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Crowther TW, Rappuoli R, Corinaldesi C, Danovaro R, Donohue TJ, Huisman J, Stein LY, Timmis JK, Timmis K, Anderson MZ, Bakken LR, Baylis M, Behrenfeld MJ, Boyd PW, Brettell I, Cavicchioli R, Delavaux CS, Foreman CM, Jansson JK, Koskella B, Milligan-McClellan K, North JA, Peterson D, Pizza M, Ramos JL, Reay D, Remais JV, Rich VI, Ripple WJ, Singh BK, Smith GR, Stewart FJ, Sullivan MB, van den Hoogen J, van Oppen MJH, Webster NS, Zohner CM, van Galen LG. Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals. Cell 2024; 187:5195-5216. [PMID: 39303686 DOI: 10.1016/j.cell.2024.07.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 07/05/2024] [Accepted: 07/27/2024] [Indexed: 09/22/2024]
Abstract
Microorganisms, including bacteria, archaea, viruses, fungi, and protists, are essential to life on Earth and the functioning of the biosphere. Here, we discuss the key roles of microorganisms in achieving the United Nations Sustainable Development Goals (SDGs), highlighting recent and emerging advances in microbial research and technology that can facilitate our transition toward a sustainable future. Given the central role of microorganisms in the biochemical processing of elements, synthesizing new materials, supporting human health, and facilitating life in managed and natural landscapes, microbial research and technologies are directly or indirectly relevant for achieving each of the SDGs. More importantly, the ubiquitous and global role of microbes means that they present new opportunities for synergistically accelerating progress toward multiple sustainability goals. By effectively managing microbial health, we can achieve solutions that address multiple sustainability targets ranging from climate and human health to food and energy production. Emerging international policy frameworks should reflect the vital importance of microorganisms in achieving a sustainable future.
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Affiliation(s)
- Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland; Restor Eco AG, Zürich 8001, Switzerland.
| | - Rino Rappuoli
- Fondazione Biotecnopolo di Siena, Siena 53100, Italy.
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona 60131, Italy; National Biodiversity Future Center, Palermo 90133, Italy
| | - Roberto Danovaro
- National Biodiversity Future Center, Palermo 90133, Italy; Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
| | - Timothy J Donohue
- Wisconsin Energy Institute, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam 94240, the Netherlands
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - James Kenneth Timmis
- Institute of Political Science, University of Freiburg, Freiburg 79085, Germany; Athena Institute for Research on Innovation and Communication in Health and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081, the Netherlands
| | - Kenneth Timmis
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig 38106, Germany
| | - Matthew Z Anderson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas 1433, Norway
| | - Matthew Baylis
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Cheshire, Neston CH64 7TE, UK
| | - Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7004, Australia
| | - Ian Brettell
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Camille S Delavaux
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Christine M Foreman
- Department of Chemical and Biological Engineering and Center for Biofilm Engineering, Montana State University, Bozeman, MT 59718, USA
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kat Milligan-McClellan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
| | - Justin A North
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Devin Peterson
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA
| | - Mariagrazia Pizza
- Department of Life Sciences, CBRB Center, Imperial College, London SW7 2AZ, UK
| | - Juan L Ramos
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada 18008, Spain
| | - David Reay
- School of GeoSciences, The University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Justin V Remais
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Virginia I Rich
- Center of Microbiome Science, Byrd Polar and Climate Research, and Microbiology Department, The Ohio State University, Columbus, OH 43214, USA
| | - William J Ripple
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5704, USA
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Gabriel Reuben Smith
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Frank J Stewart
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Center of Microbiome Science, and EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
| | - Johan van den Hoogen
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia; School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicole S Webster
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7004, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia; Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Constantin M Zohner
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Laura G van Galen
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland; Society for the Protection of Underground Networks (SPUN), Dover, DE 19901, USA.
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Mc Cartney AM, Formenti G, Mouton A, De Panis D, Marins LS, Leitão HG, Diedericks G, Kirangwa J, Morselli M, Salces-Ortiz J, Escudero N, Iannucci A, Natali C, Svardal H, Fernández R, De Pooter T, Joris G, Strazisar M, Wood JMD, Herron KE, Seehausen O, Watts PC, Shaw F, Davey RP, Minotto A, Fernández JM, Böhne A, Alegria C, Alioto T, Alves PC, Amorim IR, Aury JM, Backstrom N, Baldrian P, Baltrunaite L, Barta E, BedHom B, Belser C, Bergsten J, Bertrand L, Bilandija H, Binzer-Panchal M, Bista I, Blaxter M, Borges PAV, Dias GB, Bosse M, Brown T, Bruggmann R, Buena-Atienza E, Burgin J, Buzan E, Cariani A, Casadei N, Chiara M, Chozas S, Čiampor F, Crottini A, Cruaud C, Cruz F, Dalen L, De Biase A, Del Campo J, Delic T, Dennis AB, Derks MFL, Diroma MA, Djan M, Duprat S, Eleftheriadi K, Feulner PGD, Flot JF, Forni G, Fosso B, Fournier P, Fournier-Chambrillon C, Gabaldon T, Garg S, Gissi C, Giupponi L, Gomez-Garrido J, González J, Grilo ML, Grüning B, Guerin T, Guiglielmoni N, Gut M, Haesler MP, Hahn C, Halpern B, Harrison PW, Heintz J, Hindrikson M, Höglund J, Howe K, Hughes GM, Istace B, Cock MJ, Janžekovič F, Jonsson ZO, Joye-Dind S, Koskimäki JJ, Krystufek B, Kubacka J, Kuhl H, Kusza S, Labadie K, Lähteenaro M, Lantz H, Lavrinienko A, Leclère L, Lopes RJ, Madsen O, Magdelenat G, Magoga G, Manousaki T, Mappes T, Marques JP, Redondo GIM, Maumus F, McCarthy SA, Megens HJ, Melo-Ferreira J, Mendes SL, Montagna M, Moreno J, Mosbech MB, Moura M, Musilova Z, Myers E, Nash WJ, Nater A, Nicholson P, Niell M, Nijland R, Noel B, Noren K, Oliveira PH, Olsen RA, Ometto L, Oomen RA, Ossowski S, Palinauskas V, Palsson S, Panibe JP, Pauperio J, Pavlek M, Payen E, Pawlowska J, Pellicer J, Pesole G, Pimenta J, Pippel M, Pirttilä AM, Poulakakis N, Rajan J, M C Rego R, Resendes R, Resl P, Riesgo A, Rodin-Morch P, Soares AER, Fernandes CR, Romeiras MM, Roxo G, Rüber L, Ruiz-Lopez MJ, Saarma U, da Silva LP, Sim-Sim M, Soler L, Sousa VC, Santos CS, Spada A, Stefanovic M, Steger V, Stiller J, Stöck M, Struck TH, Sudasinghe H, Tapanainen R, Tellgren-Roth C, Trindade H, Tukalenko Y, Urso I, Vacherie B, Van Belleghem SM, Van Oers K, Vargas-Chavez C, Velickovic N, Vella N, Vella A, Vernesi C, Vicente S, Villa S, Pettersson OV, Volckaert FAM, Voros J, Wincker P, Winkler S, Ciofi C, Waterhouse RM, Mazzoni CJ. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. NPJ BIODIVERSITY 2024; 3:28. [PMID: 39289538 PMCID: PMC11408602 DOI: 10.1038/s44185-024-00054-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 07/19/2024] [Indexed: 09/19/2024]
Abstract
A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.
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Affiliation(s)
- Ann M Mc Cartney
- Genomics Institute, University of California, Santa Cruz, CA, USA.
| | - Giulio Formenti
- The Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Alice Mouton
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- InBios-Conservation Genetics Laboratory, University of Liege, Liege, Belgium
| | - Diego De Panis
- Leibniz Institut für Zoo und Wildtierforschung, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Luísa S Marins
- Leibniz Institut für Zoo und Wildtierforschung, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | | | | | - Joseph Kirangwa
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Marco Morselli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Judit Salces-Ortiz
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Nuria Escudero
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Alessio Iannucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Chiara Natali
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Rosa Fernández
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Tim De Pooter
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Geert Joris
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Katie E Herron
- School of Biology and Environmental Science, University College Dublin, Belfield, Ireland
| | - Ole Seehausen
- Aquatic Ecology & Evolution, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology & Evolution, Eawag, Kastanienbaum, Switzerland
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Felix Shaw
- The Earlham Institute, Norwich Research Park, Norwich, UK
| | - Robert P Davey
- The Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - José M Fernández
- Barcelona Supercomputing Center; Spanish National Bioinformatics Institute, ELIXIR Spain, Getafe, Spain
| | - Astrid Böhne
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Bonn, Germany
| | - Carla Alegria
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Tyler Alioto
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Paulo C Alves
- CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, InBIO Laboratorio Associado, Universidade do Porto, Vairao, Portugal
- Departamento de Biologia, Faculdade de Ciencias, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, Vairao, Portugal
| | - Isabel R Amorim
- University of the Azores, cE3c-Centre for Ecology, Evolution and Environmental Changes, Azorean Biodiversity Group, CHANGE-Global Change and Sustainability Institute, Rua Capitão João d´Ávila, Pico da Urze, Angra do Heroísmo, Portugal
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Niclas Backstrom
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | | | - Endre Barta
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Bertrand BedHom
- Institut de Systematique, Evolution, Biodiversite, Museum National d Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Faculty of Science, Stockholm University, Stockholm, Sweden
| | - Laurie Bertrand
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | | | - Mahesh Binzer-Panchal
- SciLifeLab, Solna, Sweden
- Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Iliana Bista
- Senckenberg Research Institute, Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
- Wellcome CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Paulo A V Borges
- University of the Azores, cE3c-Centre for Ecology, Evolution and Environmental Changes, Azorean Biodiversity Group, CHANGE-Global Change and Sustainability Institute, Rua Capitão João d´Ávila, Pico da Urze, Angra do Heroísmo, Portugal
| | - Guilherme Borges Dias
- SciLifeLab, Solna, Sweden
- Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Mirte Bosse
- VU University Amsterdam, Amsterdam, The Netherlands
- Animal Breeding & Genomics, Wageningen University & Research, Wageningen, The Netherlands
- Wageningen University & Research, Wageningen, The Netherlands
| | - Tom Brown
- Leibniz Institut für Zoo und Wildtierforschung, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN concept Genome Center, Dresden, Germany
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Elena Buena-Atienza
- Institute of Medical Genetics and Applied Genomics, University of Tubingen, Tubingen, Germany
- NGS Competence Center Tubingen, Tubingen, Germany
| | - Josephine Burgin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Elena Buzan
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Koper, Slovenia
- Faculty of Environmental Protection, Velenje, Slovenia
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum Universitá di Bologna, Bologna, Italy
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tubingen, Tubingen, Germany
- NGS Competence Center Tubingen, Tubingen, Germany
| | - Matteo Chiara
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Sergio Chozas
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- Sociedade Portuguesa de Botânica, Lisbon, Portugal
| | - Fedor Čiampor
- Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre Slovak Academy of Sciences, Bratislava, Slovakia
| | - Angelica Crottini
- CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, InBIO Laboratorio Associado, Universidade do Porto, Vairao, Portugal
- Departamento de Biologia, Faculdade de Ciencias, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, Vairao, Portugal
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Fernando Cruz
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Love Dalen
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Alessio De Biase
- Department of Biology and Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Javier Del Campo
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Teo Delic
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Ljubljana, Slovenia
| | - Alice B Dennis
- University of Namur, Department of Biology, URBE, ILEE, Namur, Belgium
| | - Martijn F L Derks
- Animal Breeding & Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Maria Angela Diroma
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Mihajla Djan
- Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | - Simone Duprat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Klara Eleftheriadi
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Philine G D Feulner
- Eawag Swiss Federal Institute of Aquatic Science and Technology, Department of Fish Ecology & Evolution, Kastanienbaum, Switzerland
| | - Jean-François Flot
- Department of Organismal Biology, Universite libre de Bruxelles, Brussels, Belgium
| | - Giobbe Forni
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum Universitá di Bologna, Bologna, Italy
| | - Bruno Fosso
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Pascal Fournier
- Groupe de Recherche et d Etude pour la Gestion de l Environnement, Villandraut, France
| | | | - Toni Gabaldon
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- CIBERINFEC, Instituto Carlos III, Barcelona, Spain
| | - Shilpa Garg
- NNF Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Carmela Gissi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
- CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - Luca Giupponi
- Centre of Applied Studies for the Sustainable Management and Protection of Mountain Areas CRC Ge.S.Di.Mont., University of Milan, Milan, Italy
- Department of Agricultural and Environmental Sciences-Production, Landscape and Agroenergy DiSAA, University of Milan, Milan, Italy
| | - Jessica Gomez-Garrido
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Miguel L Grilo
- Marine and Environmental Sciences Centre, Aquatic Research Network, Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisboa, Portugal
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Caparica, Portugal
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Thomas Guerin
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Marcel P Haesler
- Aquatic Ecology & Evolution, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology & Evolution, Eawag, Kastanienbaum, Switzerland
| | - Christoph Hahn
- Department of Biology, University of Graz, Graz, Austria
| | - Balint Halpern
- MME BirdLife Hungary, Budapest, Hungary
- Doctoral School of Biology, Department of Systematic Zoology and Ecology, Institute of Biology, ELTE Eotvos Lorand University, Budapest, Hungary
- HUN-REN-ELTE-MTM Integrative Ecology Research Group, Budapest, Hungary
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Julia Heintz
- SciLifeLab, Solna, Sweden
- Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jacob Höglund
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Ireland
- UCD Conway Institute, University College Dublin, Belfield, Ireland
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Mark J Cock
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universite, UPMC University Paris 06, Paris, France
- France Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Franc Janžekovič
- University of Maribor, Faculty of Natural Sciences and Mathematics, Maribor, Slovenia
| | - Zophonias O Jonsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Sagane Joye-Dind
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Janne J Koskimäki
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Boris Krystufek
- Slovenian Museum of Natural History, Ljubljana, Slovenia
- Science and Research Centre Koper, Koper, Slovenia
| | - Justyna Kubacka
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Heiner Kuhl
- Department IV Fish Biology, Fisheries and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Szilvia Kusza
- University of Debrecen, Centre for Agricultural Genomics and Biotechnology, Debrecen, Hungary
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Meri Lähteenaro
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Faculty of Science, Stockholm University, Stockholm, Sweden
| | - Henrik Lantz
- SciLifeLab, Solna, Sweden
- Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Anton Lavrinienko
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zurich, Zurich, Switzerland
| | - Lucas Leclère
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Banyuls-sur-Mer, France
| | - Ricardo Jorge Lopes
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- MHNC-UP, Natural History and Science Museum of the University of Porto, Porto, Portugal
| | - Ole Madsen
- Animal Breeding & Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Giulia Magoga
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Tereza Manousaki
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Heraklion, Crete, Greece
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Joao Pedro Marques
- CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, InBIO Laboratorio Associado, Universidade do Porto, Vairao, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, Vairao, Portugal
| | | | - Florian Maumus
- Universite Paris Saclay, INRAE, URGI, Versailles, France
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Hendrik-Jan Megens
- Animal Breeding & Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Jose Melo-Ferreira
- CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, InBIO Laboratorio Associado, Universidade do Porto, Vairao, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, Vairao, Portugal
- Departamento de Biologia, Faculdade de Ciencias da Universidade do Porto, Porto, Portugal
| | - Sofia L Mendes
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Matteo Montagna
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Interuniversity Center for Studies on Bioinspired Agro Environmental Technology, University of Naples Federico II, Naples, Italy
| | - Joao Moreno
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- MARE Marine and Environmental Sciences Centre, ARNET Aquatic Research Network, Lisboa, Portugal
| | - Mai-Britt Mosbech
- SciLifeLab, Solna, Sweden
- Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Mónica Moura
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores; Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal
- UNESCO, Chair Land Within Sea Biodiversity & Sustainability in Atlantic Islands, Portugal
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Eugene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN concept Genome Center, Dresden, Germany
| | - Will J Nash
- The Earlham Institute, Norwich Research Park, Norwich, UK
| | - Alexander Nater
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Pamela Nicholson
- Next Generation Sequencing Platform, University of Bern, Bern, Switzerland
| | - Manuel Niell
- Andorra Research and Innovation, Sant Julià de Lòria, Andorra
| | - Reindert Nijland
- Marine Animal Ecology Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Benjamin Noel
- University of the Azores, cE3c-Centre for Ecology, Evolution and Environmental Changes, Azorean Biodiversity Group, CHANGE-Global Change and Sustainability Institute, Rua Capitão João d´Ávila, Pico da Urze, Angra do Heroísmo, Portugal
| | - Karin Noren
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Pedro H Oliveira
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Remi-Andre Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Lino Ometto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
- University of New Brunswick Saint John, Saint John, New Brunswick, Canada
| | - Stephan Ossowski
- Institute for Medical Genetics and Applied Genomics, University of Tubingen, Tubingen, Germany
- NGS Competence Center Tubingen (NCCT), University of Tubingen, Tubingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tubingen, Tubingen, Germany
| | | | - Snaebjorn Palsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Jerome P Panibe
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Joana Pauperio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Emilie Payen
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | | | - Jaume Pellicer
- Institut Botànic de Barcelona, IBB (CSIC-CMCNB), Passeig del Migdia s.n., Parc de Montjüic, Barcelona, Spain
| | - Graziano Pesole
- University of Bari Aldo Moro, Department of Biosciences, Biotechnology and Environment; Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Joao Pimenta
- CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, InBIO Laboratorio Associado, Universidade do Porto, Vairao, Portugal
- Wellcome Sanger Institute, Cambridge, UK
| | - Martin Pippel
- SciLifeLab, Solna, Sweden
- Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | | | - Nikos Poulakakis
- Department of Biology, School of Sciences and Engineering, University of Crete, Voutes University Campus, Irakleio, Greece
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio, Greece
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rúben M C Rego
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores; Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal
- UNESCO, Chair Land Within Sea Biodiversity & Sustainability in Atlantic Islands, Portugal
| | - Roberto Resendes
- Universidade dos Acores, Departamento de Biologia, Ponta Delgada, Portugal
| | - Philipp Resl
- Department of Biology, University of Graz, Graz, Austria
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Madrid, Spain
| | | | - Andre E R Soares
- SciLifeLab, Solna, Sweden
- Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Carlos Rodriguez Fernandes
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- Faculdade de Psicologia, Universidade de Lisboa, Lisboa, Portugal
| | - Maria M Romeiras
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
- Portugal Centre for Ecology, Evolution and Environmental Changes, Lisbon, Portugal
| | - Guilherme Roxo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores; Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal
- UNESCO, Chair Land Within Sea Biodiversity & Sustainability in Atlantic Islands, Portugal
| | - Lukas Rüber
- Aquatic Ecology & Evolution, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland
- Naturhistorisches Museum Bern, Bern, Switzerland
| | - Maria Jose Ruiz-Lopez
- Departamento de Biología de la Conservación y Cambio Global, Estación Biológica de Doñana (EBD), CSIC, Sevilla, Spain
- CIBER of Epidemiology and Public Health, Granada, Spain
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Luis P da Silva
- CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, InBIO Laboratorio Associado, Universidade do Porto, Vairao, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, Vairao, Portugal
| | - Manuela Sim-Sim
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- Museu Nacional de História Natural e da Ciência, Lisboa, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Lucile Soler
- SciLifeLab, Solna, Sweden
- Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Vitor C Sousa
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Carla Sousa Santos
- MARE Marine and Environmental Sciences Centre, ARNET Aquatic Research Network, Lisboa, Portugal
| | - Alberto Spada
- Department of Agricultural and Environmental Sciences Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Milomir Stefanovic
- Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | - Viktor Steger
- Department of Genetics and Genomics, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Godollo, Hungary
| | - Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Stöck
- Department IV Fish Biology, Fisheries and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Torsten H Struck
- Natural History Museum, University of Oslo, Blindern, Oslo, Norway
| | - Hiranya Sudasinghe
- Naturhistorisches Museum Bern, Bern, Switzerland
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Christian Tellgren-Roth
- SciLifeLab, Solna, Sweden
- Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Helena Trindade
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Yevhen Tukalenko
- Institute for Nuclear Research of the NAS of Ukraine, Kyiv, Ukraine
| | - Ilenia Urso
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Benoit Vacherie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Steven M Van Belleghem
- Ecology, Evolution and Conservation Biology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Kees Van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Carlos Vargas-Chavez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Nevena Velickovic
- Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | - Noel Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida, Malta
| | - Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida, Malta
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre-Fondazione Edmund Mach, San Michele All'Adige, Italy
| | - Sara Vicente
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- ERISA Escola Superior de Saúde Ribeiro Sanches, IPLUSO, Lisboa, Portugal
| | - Sara Villa
- Institute for Sustainable Plant Protection, National Research Council, Sesto Fiorentino, Italy
- Department of Agricultural and Environmental Sciences, University of Milan via Giovanni Celoria 2, Milan, Italy
| | - Olga Vinnere Pettersson
- SciLifeLab, Solna, Sweden
- Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Judit Voros
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Sylke Winkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Claudio Ciofi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institut für Zoo und Wildtierforschung, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
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3
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Mc Cartney AM, Scholz AH, Groussin M, Staunton C. Benefit-Sharing by Design: A Call to Action for Human Genomics Research. Annu Rev Genomics Hum Genet 2024; 25:369-395. [PMID: 38608642 DOI: 10.1146/annurev-genom-021623-104241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
The ethical standards for the responsible conduct of human research have come a long way; however, concerns surrounding equity remain in human genetics and genomics research. Addressing these concerns will help society realize the full potential of human genomics research. One outstanding concern is the fair and equitable sharing of benefits from research on human participants. Several international bodies have recognized that benefit-sharing can be an effective tool for ethical research conduct, but international laws, including the Convention on Biological Diversity and its Nagoya Protocol on Access and Benefit-Sharing, explicitly exclude human genetic and genomic resources. These agreements face significant challenges that must be considered and anticipated if similar principles are applied in human genomics research. We propose that benefit-sharing from human genomics research can be a bottom-up effort and embedded into the existing research process. We propose the development of a "benefit-sharing by design" framework to address concerns of fairness and equity in the use of human genomic resources and samples and to learn from the aspirations and decade of implementation of the Nagoya Protocol.
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Affiliation(s)
- Ann M Mc Cartney
- Genomics Institute, University of California, Santa Cruz, California, USA;
| | - Amber Hartman Scholz
- Department of Science Policy and Internationalisation, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany;
| | - Mathieu Groussin
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany;
| | - Ciara Staunton
- School of Law, University of KwaZulu-Natal, Durban, South Africa
- Institute for Biomedicine, Eurac Research, Bolzano, Italy;
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4
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Prescott RD, Chan YL, Tong EJ, Bunn F, Onouye CT, Handel C, Lo CC, Davenport K, Johnson S, Flynn M, Saito JA, Lee H, Wong K, Lawson BN, Hiura K, Sager K, Sadones M, Hill EC, Esibill D, Cockell CS, Santomartino R, Chain PS, Decho AW, Donachie SP. Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance. ASTROBIOLOGY 2023; 23:1348-1367. [PMID: 38079228 PMCID: PMC10750312 DOI: 10.1089/ast.2023.0072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 12/22/2023]
Abstract
Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with "place" and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai'i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16AT, of the new species (DSM 112479T = NCTC 14602T). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61T, of the new species (DSM 116657T = LMG = 33184T), and Hawai'i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16ET, of the new species (DSM 112478T = NCTC 14603T).
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Affiliation(s)
- Rebecca D. Prescott
- Department of Biology, University of Mississippi, University, Mississippi, USA
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
- National Aeronautics and Space Administration, Johnson Space Center, Houston, Texas, USA
| | - Yvonne L. Chan
- Office of Community Science, ‘Iolani School, Honolulu, Hawai‘i, USA
| | - Eric J. Tong
- Office of Community Science, ‘Iolani School, Honolulu, Hawai‘i, USA
| | - Fiona Bunn
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - Chiyoko T. Onouye
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Christy Handel
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Chien-Chi Lo
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Karen Davenport
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Shannon Johnson
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Mark Flynn
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Jennifer A. Saito
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Herb Lee
- Pacific American Foundation, Kailua, Hawai‘i, USA
| | | | - Brittany N. Lawson
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Kayla Hiura
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Kailey Sager
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Mia Sadones
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Ethan C. Hill
- Office of Community Science, ‘Iolani School, Honolulu, Hawai‘i, USA
| | | | - Charles S. Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - Rosa Santomartino
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - Patrick S.G. Chain
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Alan W. Decho
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina, USA
| | - Stuart P. Donachie
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
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Handsley-Davis M, Anderson MZ, Bader AC, Ehau-Taumaunu H, Fox K, Kowal E, Weyrich LS. Microbiome ownership for Indigenous peoples. Nat Microbiol 2023; 8:1777-1786. [PMID: 37770744 DOI: 10.1038/s41564-023-01470-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
Several studies have reported increased microbial diversity, or distinct microbial community compositions, in the microbiomes of Indigenous peoples around the world. However, there is a widespread failure to include Indigenous cultures and perspectives in microbiome research programmes, and ethical issues pertaining to microbiome research involving Indigenous participants have not received enough attention. We discuss the benefits and risks arising from microbiome research involving Indigenous peoples and analyse microbiome ownership as an ethical concept in this context. We argue that microbiome ownership represents an opportunity for Indigenous peoples to steward and protect their resident microbial communities at every stage of research.
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Affiliation(s)
- Matilda Handsley-Davis
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Quebec, Canada
| | - Hanareia Ehau-Taumaunu
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College, PA, USA
| | - Keolu Fox
- Department of Anthropology, Global Health Program, and Indigenous Futures Institute, University of California, San Diego, CA, USA
| | - Emma Kowal
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Melbourne, Victoria, Australia
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
- Department of Anthropology and Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, USA.
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6
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Resnik D. Openness in Scientific Research: A Historical and Philosophical Perspective. JOURNAL OF OPEN ACCESS TO LAW 2023; 11:132. [PMID: 37994350 PMCID: PMC10665006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Openness is widely regarded as a pillar of scientific ethics because it promotes reproducibility and progress in science and benefits society. However, the sharing of scientific information can sometimes adversely impact the interests of human research participants, human communities or populations, scientists, and private research sponsors; and may threaten national security. Because openness may conflict with other important social values, solutions to ethical and policy dilemmas should include meaningful input from those who are impacted by the sharing and use of scientific information, including research participants, communities, and the public. Data sharing and use policies should be reviewed and revised periodically to account for ongoing changes in science, technology, and society.
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Affiliation(s)
- David Resnik
- National Institute of Environmental Health Sciences (NIEHS)
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7
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Te Aika B, Liggins L, Rye C, Perkins EO, Huh J, Brauning R, Godfery T, Black MA. Aotearoa genomic data repository: An āhuru mōwai for taonga species sequencing data. Mol Ecol Resour 2023. [PMID: 37712601 DOI: 10.1111/1755-0998.13866] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/04/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023]
Abstract
The Aotearoa Genomic Data Repository (AGDR) is an initiative to provide a secure within-nation option for the storage, management and sharing of non-human genomic data generated from biological and environmental samples originating in Aotearoa New Zealand. This resource has been developed to follow the principles of Māori Data Sovereignty, and to enable the right of kaitiakitanga (guardianship), so that iwi, hapū and whānau (tribes, kinship groups and families) can effectively exercise their responsibilities as guardians over biological entities that they regard as taonga (precious or treasured). While the repository is designed to facilitate the sharing of data-making it findable by researchers and interoperable with data held in other genomic repositories-the decision-making process regarding who can access the data is entirely in the hands of those holding kaitiakitanga over each data set. No data are made available to the requesting researcher until the request has been approved, and the conditions for access (which can vary by data set) have been agreed to. Here we describe the development of the AGDR, from both a cultural perspective, and a technical one, and outline the processes that underpin its operation.
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Affiliation(s)
- Ben Te Aika
- Research and Enterprise Office, University of Otago, Dunedin, New Zealand
| | - Libby Liggins
- School of Natural Sciences, Massey University, Auckland, New Zealand
- Genomics Aotearoa, New Zealand
| | - Claire Rye
- New Zealand eScience Infrastructure, University of Auckland, Auckland, New Zealand
| | - E Owen Perkins
- New Zealand eScience Infrastructure, University of Auckland, Auckland, New Zealand
| | - Jun Huh
- New Zealand eScience Infrastructure, University of Auckland, Auckland, New Zealand
| | - Rudiger Brauning
- Genomics Aotearoa, New Zealand
- Invermay Agricultural Centre, AgResearch Ltd, Mosgiel, Otago, New Zealand
| | - Tracey Godfery
- Genomics Aotearoa, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Michael A Black
- Genomics Aotearoa, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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8
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Wylie MJ, Kitson J, Russell K, Yoshizaki G, Yazawa R, Steeves TE, Wellenreuther M. Fish germ cell cryobanking and transplanting for conservation. Mol Ecol Resour 2023. [PMID: 37712134 DOI: 10.1111/1755-0998.13868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/26/2023] [Accepted: 07/18/2023] [Indexed: 09/16/2023]
Abstract
The unprecedented loss of global biodiversity is linked to multiple anthropogenic stressors. New conservation technologies are urgently needed to mitigate this loss. The rights, knowledge and perspectives of Indigenous peoples in biodiversity conservation-including the development and application of new technologies-are increasingly recognised. Advances in germplasm cryopreservation and germ cell transplantation (termed 'broodstock surrogacy') techniques offer exciting tools to preserve biodiversity, but their application has been underappreciated. Here, we use teleost fishes as an exemplar group to outline (1) the power of these techniques to preserve genome-wide genetic diversity, (2) the need to apply a conservation genomic lens when selecting individuals for germplasm cryobanking and broodstock surrogacy and (3) the value of considering the cultural significance of these genomic resources. We conclude by discussing the opportunities and challenges of these techniques for conserving biodiversity in threatened teleost fish and beyond.
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Affiliation(s)
- Matthew J Wylie
- The New Zealand Institute for Plant & Food Research Limited, Nelson, New Zealand
| | - Jane Kitson
- Kitson Consulting Ltd, Invercargill, New Zealand
| | - Khyla Russell
- Kāti Huirapa Rūnaka ki Puketeraki, Karitane, New Zealand
| | - Goro Yoshizaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ryosuke Yazawa
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Limited, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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9
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Soares GH, Hedges J, Sethi S, Poirier B, Jamieson L. From biocolonialism to emancipation: considerations on ethical and culturally respectful omics research with indigenous Australians. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2023; 26:487-496. [PMID: 37171744 PMCID: PMC10425494 DOI: 10.1007/s11019-023-10151-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/04/2023] [Indexed: 05/13/2023]
Abstract
As part of a (bio)colonial project, the biological information of Indigenous Peoples has historically been under scientific scrutiny, with very limited benefits for communities and donors. Negative past experiences have contributed to further exclude Indigenous communities from novel developments in the field of omics research. Over the past decade, new guidelines, reflections, and projects of genetic research with Indigenous Peoples have flourished in Australia, providing opportunities to move the field into a place of respect and ethical relationships. This review explores the ethical and cultural implications of the use of biological samples from Indigenous communities in biomedical research. A structured framework outlining emerging topics of interest for the development of respectful omics research partnerships with Indigenous Australians is presented. This paper highlights aspects related to Indigenous governance, community and individual consent, respectful handling of biological samples, data management, and communication in order to protect Indigenous interests and rights and to promote communities' autonomy.
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Affiliation(s)
- Gustavo H Soares
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia.
| | - Joanne Hedges
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
| | - Sneha Sethi
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
| | - Brianna Poirier
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
| | - Lisa Jamieson
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
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10
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Urban L, Perlas A, Francino O, Martí‐Carreras J, Muga BA, Mwangi JW, Boykin Okalebo L, Stanton JL, Black A, Waipara N, Fontsere C, Eccles D, Urel H, Reska T, Morales HE, Palmada‐Flores M, Marques‐Bonet T, Watsa M, Libke Z, Erkenswick G, van Oosterhout C. Real-time genomics for One Health. Mol Syst Biol 2023; 19:e11686. [PMID: 37325891 PMCID: PMC10407731 DOI: 10.15252/msb.202311686] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.
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Affiliation(s)
- Lara Urban
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Albert Perlas
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
| | - Olga Francino
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Joan Martí‐Carreras
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Brenda A Muga
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | | | | | | | - Amanda Black
- Bioprotection AotearoaLincoln UniversityLincolnNew Zealand
| | | | - Claudia Fontsere
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
| | - David Eccles
- Hugh Green Cytometry CentreMalaghan Institute of Medical ResearchWellingtonNew Zealand
| | - Harika Urel
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Tim Reska
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Hernán E Morales
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
- Department of Biology, Ecology BuildingLund UniversityLundSweden
| | - Marc Palmada‐Flores
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
| | - Tomas Marques‐Bonet
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAGCentre of Genomic AnalysisBarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaBarcelonaSpain
| | | | - Zane Libke
- Instituto Nacional de BiodiversidadQuitoEcuador
- Fundación Sumak Kawsay In SituCantón MeraEcuador
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11
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Patnaik HH, Sang MK, Park JE, Song DK, Jeong JY, Hong CE, Kim YT, Shin HJ, Ziwei L, Hwang HJ, Park SY, Kang SW, Ko JH, Lee JS, Park HS, Jo YH, Han YS, Patnaik BB, Lee YS. A review of the endangered mollusks transcriptome under the threatened species initiative of Korea. Genes Genomics 2023; 45:969-987. [PMID: 37405596 DOI: 10.1007/s13258-023-01389-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/09/2023] [Indexed: 07/06/2023]
Abstract
Transcriptome studies for conservation of endangered mollusks is a proactive approach towards managing threats and uncertainties facing these species in natural environments. The population of these species is declining due to habitat destruction, illicit wildlife trade, and global climate change. These activities risk the free movement of species across the wild landscape, loss of breeding grounds, and restrictions in displaying the physiological attributes so crucial for faunal welfare. Gastropods face the most negative ecological effects and have been enlisted under Korea's protective species consortium based on their population dynamics in the last few years. Moreover, with the genetic resources restricted for such species, conservation by informed planning is not possible. This review provides insights into the activities under the threatened species initiative of Korea with special reference to the transcriptome assemblies of endangered mollusks. The gastropods such as Ellobium chinense, Aegista chejuensis, Aegista quelpartensis, Incilaria fruhstorferi, Koreanohadra kurodana, Satsuma myomphala, and Clithon retropictus have been represented. Moreover, the transcriptome summary of bivalve Cristaria plicata and Caenogastropoda Charonia lampas sauliae is also discussed. Sequencing, de novo assembly, and annotation identified transcripts or homologs for the species and, based on an understanding of the biochemical and molecular pathways, were ascribed to predictive gene function. Mining for simple sequence repeats from the transcriptome have successfully assisted genetic polymorphism studies. A comparison of the transcriptome scheme of Korean endangered mollusks with the genomic resources of other endangered mollusks have been discussed with homologies and analogies for dictating future research.
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Affiliation(s)
- Hongray Howrelia Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Min Kyu Sang
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jie Eun Park
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Dae Kwon Song
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jun Yang Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Chan Eui Hong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Yong Tae Kim
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Hyeon Jun Shin
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Liu Ziwei
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Hee Ju Hwang
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - So Young Park
- Biodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, 37242, South Korea
| | - Se Won Kang
- Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, 56212, South Korea
| | - Jung Ho Ko
- Police Science Institute, Korean National Police University, Asan, Chungnam, 31539, South Korea
| | - Jun Sang Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 34069, South Korea
| | - Yong Hun Jo
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Bharat Bhusan Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- P.G Department of Biosciences and Biotechnology, Fakir Mohan University, Odisha, 756089, Nuapadhi, Balasore, India
| | - Yong Seok Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea.
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea.
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12
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Crandall ED, Toczydlowski RH, Liggins L, Holmes AE, Ghoojaei M, Gaither MR, Wham BE, Pritt AL, Noble C, Anderson TJ, Barton RL, Berg JT, Beskid SG, Delgado A, Farrell E, Himmelsbach N, Queeno SR, Trinh T, Weyand C, Bentley A, Deck J, Riginos C, Bradburd GS, Toonen RJ. Importance of timely metadata curation to the global surveillance of genetic diversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14061. [PMID: 36704891 PMCID: PMC10751740 DOI: 10.1111/cobi.14061] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/27/2022] [Accepted: 01/07/2023] [Indexed: 05/18/2023]
Abstract
Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.
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Affiliation(s)
- Eric D Crandall
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Rachel H Toczydlowski
- Ecology, Evolution, and Behavior Program, Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Libby Liggins
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Ann E Holmes
- Department of Animal Science, University of California, Davis, Davis, California, USA
| | - Maryam Ghoojaei
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Michelle R Gaither
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Briana E Wham
- Department of Research Informatics and Publishing, The Pennsylvania State University Libraries, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrea L Pritt
- Madlyn L. Hanes Library, The Pennsylvania State University Libraries, Pennsylvania State University, Middletown, Pennsylvania, USA
| | - Cory Noble
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Tanner J Anderson
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Randi L Barton
- Department of Marine Science, California State University Monterey Bay, Seaside, California, USA
- Moss Landing Marine Laboratories, Moss Landing, California, USA
| | - Justin T Berg
- UOG Marine Laboratory, University of Guam, Mangilao, Guam
| | - Sofia G Beskid
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Alonso Delgado
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Emily Farrell
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Nan Himmelsbach
- Department of Natural Science, Hawai'i Pacific University, Honolulu, Hawaii, USA
| | - Samantha R Queeno
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Thienthanh Trinh
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Courtney Weyand
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Andrew Bentley
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
| | - John Deck
- Berkeley Natural History Museums, University of California, Berkeley, Berkeley, California, USA
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Gideon S Bradburd
- Ecology, Evolution, and Behavior Program, Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, Hawaii, USA
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13
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Dillon EM, Dunne EM, Womack TM, Kouvari M, Larina E, Claytor JR, Ivkić A, Juhn M, Carmona PSM, Robson SV, Saha A, Villafaña JA, Zill ME. Challenges and directions in analytical paleobiology. PALEOBIOLOGY 2023; 49:377-393. [PMID: 37809321 PMCID: PMC7615171 DOI: 10.1017/pab.2023.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.
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Affiliation(s)
- Erin M. Dillon
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, U.S.A.; Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Emma M. Dunne
- GeoZentrum Nordbayern, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Tom M. Womack
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Miranta Kouvari
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom; Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Ekaterina Larina
- Jackson School of Geosciences, University of Texas, Austin, Texas 78712, U.S.A
| | - Jordan Ray Claytor
- Department of Biology, University of Washington, Seattle, Washington 98195, U.S.A; Burke Museum of Natural History and Culture, Seattle, Washington 98195, U.S.A
| | - Angelina Ivkić
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2,1090 Vienna, Austria
| | - Mark Juhn
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California 90095, U.S.A
| | - Pablo S. Milla Carmona
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ciencias Geológicas, Buenos Aires C1428EGA, Argentina; Instituto de Estudios Andinos “Don Pablo Groeber” (IDEAN, UBA-CONICET), Buenos Aires C1428EGA, Argentina
| | - Selina Viktor Robson
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Anwesha Saha
- Institute of Palaeobiology, Polish Academy of Sciences, ul. Twarda 51/55, 00-818 Warsaw, Poland; Laboratory of Paleogenetics and Conservation Genetics, Centre of New Technologies (CeNT), University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Jaime A. Villafaña
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria; Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O ‘Higgins, Santiago 8370993, Chile
| | - Michelle E. Zill
- Department of Earth and Planetary Sciences, University of California Riverside, Riverside, California 92521, U.S.A
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14
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Hutchins L, Mc Cartney A, Graham N, Gillespie R, Guzman A. Arthropods are kin: Operationalizing Indigenous data sovereignty to respectfully utilize genomic data from Indigenous lands. Mol Ecol Resour 2023. [PMID: 37455607 DOI: 10.1111/1755-0998.13822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023]
Abstract
Indigenous peoples have cultivated biodiverse agroecosystems since time immemorial. The rise of metagenomics and high-throughput sequencing technologies in biodiversity studies has rapidly expanded the scale of data collection from these lands. A respectful approach to the data life cycle grounded in the sovereignty of indigenous communities is imperative to not perpetuate harm. In this paper, we operationalize an indigenous data sovereignty (IDS) framework to outline realistic considerations for genomic data that span data collection, governance, and communication. As a case study for this framework, we use arthropod genomic data collected from diversified and simplified farm sites close to and far from natural habitats within a historic Kānaka 'Ōiwi (Indigenous Hawaiian) agroecosystem. Diversified sites had the highest Operational Taxonomic Unit (OTU) richness for native and introduced arthropods. There may be a significant spillover effect between forest and farm sites, as farm sites near a natural habitat had higher OTU richness than those farther away. We also provide evidence that management factors such as the number of Polynesian crops cultivated may drive arthropod community composition. Through this case study, we emphasize the context-dependent opportunities and challenges for operationalizing IDS by utilizing participatory research methods, expanding novel data management tools through the Local Contexts Hub, and developing and nurturing community partnerships-all while highlighting the potential of agroecosystems for arthropod conservation. Overall, the workflow and the example presented here can help researchers take tangible steps to achieve IDS, which often seems elusive with the expanding use of genomic data.
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Affiliation(s)
- Leke Hutchins
- Department of Environmental Sciences Policy and Management, University of California Berkeley, Berkeley, California, USA
| | - Ann Mc Cartney
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Natalie Graham
- Department of Environmental Sciences Policy and Management, University of California Berkeley, Berkeley, California, USA
| | - Rosemary Gillespie
- Department of Environmental Sciences Policy and Management, University of California Berkeley, Berkeley, California, USA
| | - Aidee Guzman
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
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15
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Hudson M, Carroll SR, Anderson J, Blackwater D, Cordova-Marks FM, Cummins J, David-Chavez D, Fernandez A, Garba I, Hiraldo D, Jäger MB, Jennings LL, Martinez A, Sterling R, Walker JD, Rowe RK. Indigenous Peoples' Rights in Data: a contribution toward Indigenous Research Sovereignty. Front Res Metr Anal 2023; 8:1173805. [PMID: 37215248 PMCID: PMC10192690 DOI: 10.3389/frma.2023.1173805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/31/2023] [Indexed: 05/24/2023] Open
Abstract
Indigenous Peoples' right to sovereignty forms the foundation for advocacy and actions toward greater Indigenous self-determination and control across a range of domains that impact Indigenous Peoples' communities and cultures. Declarations for sovereignty are rising throughout Indigenous communities and across diverse fields, including Network Sovereignty, Food Sovereignty, Energy Sovereignty, and Data Sovereignty. Indigenous Research Sovereignty draws in the sovereignty discourse of these initiatives to consider their applications to the broader research ecosystem. Our exploration of Indigenous Research Sovereignty, or Indigenous self-determination in the context of research activities, has been focused on the relationship between Indigenous Data Sovereignty and efforts to describe Indigenous Peoples' Rights in data.
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Affiliation(s)
- Maui Hudson
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | - Stephanie Russo Carroll
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Jane Anderson
- Anthropology and Program in Museum Studies, New York University, New York, NY, United States
| | | | - Felina M. Cordova-Marks
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
| | - Jewel Cummins
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Dominique David-Chavez
- Forest and Rangeland Stewardship Department, Colorado State University, Fort Collins, CO, United States
| | - Adam Fernandez
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Ibrahim Garba
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Danielle Hiraldo
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
- American Indian Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Mary Beth Jäger
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Lydia L. Jennings
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Andrew Martinez
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Rogena Sterling
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | | | - Robyn K. Rowe
- School of Computing, Queen's University, Kingston, ON, Canada
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16
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Mc Cartney AM, Head MA, Tsosie KS, Sterner B, Glass JR, Paez S, Geary J, Hudson M. Indigenous peoples and local communities as partners in the sequencing of global eukaryotic biodiversity. NPJ BIODIVERSITY 2023; 2:8. [PMID: 38693997 PMCID: PMC11062294 DOI: 10.1038/s44185-023-00013-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/17/2023] [Indexed: 05/03/2024]
Abstract
The aim to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity is the shared mission of many ongoing large-scale biodiversity genomics initiatives. Reference genomes of global flora and fauna have the potential to inform a broad range of major issues facing both biodiversity and humanity, such as the impact of climate change, the conservation of endangered species and ecosystems, public health crises, and the preservation and enhancement of ecosystem services. Biodiversity is dramatically declining: 28% of species being assessed by the IUCN are threatened with extinction, and recent reports suggest that a transformative change is needed to conserve and protect what remains. To provide a collective and global genomic response to the biodiversity crisis, many biodiversity genomics initiatives have come together, creating a network of networks under the Earth BioGenome Project. This network seeks to expedite the creation of an openly available, "public good" encyclopedia of high-quality eukaryotic reference genomes, in the hope that by advancing our basic understanding of nature, it can lead to the transformational scientific developments needed to conserve and protect global biodiversity. Key to completing this ambitious encyclopedia of reference genomes, is the ability to responsibly, ethically, legally, and equitably access and use samples from all of the eukaryotic species across the planet, including those that are under the custodianship of Indigenous Peoples and Local Communities. Here, the biodiversity genomics community is subject to the provisions codified in international, national, and local legislations and customary community norms, principles, and protocols. We propose a framework to support biodiversity genomic researchers, projects, and initiatives in building trustworthy and sustainable partnerships with communities, providing minimum recommendations on how to access, utilize, preserve, handle, share, analyze, and communicate samples, genomics data, and associated Traditional Knowledge obtained from, and in partnership with, Indigenous Peoples and Local Communities across the data-lifecycle.
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Affiliation(s)
| | - M. A. Head
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | - K. S. Tsosie
- Native BioData Consortium, Eagle Butte, SD USA
- School of Life Sciences, Arizona State University, Tempe, AZ USA
| | - B. Sterner
- School of Life Sciences, Arizona State University, Tempe, AZ USA
| | - J. R. Glass
- Department of Fisheries, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK USA
| | - S. Paez
- Neurogenetics of Language, The Rockefeller University, New York, NY USA
| | - J. Geary
- School for the Future of Innovation in Society, Arizona State University, Tempe, AZ USA
| | - M. Hudson
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
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17
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Wold JR, Guhlin JG, Dearden PK, Santure AW, Steeves TE. The promise and challenges of characterizing genome-wide structural variants: A case study in a critically endangered parrot. Mol Ecol Resour 2023. [PMID: 36916824 DOI: 10.1111/1755-0998.13783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023]
Abstract
There is growing interest in the role of structural variants (SVs) as drivers of local adaptation and speciation. From a biodiversity genomics perspective, the characterization of genome-wide SVs provides an exciting opportunity to complement single nucleotide polymorphisms (SNPs). However, little is known about the impacts of SV discovery and genotyping strategies on the characterization of genome-wide SV diversity within and among populations. Here, we explore a near whole-species resequence data set, and long-read sequence data for a subset of highly represented individuals in the critically endangered kākāpō (Strigops habroptilus). We demonstrate that even when using a highly contiguous reference genome, different discovery and genotyping strategies can significantly impact the type, size and location of SVs characterized genome-wide. Further, we found that the mean number of SVs in each of two kākāpō lineages differed both within and across generations. These combined results suggest that genome-wide characterization of SVs remains challenging at the population-scale. We are optimistic that increased accessibility to long-read sequencing and advancements in bioinformatic approaches including multireference approaches like genome graphs will alleviate at least some of the challenges associated with resolving SV characteristics below the species level. In the meantime, we address caveats, highlight considerations, and provide recommendations for the characterization of genome-wide SVs in biodiversity genomic research.
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Affiliation(s)
- Jana R Wold
- University of Canterbury, Christchurch, New Zealand
| | - Joseph G Guhlin
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Peter K Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
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18
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Cortez AD, Lippert D, Davis JL, Nicholas G, Malhi RS, Weyrich LS, Claw KG, Bader AC, Colwell C. Extracting the practices of paleogenomics: A study of ancient DNA labs and research in relation to Native Americans and Indigenous peoples. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 36799477 DOI: 10.1002/ajpa.24714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
OBJECTIVES The field of paleogenomics has rapidly grown, influencing a range of scientific fields and drawing notice from the public. In the United States, this work is especially salient for Native Americans, who are frequently the subject of ancient DNA analyses, but are less frequently included as researchers, collaborators, or advisors. This article seeks to deepen our understanding of the current state of paleogenomics so that the field can center Indigenous peoples and their experiences, knowledges, and stakes in the research process. MATERIALS AND METHODS We conducted 31 semi-structured interviews with researchers from three paleogenomics labs located in North America and Europe. We used a responsive interviewing technique where the interview resembled a conversation around a set of questions that could change depending upon the interviewee's answers and experiences. We then employed a theme-based analysis of the interviews. RESULTS Through this analysis, we are able to identify practices in the field related to training, the structuring of labs and projects, consent, data control, Ancestor care, and funding that influence various forms of engagement with Indigenous peoples, and which foster or delimit ethical commitments to descendant communities. DISCUSSION This research not only elucidates contemporary practices in paleogenomics labs but also identifies specific areas of potential intervention to help researchers work toward ethical and collaborative paleogenomic research with Indigenous peoples. Using these results, researchers and community advocates can work toward reorienting the field of paleogenomics toward ethical research with Indigenous peoples.
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Affiliation(s)
| | - Dorothy Lippert
- Repatriation Office, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jenny L Davis
- American Indian Studies, Department of Anthropology, University of Illinois Urbana Champaign, Champaign, Illinois, USA
| | - George Nicholas
- Department of Archaeology, Simon Fraser University, Burnaby, Canada
| | - Ripan S Malhi
- Department of Anthropology, Carl R Woese Institute for Genomic Biology, University of Illinois Urbana Champaign, Champaign, Illinois, USA
| | - Laura S Weyrich
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Katrina G Claw
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Canada
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19
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Abstract
The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article "Ethics of DNA research on human remains: five globally applicable guidelines" published in 2021 in Nature by a large group of aDNA researchers and collaborators. We argue that these guidelines do not sufficiently consider the interests of community stakeholders, including descendant communities and communities with potential, but yet unestablished, ties to Ancestors. We focus on three main areas of concern with the guidelines. First is the false separation of "scientific" and "community" concerns and the consistent privileging of researcher perspectives over those of community members. Second, the commitment of the guidelines' authors to open data ignores the principles and practice of Indigenous Data Sovereignty. Further, the authors argue that involving community members in decisions about publication and data sharing is unethical. We argue that excluding community perspectives on "ethical" grounds is convenient for researchers, but it is not, in fact, ethical. Third, we stress the risks of not consulting communities that have established or potential ties to Ancestors, using two recent examples from the literature. Ancient DNA researchers cannot focus on the lowest common denominator of research practice, the bare minimum that is legally necessary. Instead, they should be leading multidisciplinary efforts to create processes to ensure communities from all regions of the globe are identified and engaged in research that affects them. This will often present challenges, but we see these challenges as part of the research, rather than a distraction from the scientific endeavor. If a research team does not have the capacity to meaningfully engage communities, questions must be asked about the value and benefit of their research.
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20
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Batley J, Hufton AL, Oliveira G, Varshney RK. Global Action on Biodiversity May Hinge on Genetic Data Sharing Agreement. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2200031. [PMID: 36911288 PMCID: PMC9993466 DOI: 10.1002/ggn2.202200031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jacqueline Batley
- School of Biological Sciences The University of Western Australia Crawley WA 6009 Australia
| | | | | | - Rajeev K Varshney
- Centre for Crop & Food Innovation State Agricultural Biotechnology Centre Food Futures Institute Murdoch University Murdoch WA 6150 Australia
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21
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Golan J, Riddle K, Hudson M, Anderson J, Kusabs N, Coltman T. Benefit sharing: Why inclusive provenance metadata matter. Front Genet 2022; 13:1014044. [PMID: 36212139 PMCID: PMC9532573 DOI: 10.3389/fgene.2022.1014044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/30/2022] [Indexed: 11/25/2022] Open
Abstract
Fair and equitable benefit sharing of genetic resources is an expectation of the Nagoya Protocol. Although the Nagoya Protocol does not yet formally apply to Digital Sequence Information (“DSI”), discussions are currently underway regarding to include such data through ongoing Convention on Biological Diversity (“CBD”) negotiations. While Indigenous Peoples and Local Communities (“IPLC”) expect the value generated from genomic data to be subject to benefit sharing arrangements, a range of views are currently being expressed by Nation States, IPLC and other stakeholders. The use of DSI gives rise to unique considerations, creating a gray area as to how it should be considered under the Nagoya Protocol’s Access and Benefit Sharing (“ABS”) principles. One way for benefit sharing to be enhanced is through the connection of data to proper provenance information. A significant development is the use of digital labeling systems to ensure that the origin of samples is appropriately disclosed. The Traditional Knowledge and Biocultural Labels initiative offers a practical option for data provided to genomic databases. In particular, the BioCultural Labels (“BC Labels”) are a mechanism for Indigenous communities to identify and maintain provenance, origin and authority over biocultural material and data generated from Indigenous land and waters held in research, cultural institutions and data repositories. This form of cultural metadata adds value to the research endeavor and the creation of Indigenous fields within databases adds transparency and accountability to the research environment.
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Affiliation(s)
- Jacob Golan
- School of Law, New York University, New York, NY, United States
- *Correspondence: Jacob Golan, ; KatieLee Riddle,
| | - KatieLee Riddle
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
- *Correspondence: Jacob Golan, ; KatieLee Riddle,
| | - Maui Hudson
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | - Jane Anderson
- Engelberg Center of Innovation Law and Policy, School of Law, New York University, New York, NY, United States
| | - Natalie Kusabs
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | - Tim Coltman
- Waikato Management School, University of Waikato, Hamilton, New Zealand
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22
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Liggins L, Arranz V, Braid HE, Carmelet-Rescan D, Elleouet J, Egorova E, Gemmell MR, Hills SFK, Holland LP, Koot EM, Lischka A, Maxwell KH, McCartney LJ, Nguyen HTT, Noble C, Olmedo Rojas P, Parvizi E, Pearman WS, Sweatman JAN, Kaihoro TR, Walton K, Aguirre JD, Stewart LC. The future of molecular ecology in Aotearoa New Zealand: an early career perspective. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2097709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Libby Liggins
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Vanessa Arranz
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Heather E. Braid
- AUT Lab for Cephalopod Ecology and Systematics, School of Science, Auckland University of Technology, Auckland, New Zealand
| | | | | | - Ekaterina Egorova
- Massey Geoinformatics Collaboratory, School of Mathematical and Computational Sciences, Auckland, New Zealand
| | - Michael R. Gemmell
- Plant Health and Environment Lab, Ministry for Primary Industries, Auckland, New Zealand
| | - Simon F. K. Hills
- Ngāti Porou
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Emily M. Koot
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North, New Zealand
| | - Alexandra Lischka
- AUT Lab for Cephalopod Ecology and Systematics, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Kimberley H. Maxwell
- Ngāti Porou
- Te Whakatōhea, Te Whānau-a-Apanui, Ngāitai, Ngāti Tūwharetoa
- Te Kōtahi Research Institute, Faculty of Māori and Indigenous Studies, University of Waikato, Hamilton, New Zealand
| | | | - Hang T. T. Nguyen
- Faculty of Fisheries, University of Agriculture and Forestry, Hue University, Vietnam
| | - Cory Noble
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | | | - Elahe Parvizi
- School of Science, University of Waikato, Hamilton, New Zealand
| | | | | | | | - Kerry Walton
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - J. David Aguirre
- School of Natural Sciences, Massey University, Auckland, New Zealand
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23
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Villanea FA, Witt KE. Underrepresented Populations at the Archaic Introgression Frontier. Front Genet 2022; 13:821170. [PMID: 35281795 PMCID: PMC8914065 DOI: 10.3389/fgene.2022.821170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fernando A Villanea
- Department of Anthropology, College of Arts and Sciences, University of Colorado Boulder, Boulder, CO, United States
- *Correspondence: Fernando A Villanea,
| | - Kelsey E. Witt
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
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24
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Stephan T, Burgess SM, Cheng H, Danko CG, Gill CA, Jarvis ED, Koepfli KP, Koltes JE, Lyons E, Ronald P, Ryder OA, Schriml LM, Soltis P, VandeWoude S, Zhou H, Ostrander EA, Karlsson EK. Darwinian genomics and diversity in the tree of life. Proc Natl Acad Sci U S A 2022; 119:e2115644119. [PMID: 35042807 PMCID: PMC8795533 DOI: 10.1073/pnas.2115644119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Genomics encompasses the entire tree of life, both extinct and extant, and the evolutionary processes that shape this diversity. To date, genomic research has focused on humans, a small number of agricultural species, and established laboratory models. Fewer than 18,000 of ∼2,000,000 eukaryotic species (<1%) have a representative genome sequence in GenBank, and only a fraction of these have ancillary information on genome structure, genetic variation, gene expression, epigenetic modifications, and population diversity. This imbalance reflects a perception that human studies are paramount in disease research. Yet understanding how genomes work, and how genetic variation shapes phenotypes, requires a broad view that embraces the vast diversity of life. We have the technology to collect massive and exquisitely detailed datasets about the world, but expertise is siloed into distinct fields. A new approach, integrating comparative genomics with cell and evolutionary biology, ecology, archaeology, anthropology, and conservation biology, is essential for understanding and protecting ourselves and our world. Here, we describe potential for scientific discovery when comparative genomics works in close collaboration with a broad range of fields as well as the technical, scientific, and social constraints that must be addressed.
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Affiliation(s)
- Taylorlyn Stephan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20817
| | - Shawn M Burgess
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20817
| | - Hans Cheng
- Avian Disease and Oncology Laboratory, Agricultural Research Service, US Department of Agriculture, East Lansing, MI 48823
| | - Charles G Danko
- Department of Biomedical Sciences, Baker Institute for Animal Health, Cornell University, Ithaca, NY 14850
| | - Clare A Gill
- Department of Animal Science, Texas A&M University, College Station, TX 77843
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- HHMI, Chevy Chase, MD 20815
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA 50011
| | - Eric Lyons
- School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721
| | - Pamela Ronald
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
- The Innovative Genomics Institute, University of California, Berkeley, CA 94720
- Grass Genetics, Joint Bioenergy Institute, Emeryville, CA 94608
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Department of Evolution, Behavior, and Ecology, University of California San Diego, La Jolla, CA 92093
| | - Lynn M Schriml
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Pamela Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
| | - Sue VandeWoude
- Department of Micro-, Immuno-, and Pathology, Colorado State University, Fort Collins, CO 80532
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA 95616
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20817
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655;
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
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