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Thorogood R, Mustonen V, Aleixo A, Aphalo PJ, Asiegbu FO, Cabeza M, Cairns J, Candolin U, Cardoso P, Eronen JT, Hällfors M, Hovatta I, Juslén A, Kovalchuk A, Kulmuni J, Kuula L, Mäkipää R, Ovaskainen O, Pesonen AK, Primmer CR, Saastamoinen M, Schulman AH, Schulman L, Strona G, Vanhatalo J. Understanding and applying biological resilience, from genes to ecosystems. NPJ BIODIVERSITY 2023; 2:16. [PMID: 39242840 PMCID: PMC11332022 DOI: 10.1038/s44185-023-00022-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/07/2023] [Indexed: 09/09/2024]
Abstract
The natural world is under unprecedented and accelerating pressure. Much work on understanding resilience to local and global environmental change has, so far, focussed on ecosystems. However, understanding a system's behaviour requires knowledge of its component parts and their interactions. Here we call for increased efforts to understand 'biological resilience', or the processes that enable components across biological levels, from genes to communities, to resist or recover from perturbations. Although ecologists and evolutionary biologists have the tool-boxes to examine form and function, efforts to integrate this knowledge across biological levels and take advantage of big data (e.g. ecological and genomic) are only just beginning. We argue that combining eco-evolutionary knowledge with ecosystem-level concepts of resilience will provide the mechanistic basis necessary to improve management of human, natural and agricultural ecosystems, and outline some of the challenges in achieving an understanding of biological resilience.
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Affiliation(s)
- Rose Thorogood
- HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
| | - Ville Mustonen
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Computer Science, Faculty of Science, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, HiLIFE Helsinki Institute for Life Science, University of Helsinki, Helsinki, Finland
| | - Alexandre Aleixo
- LUOMUS Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Pedro J Aphalo
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Fred O Asiegbu
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Mar Cabeza
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- HELSUS Helsinki Institute of Sustainability Science, University of Helsinki, Helsinki, Finland
| | - Johannes Cairns
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
| | - Ulrika Candolin
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pedro Cardoso
- LUOMUS Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- CE3C - Centre for Ecology, Evolution and Environmental Changes, CHANGE-Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Jussi T Eronen
- HELSUS Helsinki Institute of Sustainability Science, University of Helsinki, Helsinki, Finland
- Research Programme in Ecosystems and Environment, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- BIOS Research Unit, Helsinki, Finland
| | - Maria Hällfors
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Centre for Ecological Change, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Syke Finnish Environment Institute, Helsinki, Finland
| | - Iiris Hovatta
- SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Neuroscience Center, HiLIFE Helsinki Institute for Life Science, University of Helsinki, Helsinki, Finland
| | - Aino Juslén
- LUOMUS Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Syke Finnish Environment Institute, Helsinki, Finland
| | - Andriy Kovalchuk
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
- Onego Bio Ltd, Helsinki, Finland
| | - Jonna Kulmuni
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Liisa Kuula
- SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Raisa Mäkipää
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Otso Ovaskainen
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anu-Katriina Pesonen
- SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Craig R Primmer
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, HiLIFE Helsinki Institute for Life Science, University of Helsinki, Helsinki, Finland
| | - Marjo Saastamoinen
- HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Centre for Ecological Change, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Alan H Schulman
- Institute of Biotechnology, HiLIFE Helsinki Institute for Life Science, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Leif Schulman
- LUOMUS Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Syke Finnish Environment Institute, Helsinki, Finland
| | - Giovanni Strona
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Centre for Ecological Change, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- European Commission, Joint Research Centre, Directorate D - Sustainable Resources, Ispra, Italy
| | - Jarno Vanhatalo
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Centre for Ecological Change, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, Faculty of Science, University of Helsinki, Helsinki, Finland
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Arredondo A, Mourato B, Nguyen K, Boitard S, Rodríguez W, Noûs C, Mazet O, Chikhi L. Inferring number of populations and changes in connectivity under the n-island model. Heredity (Edinb) 2021; 126:896-912. [PMID: 33846579 PMCID: PMC8178352 DOI: 10.1038/s41437-021-00426-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 12/11/2022] Open
Abstract
Inferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, ignoring population structure. Alternatively, when structure is assumed, it is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate). The IICR can be estimated for a single diploid individual using the PSMC method of Li and Durbin (2011). For an isolated panmictic population, the IICR matches the population size history, and this is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme with limited connection to population size changes. Our method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise stationary symmetrical island models. In our models we assume a fixed number of time periods during which gene flow is constant, but gene flow is allowed to change between time periods. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent.
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Affiliation(s)
- Armando Arredondo
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France. .,Institut de Mathématiques de Toulouse; UMR5219. Université de Toulouse, Toulouse, France.
| | - Beatriz Mourato
- Institut de Mathématiques de Toulouse; UMR5219. Université de Toulouse, Toulouse, France.,Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Khoa Nguyen
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France
| | - Simon Boitard
- CBGP, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Willy Rodríguez
- Institut de Mathématiques de Toulouse; UMR5219. Université de Toulouse, Toulouse, France.,ENAC - Ecole Nationale de l'Aviation Civile, Université de Toulouse, Toulouse, France
| | | | - Olivier Mazet
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France.,Institut de Mathématiques de Toulouse; UMR5219. Université de Toulouse, Toulouse, France
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, Oeiras, Portugal. .,Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), CNRS, IRD, UPS, Université de Toulouse Midi-Pyrénées, Toulouse, France.
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