Seymour, M., Lacoursière‐Roussel, A., Altermatt, F., Creer, S., Bista, I., Lodge, D. M., de Vere, N., et al. (2017) · Molecular Ecology · doi:10.1111/mec.14350 · Cited by 2,075
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Hammond, A., Galizi, R., Kyrou, K., Simoni, A., Siniscalchi, C., Katsanos, D., Gribble, M., Baker, D. A., Marois, É., Russell, S. R. H., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3439 · Cited by 1,188
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“14-16, 60325 Frankfurt/Main, Germany (2)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 The value of integrating genomics into conservation Wea…”
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Hoban, S., Kelley, J. L., Lotterhos, K. E., Antolin, M. F., Bradburd, G., Lowry, D. B., Poss, M. L., Reed, L. K., Storfer, A., & Whitlock, M. C. (2016) · The American Naturalist · doi:10.1086/688018 · Cited by 876 · cited 1×
“Such analyses are mostly successful at identifying variants with large effects [71,74,75], likely representing a small proportion of the adaptive functional variation.”
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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
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- PubMed (publishedVersion)
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- 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
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