Understanding and applying biological resilience, from genes to ecosystems.
Journal
npj biodiversity
ISSN: 2731-4243
Titre abrégé: NPJ Biodivers
Pays: England
ID NLM: 9918804277406676
Informations de publication
Date de publication:
28 Aug 2023
28 Aug 2023
Historique:
received:
16
03
2022
accepted:
07
08
2023
medline:
7
9
2024
pubmed:
7
9
2024
entrez:
6
9
2024
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 39242840
doi: 10.1038/s44185-023-00022-6
pii: 10.1038/s44185-023-00022-6
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
16Informations de copyright
© 2023. The Author(s).
Références
Lewis, S. L. & Maslin, M. A. Defining the Anthropocene. Nature 519, 171–180 (2015).
pubmed: 25762280
doi: 10.1038/nature14258
Ellis, E. C. Ecology in an anthropogenic biosphere. Ecol. Monogr. 85, 287–331 (2015).
doi: 10.1890/14-2274.1
van Kleunen, M. et al. Global exchange and accumulation of non-native plants. Nature 525, 100–103 (2015).
pubmed: 26287466
doi: 10.1038/nature14910
Scheffer, M., Carpenter, S., Foley, J. A., Folke, C. & Walker, B. Catastrophic shifts in ecosystems. Nature 413, 591–596 (2001).
pubmed: 11595939
doi: 10.1038/35098000
Foley, J. A. Global consequences of land use. Science 309, 570–574 (2005).
pubmed: 16040698
doi: 10.1126/science.1111772
Sullivan, A. P., Bird, D. W. & Perry, G. H. Human behaviour as a long-term ecological driver of non-human evolution. Nat. Ecol. Evol. 1, 0065 (2017).
doi: 10.1038/s41559-016-0065
Sutherland, W. J. et al. Identification of 100 fundamental ecological questions. J. Ecol.101, 58–67 (2013).
doi: 10.1111/1365-2745.12025
Weise, H. et al. Resilience trinity: safeguarding ecosystem functioning and services across three different time horizons and decision contexts. Oikos 129, 445–456 (2020).
doi: 10.1111/oik.07213
Helfgott, A. Operationalising systemic resilience. Eur. J. Oper. Res. 268, 852–864 (2018).
doi: 10.1016/j.ejor.2017.11.056
Dakos, V. & Kéfi, S. Ecological resilience: what to measure and how. Environ. Res. Lett.17, 043003 (2022).
doi: 10.1088/1748-9326/ac5767
Yi, C. & Jackson, N. A review of measuring ecosystem resilience to disturbance. Environ. Res. Lett. 16, 053008 (2021).
doi: 10.1088/1748-9326/abdf09
Pimm, S. L. The complexity and stability of ecosystems. Nature 307, 321–326 (1984).
doi: 10.1038/307321a0
Holling, C. S. Resilience and stability of ecological systems. Ann. Rev. Ecol. Syst. 4, 1–23 (1973).
doi: 10.1146/annurev.es.04.110173.000245
Oliver, T. H. et al. Biodiversity and resilience of ecosystem functions. Trends Ecol. Evol. 30, 673–684 (2015).
pubmed: 26437633
doi: 10.1016/j.tree.2015.08.009
Ingrisch, J. & Bahn, M. Towards a comparable quantification of resilience. Trends Ecol. Evol. 33, 251–259 (2018).
pubmed: 29477443
doi: 10.1016/j.tree.2018.01.013
Capdevila, P. et al. Reconciling resilience across ecological systems, species and subdisciplines. J. Ecol. 109, 3102–3113 (2021).
doi: 10.1111/1365-2745.13775
Gladstone-Gallagher, R. V., Pilditch, C. A., Stephenson, F. & Thrush, S. F. Linking traits across ecological scales determines functional resilience. Trends Ecol. Evol. 34, 1080–1091 (2019).
pubmed: 31422892
doi: 10.1016/j.tree.2019.07.010
Levin, S. A. The problem of pattern and scale in ecology: the Robert H. MacArthur Award lecture. Ecology 73, 1943–1967 (1992).
doi: 10.2307/1941447
Gallagher, R. & Appenzeller, T. Beyond reductionism. Science 284, 79–79 (1999).
doi: 10.1126/science.284.5411.79
McGill, B. J. et al. Unifying macroecology and macroevolution to answer fundamental questions about biodiversity. Global Ecol. Biogeogr. 28, 1925–1936 (2019).
doi: 10.1111/geb.13020
Cant, J., Capdevila, P., Beger, M. & Salguero‐Gómez, R. Recent exposure to environmental stochasticity does not determine the demographic resilience of natural populations. Ecol. Lett. 26, 1186–1199 (2023).
pubmed: 37158011
doi: 10.1111/ele.14234
Dakos, V. et al. Ecosystem tipping points in an evolving world. Nat. Ecol. Evol. 3, 355–362 (2019).
pubmed: 30778190
doi: 10.1038/s41559-019-0797-2
Morris, D. W. Adaptation and habitat selection in the eco-evolutionary process. Proc. R. Soc. B: Biol. Sci. 278, 2401–2411 (2011).
doi: 10.1098/rspb.2011.0604
Tylianakis, J. M. & Maia, L. F. The patchwork of evolutionary landscapes. Nat. Ecol. Evol. 4, 672–673 (2020).
pubmed: 32286502
doi: 10.1038/s41559-020-1184-8
Carroll, S. P. et al. Applying evolutionary biology to address global challenges. Science 346, 1245993–1245993 (2014).
pubmed: 25213376
pmcid: 4245030
doi: 10.1126/science.1245993
Desai, M. M. Reverse evolution and evolutionary memory. Nat. Genet. 41, 142–143 (2009).
pubmed: 19174835
doi: 10.1038/ng0209-142
Donohue, I. et al. Navigating the complexity of ecological stability. Ecol. Lett. 19, 1172–1185 (2016).
pubmed: 27432641
doi: 10.1111/ele.12648
Bartholomé, J. et al. The genetics of exapted resistance to two exotic pathogens in pedunculate oak. New Phytol. 226, 1088–1103 (2020).
pubmed: 31711257
doi: 10.1111/nph.16319
Donelson, J. M. et al. Understanding interactions between plasticity, adaptation and range shifts in response to marine environmental change. Philos. Trans. R. Soc. B 374, 20180186 (2019).
doi: 10.1098/rstb.2018.0186
Oostra, V., Saastamoinen, M., Zwaan, B. J. & Wheat, C. W. Strong phenotypic plasticity limits potential for evolutionary responses to climate change. Nat. Commun. 9, 1005 (2018).
pubmed: 29520061
pmcid: 5843647
doi: 10.1038/s41467-018-03384-9
Hang, D., Torng, E., Ofria, C. & Schmidt, T. M. The effect of natural selection on the performance of maximum parsimony. BMC Evol. Biol. 7, 1–15 (2007).
doi: 10.1186/1471-2148-7-94
Sun, M. et al. Recent accelerated diversification in rosids occurred outside the tropics. Nat. Commun. 11, 1–12 (2020).
Zitnik, M., Sosič, R., Feldman, M. W. & Leskovec, J. Evolution of resilience in protein interactomes across the tree of life. Proc. Natl Acad. Sci. USA 116, 4426–4433 (2019).
pubmed: 30765515
pmcid: 6410798
doi: 10.1073/pnas.1818013116
Hecht, L. B., Thompson, P. C. & Rosenthal, B. M. Assessing the evolutionary persistence of ecological relationships: a review and preview. Infect. Genet. Evol. 84, 104441 (2020).
pubmed: 32622083
pmcid: 7327472
doi: 10.1016/j.meegid.2020.104441
Mathur, S., Tomeček, J. M., Tarango-Arámbula, L. A., Perez, R. M. & DeWoody, J. A. An evolutionary perspective on genetic load in small, isolated populations as informed by whole genome resequencing and forward-time simulations. Evolution 77, 690–704 (2023).
pubmed: 36626799
doi: 10.1093/evolut/qpac061
Louis, M. et al. Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros. Proc. R. Soc. B 287, 20192964 (2020).
pubmed: 32315590
pmcid: 7211449
doi: 10.1098/rspb.2019.2964
Cortés, A. J., López-Hernández, F. & Osorio-Rodriguez, D. Predicting thermal adaptation by looking into populations’ genomic past. Front. Genet. 11, 564515 (2020).
pubmed: 33101385
pmcid: 7545011
doi: 10.3389/fgene.2020.564515
Fox, R. J., Donelson, J. M., Schunter, C., Ravasi, T. & Gaitán-Espitia, J. D. Beyond buying time: the role of plasticity in phenotypic adaptation to rapid environmental change. Philos. Trans. R.Soc. B 374, 20180174 (2019).
doi: 10.1098/rstb.2018.0174
Ghalambor, C. K., McKay, J. K., Carroll, S. P. & Reznick, D. N. Adaptive versus non‐adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments. Funct. Ecol. 21, 394–407 (2007).
doi: 10.1111/j.1365-2435.2007.01283.x
Thebault, E. & Fontaine, C. Stability of ecological communities and the architecture of mutualistic and trophic networks. Science 329, 853–856 (2010).
pubmed: 20705861
doi: 10.1126/science.1188321
Turcotte, M. M. & Levine, J. M. Phenotypic plasticity and species coexistence. Trends Ecol. Evol. 31, 803–813 (2016).
pubmed: 27527257
doi: 10.1016/j.tree.2016.07.013
Hess, C., Levine, J. M., Turcotte, M. M. & Hart, S. P. Phenotypic plasticity promotes species coexistence. Nat. Ecol. Evol. 6, 1256–1261 (2022).
pubmed: 35927317
doi: 10.1038/s41559-022-01826-8
Holeski, L. M., Jander, G. & Agrawal, A. A. Transgenerational defense induction and epigenetic inheritance in plants. Trends Ecol. Evol. 27, 618–626 (2012).
pubmed: 22940222
doi: 10.1016/j.tree.2012.07.011
Pazzaglia, J., Reusch, T. B. H., Terlizzi, A., Marín‐Guirao, L. & Procaccini, G. Phenotypic plasticity under rapid global changes: the intrinsic force for future seagrasses survival. Evol. Appl. 14, 1181–1201 (2021).
pubmed: 34025759
pmcid: 8127715
doi: 10.1111/eva.13212
Grottoli, A. G., Rodrigues, L. J. & Palardy, J. E. Heterotrophic plasticity and resilience in bleached corals. Nature 440, 1186–1189 (2006).
pubmed: 16641995
doi: 10.1038/nature04565
Seebacher, F., White, C. R. & Franklin, C. E. Physiological plasticity increases resilience of ectothermic animals to climate change. Nat. Clim. Change 5, 61–66 (2015).
doi: 10.1038/nclimate2457
Taylor, B. M. et al. Demographic plasticity facilitates ecological and economic resilience in a commercially important reef fish. J. Anim. Ecol. 88, 1888–1900 (2019).
pubmed: 31429473
doi: 10.1111/1365-2656.13095
Valladares, F. et al. The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change. Ecol. Lett. 17, 1351–1364 (2014).
pubmed: 25205436
doi: 10.1111/ele.12348
McNamara, J. M., Dall, S. R. X., Hammerstein, P. & Leimar, O. Detection vs. selection: integration of genetic, epigenetic and environmental cues in fluctuating environments. Ecol. Lett. 19, 1267–1276 (2016).
pubmed: 27600658
doi: 10.1111/ele.12663
Barnosky, A. D. et al. Approaching a state shift in Earth’s biosphere. Nature 486, 52–58 (2012).
pubmed: 22678279
doi: 10.1038/nature11018
Legrand, D. et al. Eco-evolutionary dynamics in fragmented landscapes. Ecography 40, 9–25 (2017).
doi: 10.1111/ecog.02537
Hämäläinen, L., M. Rowland, H., Mappes, J. & Thorogood, R. Social information use by predators: expanding the information ecology of prey defences. Oikos 2022, e08743 (2022).
doi: 10.1111/oik.08743
Fukami, T. Historical contingency in community assembly: integrating niches, species pools, and priority effects. Ann. Rev. Ecol. Evol. Syst. 46, 1–23 (2015).
doi: 10.1146/annurev-ecolsys-110411-160340
Baruah, G., Clements, C. F. & Ozgul, A. Eco‐evolutionary processes underlying early warning signals of population declines. J. Anim. Ecol. 89, 436–448 (2020).
pubmed: 31433863
doi: 10.1111/1365-2656.13097
Strona, G. et al. Global tropical reef fish richness could decline by around half if corals are lost. Proc. R. Soc. Lond. B 288, 20210274 (2021).
Massot, M., Legendre, S., Fédérici, P. & Clobert, J. Climate warming: a loss of variation in populations can accompany reproductive shifts. Ecol. Lett. 20, 1140–1147 (2017).
pubmed: 28712117
doi: 10.1111/ele.12811
Sgrò, C. M., Lowe, A. J. & Hoffmann, A. A. Building evolutionary resilience for conserving biodiversity under climate change. Evol. Appl. 4, 326–337 (2011).
pubmed: 25567976
doi: 10.1111/j.1752-4571.2010.00157.x
Fahrig, L. Effects of habitat fragmentation on biodiversity. Ann. Rev. Ecol. Evol. Syst. 34, 487–515 (2003).
doi: 10.1146/annurev.ecolsys.34.011802.132419
Baguette, M. & Van Dyck, H. Landscape connectivity and animal behavior: functional grain as a key determinant for dispersal. Landsc. Ecol. 22, 1117–1129 (2007).
doi: 10.1007/s10980-007-9108-4
Anderson, C. D. et al. Considering spatial and temporal scale in landscape-genetic studies of gene flow. Mol. Ecol. 19, 3565–3575 (2010).
pubmed: 20723051
doi: 10.1111/j.1365-294X.2010.04757.x
Clark, A. T. et al. General statistical scaling laws for stability in ecological systems. Ecol. Lett. 24, 1474–1486 (2021).
pubmed: 33945663
doi: 10.1111/ele.13760
Yamamichi, M., Gibbs, T. & Levine, J. M. Integrating eco‐evolutionary dynamics and modern coexistence theory. Ecol. Lett. 25, 2091–2106 (2022).
pubmed: 35962483
pmcid: 9804941
doi: 10.1111/ele.14078
Cavigelli, S., Leips, J., Xiang, Q. Y., Lemke, D. & Konow, N. Next steps in integrative biology: mapping interactive processes across levels of biological organization. Integr. Comp. Biol. 61, 2066–2074 (2021).
doi: 10.1093/icb/icab161
Meredith, H. R. et al. Applying ecological resistance and resilience to dissect bacterial antibiotic responses. Sci. Adv. 4, eaau1873 (2018).
Waldvogel, A. et al. Evolutionary genomics can improve prediction of species’ responses to climate change. Evol. Lett. 4, 4–18 (2020).
pubmed: 32055407
pmcid: 7006467
doi: 10.1002/evl3.154
Waples, R. S., Beechie, T. & Pess, G. R. Evolutionary history, habitat disturbance regimes, and Anthropogenic changes: what do these mean for resilience of Pacific salmon populations?. Ecol. Soc. 14, art3 (2009).
doi: 10.5751/ES-02626-140103
Stange, M., Barrett, R. D. H. & Hendry, A. P. The importance of genomic variation for biodiversity, ecosystems and people. Nat. Rev. Genet. 22, 89–105 (2021).
pubmed: 33067582
doi: 10.1038/s41576-020-00288-7
Hughes, T. P., Graham, N. A., Jackson, J. B., Mumby, P. J. & Steneck, R. S. Rising to the challenge of sustaining coral reef resilience. Trends Ecol. Evolu. 25, 633–642 (2010).
doi: 10.1016/j.tree.2010.07.011
Roff, G. Evolutionary history drives biogeographic patterns of coral reef resilience. Bioscience 71, 26–39 (2021).
Fuller, Z. L. et al. Population genetics of the coral Acropora millepora: toward genomic prediction of bleaching. Science 369, eaba4674 (2020).
pubmed: 32675347
doi: 10.1126/science.aba4674
van Oppen, M. J. H., Oliver, J. K., Putnam, H. M. & Gates, R. D. Building coral reef resilience through assisted evolution. Proc. Natl Acad. Sci. USA 112, 2307–2313 (2015).
pubmed: 25646461
pmcid: 4345611
doi: 10.1073/pnas.1422301112
Bay, R. A. & Guerrero, L. Can genomes predict coral bleaching? Science 369, 249–250 (2020).
pubmed: 32675359
doi: 10.1126/science.abc9342
Papakostas, S. et al. A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus). Mol. Ecol. 21, 3516–3530 (2012).
pubmed: 22486940
doi: 10.1111/j.1365-294X.2012.05553.x
Thom, D. et al. The climate sensitivity of carbon, timber, and species richness covaries with forest age in boreal–temperate North America. Glob. Change Biol. 25, 2446–2458 (2019).
doi: 10.1111/gcb.14656
Strayer, D. L. Alien species in fresh waters: ecological effects, interactions with other stressors, and prospects for the future. Freshw. Biol. 55, 152–174 (2010).
doi: 10.1111/j.1365-2427.2009.02380.x
López-Maury, L., Marguerat, S. & Bähler, J. Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat. Rev. Genet. 9, 583–593 (2008).
pubmed: 18591982
doi: 10.1038/nrg2398
Kokko, H. et al. Can evolution supply what ecology demands? Trends Ecol. Evol. 32, 187–197 (2017).
pubmed: 28087070
doi: 10.1016/j.tree.2016.12.005
Verhagen, I., Tomotani, B. M., Gienapp, P. & Visser, M. E. Temperature has a causal and plastic effect on timing of breeding in a small songbird. The J. Exp. Biol. 223, jeb218784 (2020).
pubmed: 32205357
doi: 10.1242/jeb.218784
Grant, P. R. et al. Evolution caused by extreme events. Philos. Trans. R. Soc. B: Biol. Sci. 372, 20160146 (2017).
doi: 10.1098/rstb.2016.0146
Ellegren, H., Lindgren, G., Primmer, C. R. & Møller, A. P. Fitness loss and germline mutations in barn swallows breeding in Chernobyl. Nature 389, 593–596 (1997).
pubmed: 9335497
doi: 10.1038/39303
Bergen, E. et al. The effect of summer drought on the predictability of local extinctions in a butterfly metapopulation. Conserv. Biol. 34, 1503–1511 (2020).
pubmed: 32298001
doi: 10.1111/cobi.13515
Fraser, D. et al. Investigating biotic interactions in deep time. Trends Ecol. Evol. 36, 61–75 (2020).
pubmed: 33067015
doi: 10.1016/j.tree.2020.09.001
Lyons, S. K. et al. Holocene shifts in the assembly of plant and animal communities implicate human impacts. Nature 529, 80–83 (2016).
pubmed: 26675730
doi: 10.1038/nature16447
Frisch, D. et al. A millennial-scale chronicle of evolutionary responses to cultural eutrophication in Daphnia. Ecol. Lett. 17, 360–368 (2014).
pubmed: 24400978
doi: 10.1111/ele.12237
Hendry, A. P. A critique for eco‐evolutionary dynamics. Funct. Ecol. 33, 84–94 (2019).
doi: 10.1111/1365-2435.13244
Carpenter, S. R. et al. Early warnings of regime shifts: a whole-ecosystem experiment. Science 332, 1079–1082 (2011).
pubmed: 21527677
doi: 10.1126/science.1203672
Franks, V. R. et al. Changes in social groups across reintroductions and effects on post-release survival. Anim. Conserv. 23, 443–454 (2020).
doi: 10.1111/acv.12557
Goldenberg, S. Z. et al. Increasing conservation translocation success by building social functionality in released populations. Glob. Ecol. Conserv. 18, e00604 (2019).
Koch, E. L. & Guillaume, F. Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum. PLoS Genet. 16, e1008768 (2020).
pubmed: 32379753
pmcid: 7238888
doi: 10.1371/journal.pgen.1008768
Sun, S.-J. & Kilner, R. M. Temperature stress induces mites to help their carrion beetle hosts by eliminating rival blowflies. ELife 9, e55649 (2020).
pubmed: 32755542
pmcid: 7431131
doi: 10.7554/eLife.55649
Papakostas, S. et al. Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions. Nat. Commun. 5, 4071 (2014).
pubmed: 24892934
doi: 10.1038/ncomms5071
Bustos‐Korts, D. et al. Exome sequences and multi‐environment field trials elucidate the genetic basis of adaptation in barley. Plant J. 99, 1172–1191 (2019).
pubmed: 31108005
pmcid: 6851764
doi: 10.1111/tpj.14414
Franks, S. J. et al. The resurrection initiative: storing ancestral genotypes to capture evolution in action. BioScience 58, 870–873 (2008).
doi: 10.1641/B580913
National Library of Medicine (US) & National Center for Biotechnology Information. National Center for Biotechnology Information (NCBI). https://www.ncbi.nlm.nih.gov/ (2020).
Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29 (2000).
pubmed: 10802651
pmcid: 3037419
doi: 10.1038/75556
Kanehisa, M., Sato, Y., Furumichi, M., Morishima, K. & Tanabe, M. New approach for understanding genome variations in KEGG. Nucleic Acids Res. 47, D590–D595 (2019).
pubmed: 30321428
doi: 10.1093/nar/gky962
Primmer, C. R., Papakostas, S., Leder, E. H., Davis, M. J. & Ragan, M. A. Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research. Mol. Ecol. 22, 3216–3241 (2013).
pubmed: 23763602
doi: 10.1111/mec.12309
European Union, Copernicus Land Monitoring Service 2018, European Environment Agency. CORINE Land Cover. https://land.copernicus.eu/pan-european/corine-land-cover (2023).
Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).
doi: 10.1002/joc.5086
Karger, D. N. et al. Climatologies at high resolution for the earth’s land surface areas. Sci. Data 4, 170122 (2017).
pubmed: 28872642
pmcid: 5584396
doi: 10.1038/sdata.2017.122
GBIF.org. GBIF Home Page. https://www.gbif.org (2020).
Kattge, J. et al. TRY plant trait database – enhanced coverage and open access. Glob. Change Biol. 26, 119–188 (2020).
doi: 10.1111/gcb.14904
Ovaskainen, O. et al. Chronicles of nature calendar, a long-term and large-scale multitaxon database on phenology. Sci. Data 7, 47 (2020).
pubmed: 32047153
pmcid: 7012846
doi: 10.1038/s41597-020-0376-z
The NOW Community. NOW—New and Old Worlds: Database of fossil mammals. Zenodo https://zenodo.org/record/4268068 (2020),
Kotta, J. et al. Integrating experimental and distribution data to predict future species patterns. Sci. Rep. 9, 1821 (2019).
pubmed: 30755688
pmcid: 6372580
doi: 10.1038/s41598-018-38416-3
Barone, L., Williams, J. & Micklos, D. Unmet needs for analyzing biological big data: a survey of 704 NSF principal investigators. PLoS Comput. Biol. 13, e1005755 (2017).
pubmed: 29049281
pmcid: 5654259
doi: 10.1371/journal.pcbi.1005755
Waese, J. et al. ePlant: visualizing and exploring multiple levels of data for hypothesis generation in plant biology. Plant Cell 29, 1806–1821 (2017).
pubmed: 28808136
pmcid: 5590499
doi: 10.1105/tpc.17.00073
Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).
pubmed: 30944313
pmcid: 6447622
doi: 10.1038/s41467-019-09234-6
Ovaskainen, O., & Abrego, N. Joint Species Distribution Modeling with Applications in R. (Cambridge University Press, 2020).
DeAngelis, D. L. & Grimm, V. Individual-based models in ecology after four decades. F1000Prime Rep. 6, 39 (2014).
pubmed: 24991416
pmcid: 4047944
doi: 10.12703/P6-39
Cardoso, P. et al. Automated discovery of relationships, models, and principles in ecology. Front. Ecol. Evol. 8, 530135 (2020).
doi: 10.3389/fevo.2020.530135
Foster, S. D. et al. Effects of ignoring survey design information for data reuse. Ecol. Appl. 31, e02360 (2021).
pubmed: 33899304
doi: 10.1002/eap.2360
Dunbar, W. et al. in Managing Socio-ecological Production Landscapes and Seascapes for Sustainable Communities in Asia: Mapping and Navigating Stakeholders, Policy and Action (Saito, O., Subramanian, S. M., Hashimoto, S. & Takeuchi, K.) 93–116 (Springer Singapore, 2020).
Standish, R. J. et al. Resilience in ecology: abstraction, distraction, or where the action is? Biol. Conserv. 177, 43–51 (2014).
doi: 10.1016/j.biocon.2014.06.008
Kettenring, K. M., Mercer, K. L., Reinhardt Adams, C. & Hines, J. Application of genetic diversity-ecosystem function research to ecological restoration. J. Appl. Ecol. 51, 339–348 (2014).
doi: 10.1111/1365-2664.12202
Dhankher, O. P. & Foyer, C. H. Climate resilient crops for improving global food security and safety. Plant Cell Environ. 41, 877–884 (2018).
pubmed: 29663504
doi: 10.1111/pce.13207
Millar, C. I., Stephenson, N. L. & Stephens, S. L. Climate change and forests of the future: managing in the face of uncertainty. Ecol. Appl. 17, 2145–2151 (2007).
pubmed: 18213958
doi: 10.1890/06-1715.1
Yang, Q., Fowler, M. S., Jackson, A. L. & Donohue, I. The predictability of ecological stability in a noisy world. Nat. Ecol. Evol. 3, 251–259 (2019).
pubmed: 30697002
doi: 10.1038/s41559-018-0794-x
Cardoso, P. & Leather, S. R. Predicting a global insect apocalypse. Insect Conser. Divers. 12, 263–267 (2019).
doi: 10.1111/icad.12367
Wilkinson, M. D. et al. The FAIR guiding principles for scientific data management and stewardship. Sci. Data 3, 160018 (2016).
pubmed: 26978244
pmcid: 4792175
doi: 10.1038/sdata.2016.18
Molinelli, E. J. et al. Perturbation biology: inferring signaling networks in cellular systems. PLoS Comput. Biol. 9, e1003290 (2013).
pubmed: 24367245
pmcid: 3868523
doi: 10.1371/journal.pcbi.1003290
Jansen, R. C. Studying complex biological systems using multifactorial perturbation. Nat. Rev. Genet. 4, 145–151 (2003).
pubmed: 12560811
doi: 10.1038/nrg996
Billman, G. E. Homeostasis: the underappreciated and far too often ignored central organizing principle of physiology. Front. Physiol. 11, 200 (2020).
pubmed: 32210840
pmcid: 7076167
doi: 10.3389/fphys.2020.00200
Harmange, G., et al. Disrupting cellular memory to overcome drug resistance. Preprint at bioRxiv https://doi.org/10.1101/2022.06.16.496161 (2022).
Stockmaier, S., Ulrich, Y., Albery, G. F., Cremer, S. & Lopes, P. C. Behavioural defences against parasites across host social structures. Funct. Ecol. 37, 809–820 (2023).
doi: 10.1111/1365-2435.14310
Craine, J. M. et al. Global diversity of drought tolerance and grassland climate-change resilience. Nat. Clim. Change 3, 63–67 (2013).
doi: 10.1038/nclimate1634
Rivera, H. E. et al. A framework for understanding gene expression plasticity and its influence on stress tolerance. Mol. Ecol. 30, 1381–1397 (2021).
pubmed: 33503298
doi: 10.1111/mec.15820
Júnior, E. C. B., Rios, V. P., Dodonov, P., Vilela, B. & Japyassú, H. F. Effect of behavioural plasticity and environmental properties on the resilience of communities under habitat loss and fragmentation. Ecol. Modell. 472, 110071 (2022).
doi: 10.1016/j.ecolmodel.2022.110071
Leivesley, J. A. et al. Survival costs of reproduction are mediated by parasite infection in wild Soay sheep. Ecol. Lett. 22, ele.13275 (2019).
doi: 10.1111/ele.13275
Krause, S. M. B. et al. Environmental legacy contributes to the resilience of methane consumption in a laboratory microcosm system. Sci. Rep. 8, 8862 (2018).
pubmed: 29892072
pmcid: 5995846
doi: 10.1038/s41598-018-27168-9
Barnosky, A. D. et al. Merging paleobiology with conservation biology to guide the future of terrestrial ecosystems. Science 355, eaah4787 (2017).
pubmed: 28183912
doi: 10.1126/science.aah4787
de Mazancourt, C., Johnson, E. & Barraclough, T. G. Biodiversity inhibits species’ evolutionary responses to changing environments. Ecol. Lett. 11, 380–388 (2008).
pubmed: 18248449
doi: 10.1111/j.1461-0248.2008.01152.x
Simberloff, D. et al. Impacts of biological invasions: what’s what and the way forward. Trends Ecol. Evol. 28, 58–66 (2013).
pubmed: 22889499
doi: 10.1016/j.tree.2012.07.013
Steane, D. A. et al. Genome-wide scans detect adaptation to aridity in a widespread forest tree species. Mol. Ecol. 23, 2500–2513 (2014).
pubmed: 24750317
doi: 10.1111/mec.12751
Bell, G. Evolutionary rescue and the limits of adaptation. Philos. Trans. R. Soc. B: Biol. Sci. 368, 20120080 (2013).
doi: 10.1098/rstb.2012.0080
Ware, I. M. et al. Feedbacks link ecosystem ecology and evolution across spatial and temporal scales: empirical evidence and future directions. Funct. Ecol. 33, 31–42 (2019).
doi: 10.1111/1365-2435.13267
Bassar, R. D., Coulson, T., Travis, J. & Reznick, D. N. Towards a more precise—and accurate—view of eco‐evolution. Ecol. Lett. 24, 623–625 (2021).
pubmed: 33617684
doi: 10.1111/ele.13712
Hanski, I. Eco‐evolutionary dynamics in a changing world. Ann. N. Y. Acad. Sci. 1249, 1–17 (2012).
pubmed: 22335524
doi: 10.1111/j.1749-6632.2011.06419.x
Schoener, T. W. The newest synthesis: understanding the interplay of evolutionary and ecological dynamics. Science 331, 426–429 (2011).
pubmed: 21273479
doi: 10.1126/science.1193954
Palkovacs, E. P. & Hendry, A. P. Eco-evolutionary dynamics: Intertwining ecological and evolutionary processes in contemporary time. F1000 Biol. Rep. 2, 1 (2010).
pubmed: 20948823
pmcid: 2948349
doi: 10.3410/B2-1
Govaert, L. et al. Eco‐evolutionary feedbacks—theoretical models and perspectives. Funct. Ecol. 33, 13–30 (2019).
doi: 10.1111/1365-2435.13241
Nadeau, C. P. & Urban, M. C. Eco-evolution on the edge during climate change. Ecography 42, 1280–1297 (2019).
doi: 10.1111/ecog.04404
Coblentz, K. E., & DeLong, J. P. Ecological boundaries and constraints on viable eco‐evolutionary pathways. Oikos https://doi.org/10.1111/oik.09893 (2023).
Yanniris, C. & Frankel, V. M. Bridging valleys: expanding the adaptive landscape concept beyond theoretical space: with applications in ecology and evolution. Ideas Ecol. Evol. 11, 10–18 (2018).
Kelly, R. et al. Ten tips for developing interdisciplinary socio-ecological researchers. Socio-Ecol. Pract. Res. 1, 149–161 (2019).
doi: 10.1007/s42532-019-00018-2
Svensson, E. I. & Råberg, L. Resistance and tolerance in animal enemy–victim coevolution. Trends Ecol. Evol. 25, 267–274 (2010).
pubmed: 20092909
doi: 10.1016/j.tree.2009.12.005
Roy, B. A. & Kirchner, J. W. Evolutionary dynamics of pathogen resistance and tolerance. Evolution 54, 51–63 (2000).
pubmed: 10937183
Czorlich, Y., Aykanat, T., Erkinaro, J., Orell, P. & Primmer, C. R. Rapid evolution in salmon life history induced by direct and indirect effects of fishing. Science 376, 420–423 (2022).
pubmed: 35201899
doi: 10.1126/science.abg5980
Czorlich, Y., Aykanat, T., Erkinaro, J., Orell, P. & Primmer, C. R. Rapid sex-specific evolution of age at maturity is shaped by genetic architecture in Atlantic salmon. Nat. Ecol. Evol. 2, 1800–1807 (2018).
pubmed: 30275465
pmcid: 6322654
doi: 10.1038/s41559-018-0681-5
Debes, P. V. et al. Polygenic and major‐locus contributions to sexual maturation timing in Atlantic salmon. Mol. Ecol. 30, 4505–4519 (2021).
pubmed: 34228841
doi: 10.1111/mec.16062
Halperin, D. S., Pan, C., Lusis, A. J. & Tontonoz, P. Vestigial-like 3 is an inhibitor of adipocyte differentiation. J. Lipid Res. 54, 473–481 (2013).
pubmed: 23152581
pmcid: 3541706
doi: 10.1194/jlr.M032755
Sävilammi, T. et al. Cytosine methylation patterns suggest a role of methylation in plastic and adaptive responses to temperature in European grayling (Thymallus thymallus) populations. Epigenetics 16, 271–288 (2020).
pubmed: 32660325
pmcid: 7901546
doi: 10.1080/15592294.2020.1795597
Atmore, L. M. et al. Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics. Proc. Natl Acad. Sci. USA 119, e2208703119 (2022).
pubmed: 36282902
pmcid: 9659336
doi: 10.1073/pnas.2208703119
Lamarins, A. et al. Importance of interindividual interactions in eco-evolutionary population dynamics: the rise of demo-genetic agent-based models. Evol. Appli. 15, 1988–2001 (2022).
doi: 10.1111/eva.13508
Swinfield, T. et al. Imaging spectroscopy reveals the effects of topography and logging on the leaf chemistry of tropical forest canopy trees. Glob. Change Biol. 26, 989–1002 (2020).
doi: 10.1111/gcb.14903
Ives, A. R. et al. Self-perpetuating ecological–evolutionary dynamics in an agricultural host–parasite system. Nat. Ecol. Evol. 4, 702–711 (2020).
pubmed: 32203477
doi: 10.1038/s41559-020-1155-0
Chang, Y. et al. Epigenetic regulation in plant abiotic stress responses. J. Int. Plant Biol. 62, 563–580 (2020).
doi: 10.1111/jipb.12901
Friedrich, T., Faivre, L., Bäurle, I. & Schubert, D. Chromatin-based mechanisms of temperature memory in plants. Plant, Cell Environ. 42, 762–770 (2019).
pubmed: 29920687
doi: 10.1111/pce.13373
Rudgers, J. A. et al. Climate disruption of plant-microbe interactions. Ann. Rev. Ecol. Evol. Syst. 51, 561–586 (2020).
doi: 10.1146/annurev-ecolsys-011720-090819
Messier, C. et al. The functional complex network approach to foster forest resilience to global changes. For. Ecosyst. 6, 21 (2019).
doi: 10.1186/s40663-019-0166-2
Bernstein, A. All creatures great and small. BMJ https://doi.org/10.1136/bmj.l2385 (2019).
Mason, I. C., Qian, J., Adler, G. K. & Scheer, F. A. J. L. Impact of circadian disruption on glucose metabolism: implications for type 2 diabetes. Diabetologia 63, 462–472 (2020).
pubmed: 31915891
pmcid: 7002226
doi: 10.1007/s00125-019-05059-6
Maley, C. C. et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat. Genet. 38, 468–473 (2006).
pubmed: 16565718
doi: 10.1038/ng1768
Alexandrov, L. B., Nik-Zainal, S., Siu, H. C., Leung, S. Y. & Stratton, M. R. A mutational signature in gastric cancer suggests therapeutic strategies. Nat. Commun. 6, 8683 (2015).
pubmed: 26511885
pmcid: 4918743
doi: 10.1038/ncomms9683