Open questions for systems ecology

Main Article Content

Serguei Saavedra
Sonia Kéfi

Abstract

Systems ecology seeks to understand how interactions among ecological components generate system-level patterns, dynamics, and responses to change. In this founding editorial, we outline the motivation and scope of Systems Ecology, a diamond open-access journal organized around systems-level ecological questions rather than disciplinary boundaries. We introduce the journal's Field Map as a living framework for connecting contributions across ecological systems and identify a set of open questions spanning emergence, energy and material constraints, persistence and fragility, transformation, recovery, scaling, spatial connectivity, and inference and prediction. We argue for a publishing model in which synthesis, theory, empirical work, methods, and cross-system comparisons contribute collectively to cumulative understanding in systems ecology.

Article Details

How to Cite
Saavedra, S., & Kéfi, S. (2026). Open questions for systems ecology. Systems Ecology, 1. https://doi.org/10.67837/2341
Section
Editorials

References

International Association of Scientific, Technical and Medical Publishers. STM Global Brief 2021: Economics and Market Size. STM Association report. 2021.

Hanson MA, Gómez Barreiro P, Crosetto P, Brockington D. The Strain on Scientific Publishing. Quantitative Science Studies. 2024;5(4):823. https://doi.org/10.1162/qss_a_00327

Kovanis M, Porcher R, Ravaud P, Trinquart L. The Global Burden of Journal Peer Review in the Biomedical Literature: Strong Imbalance in the Collective Enterprise. PLOS ONE. 2016;11(11):e0166387. https://doi.org/10.1371/journal.pone.0166387

Larivière V, Haustein S, Mongeon P. The Oligopoly of Academic Publishers in the Digital Era. PLOS ONE. 2015;10(6):e0127502. https://doi.org/10.1371/journal.pone.0127502

Fortunato S, Bergstrom CT, Börner K, Evans JA, Helbing D, Milojević S, Petersen AM, Radicchi F, Sinatra R, Uzzi B, Vespignani A, Waltman L, Wang D, Barabási AL. Science of Science. Science. 2018;359(6379):eaao0185. https://doi.org/10.1126/science.aao0185

Sugimoto CR, Larivière V. Measuring Research: What Everyone Needs to Know. New York: Oxford University Press; 2018. https://doi.org/10.1093/wentk/9780190640118.001.0001

Evans JA. Electronic Publication and the Narrowing of Science and Scholarship. Science. 2008;321(5887):395–399. https://doi.org/10.1126/science.1150473

Uzzi B, Mukherjee S, Stringer M, Jones B. Atypical Combinations and Scientific Impact. Science. 2013;342(6157):468–472. https://doi.org/10.1126/science.1240474

Foster JG, Rzhetsky A, Evans JA. Tradition and Innovation in Scientists' Research Strategies. American Sociological Review. 2015;80(5):875–908. https://doi.org/10.1177/0003122415601618

Wang D, Song C, Barabási AL. Quantifying Long-Term Scientific Impact. Science. 2013;342(6154):127–132. https://doi.org/10.1126/science.1237825

Sinatra R, Wang D, Deville P, Song C, Barabási AL. Quantifying the Evolution of Individual Scientific Impact. Science. 2016;354(6312):aaf5239. https://doi.org/10.1126/science.aaf5239

Clauset A, Larremore DB, Sinatra R. Data-Driven Predictions in the Science of Science. Science. 2017;355(6324):477–480. https://doi.org/10.1126/science.aal4217

Head ML, Holman L, Lanfear R, Kahn AT, Jennions MD. The Extent and Consequences of P-Hacking in Science. PLOS Biology. 2015;13(3):e1002106. https://doi.org/10.1371/journal.pbio.1002106

Fidler F, Chee YE, Wintle BC, Burgman MA, McCarthy MA, Gordon A. Metaresearch for Evaluating Reproducibility in Ecology and Evolution. BioScience. 2017;67(3):282–289. https://doi.org/10.1093/biosci/biw159

Hicks D, Wouters P, Waltman L, de Rijcke S, Rafols I. Bibliometrics: The Leiden Manifesto for Research Metrics. Nature. 2015;520:429–431. https://doi.org/10.1038/520429a

American Society for Cell Biology. San Francisco Declaration on Research Assessment (DORA). 2012.

de Rijcke S, Wouters PF, Rushforth AD, Franssen TP, Hammarfelt B. Evaluation Practices and Effects of Indicator Use—A Literature Review. Research Evaluation. 2016;25(2):161–169. https://doi.org/10.1093/reseval/rvv038

Hutchinson GE. Homage to Santa Rosalia or Why Are There So Many Kinds of Animals? The American Naturalist. 1959;93(870):145–159. https://doi.org/10.1086/282070

May RM. Will a Large Complex System Be Stable? Nature. 1972;238(5364):413–414. https://doi.org/10.1038/238413a0

Allesina S, Tang S. Stability Criteria for Complex Ecosystems. Nature. 2012;483(7388):205–208. https://doi.org/10.1038/nature10832

Levin SA. The Problem of Pattern and Scale in Ecology. Ecology. 1992;73(6):1943–1967. https://doi.org/10.2307/1941447

Holling CS. Resilience and Stability of Ecological Systems. Annual Review of Ecology and Systematics. 1973;4:1–23. https://doi.org/10.1146/annurev.es.04.110173.000245

Scheffer M, Carpenter S, Foley JA, Folke C, Walker B. Catastrophic Shifts in Ecosystems. Nature. 2001;413:591–596. https://doi.org/10.1038/35098000

Anderson PW. More Is Different. Science. 1972;177(4047):393–396. https://doi.org/10.1126/science.177.4047.393

Levin SA. Ecosystems and the Biosphere as Complex Adaptive Systems. Ecosystems. 1998;1(5):431–436. https://doi.org/10.1007/s100219900037

Tansley AG. The Use and Abuse of Vegetational Concepts and Terms. Ecology. 1935;16(3):284–307. https://doi.org/10.2307/1930070

Odum EP. The Strategy of Ecosystem Development. Science. 1969;164(3877):262–270. https://doi.org/10.1126/science.164.3877.262

Margalef R. On Certain Unifying Principles in Ecology. The American Naturalist. 1963;97(897):357–374. https://doi.org/10.1086/282286

Prigogine I, Stengers I. Order Out of Chaos: Man's New Dialogue with Nature. New York: Bantam Books; 1984.

Solé RV, Bascompte J. Self-Organization in Complex Ecosystems. Princeton: Princeton University Press; 2006. https://doi.org/10.1515/9781400842933

Allesina S, Tang S. The Stability–Complexity Relationship at Age 40: A Random Matrix Perspective. Population Ecology. 2015;57(1):63–75. https://doi.org/10.1007/s10144-014-0471-0

Pecl GT, Araújo MB, Bell JD, Blanchard J, Bonebrake TC, Chen IC, Clark TD, Colwell RK, Danielsen F, Evengård B, Falconi L, Ferrier S, Frusher S, Garcia RA, Griffis RB, Hobday AJ, Janion-Scheepers C, Jarzyna MA, Jennings S, Lenoir J, Linnetved HI, Martin VY, McCormack PC, McDonald J, Mitchell NJ, Mustonen T, Pandolfi JM, Pettorelli N, Popova E, Robinson SA, Scheffers BR, Shaw JD, Sorte CJB, Strugnell JM, Sunday JM, Tuanmu MN, Vergés A, Villanueva C, Wernberg T, Wapstra E, Williams SE. Biodiversity Redistribution Under Climate Change: Impacts on Ecosystems and Human Well-Being. Science. 2017;355(6332):eaai9214. https://doi.org/10.1126/science.aai9214

Trisos CH, Merow C, Pigot AL. The Projected Timing of Abrupt Ecological Disruption from Climate Change. Nature. 2020;580:496–501. https://doi.org/10.1038/s41586-020-2189-9

Lenton TM, Held H, Kriegler E, Hall JW, Lucht W, Rahmstorf S, Schellnhuber HJ. Tipping Elements in the Earth's Climate System. Proceedings of the National Academy of Sciences. 2008;105(6):1786–1793. https://doi.org/10.1073/pnas.0705414105

Rohr RP, Saavedra S, Bascompte J. On the Structural Stability of Mutualistic Systems. Science. 2014;345(6195):1253497. https://doi.org/10.1126/science.1253497

Grilli J, Adorisio M, Suweis S, Barabás G, Banavar JR, Allesina S, Maritan A. Feasibility and Coexistence of Large Ecological Communities. Nature Communications. 2017;8:14389. https://doi.org/10.1038/ncomms14389

Kéfi S, Domínguez-García V, Donohue I, Fontaine C, Thébault E, Dakos V. Advancing Our Understanding of Ecological Stability. Ecology Letters. 2019;22(9):1349–1356. https://doi.org/10.1111/ele.13340

Wickman J, Klausmeier CA, Litchman E. Antifragility: A Cross-Cutting Concept for Understanding Ecological Responses to Variability. The American Naturalist. 2026;207(6):763–770.

Suding KN, Gross KL, Houseman GR. Alternative States and Positive Feedbacks in Restoration Ecology. Trends in Ecology & Evolution. 2004;19(1):46–53. https://doi.org/10.1016/j.tree.2003.10.005

Fukami T. Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects. Annual Review of Ecology, Evolution, and Systematics. 2015;46:1–23. https://doi.org/10.1146/annurev-ecolsys-110411-160340

Jones HP, Schmitz OJ. Rapid Recovery of Damaged Ecosystems. PLOS ONE. 2009;4(5):e5653. https://doi.org/10.1371/journal.pone.0005653

Suding KN, Hobbs RJ. Threshold Models in Restoration and Conservation: A Developing Framework. Trends in Ecology & Evolution. 2009;24(5):271–279. https://doi.org/10.1016/j.tree.2008.11.012

O'Connor MI, Bernhardt JR, Sunday JM, Marshall DJ. Scaling Temperature Effects on Metabolism from Individuals to Ecosystems. Annual Review of Ecology, Evolution, and Systematics. 2025;56:543–569.

Litchman E, Klausmeier CA, Schofield OM, Falkowski PG. The Role of Functional Traits and Trade-Offs in Structuring Phytoplankton Communities: Scaling from Cellular to Ecosystem Level. Ecology Letters. 2007;10:1170–1181. https://doi.org/10.1111/j.1461-0248.2007.01117.x

Kéfi S, Rietkerk M, Roy M, Franc A, de Ruiter PC, Pascual M. Robust Scaling in Ecosystems and the Meltdown of Patch-Size Distributions before Extinction. Ecology Letters. 2011;14(1):29–35. https://doi.org/10.1111/j.1461-0248.2010.01553.x

Fahrig L. Effects of Habitat Fragmentation on Biodiversity. Annual Review of Ecology, Evolution, and Systematics. 2003;34:487–515. https://doi.org/10.1146/annurev.ecolsys.34.011802.132419

Auger-Méthé M, Newman K, Cole D, Empacher F, Gryba R, King AA, Leos-Barajas V, Mills Flemming J, Nielsen A, Petris G, Thomas L. A Guide to State-Space Modeling of Ecological Time Series. Ecological Monographs. 2021;91(4):e01470. https://doi.org/10.1002/ecm.1470

Bowker GC, Star SL. Sorting Things Out: Classification and Its Consequences. Cambridge, MA: MIT Press; 1999. https://doi.org/10.7551/mitpress/6352.001.0001

Nosek BA, Alter G, Banks GC, Borsboom D, Bowman SD, Breckler SJ, Buck S, Chambers CD, Chin G, Christensen G, Contestabile M, Dafoe A, Eich E, Freese J, Glennerster R, Goroff D, Green DP, Hesse B, Humphreys M, Ishiyama J, Karlan D, Kraut A, Lupia A, Mabry P, Madon T, Malhotra N, Mayo-Wilson E, McNutt M, Miguel E, Paluck EL, Simonsohn U, Soderberg C, Spellman BA, Turitto J, VandenBos G, Vazire S, Wagenmakers EJ, Wilson R, Yarkoni T. Promoting an Open Research Culture. Science. 2015;348(6242):1422–1425. https://doi.org/10.1126/science.aab2374

Culina A, van den Berg I, Evans S, Sánchez-Tójar A. Low Availability of Code in Ecology: A Call for Urgent Action. PLOS Biology. 2020;18(7):e3000763. https://doi.org/10.1371/journal.pbio.3000763

Allesina S. Accelerating the Pace of Discovery by Changing the Peer Review Algorithm. arXiv. 2009. arXiv:0911.0344.

Powers SM, Hampton SE. Open Science, Reproducibility, and Transparency in Ecology. Ecological Applications. 2019;29(1):e01822. https://doi.org/10.1002/eap.1822

Munafò MR, Nosek BA, Bishop DVM, Button KS, Chambers CD, du Sert NP, Simonsohn U, Wagenmakers EJ, Ware JJ, Ioannidis JPA. A Manifesto for Reproducible Science. Nature Human Behaviour. 2017;1:0021. https://doi.org/10.1038/s41562-016-0021

Grossmann A, Brembs B. Current Market Rates for Scholarly Publishing Services. F1000Research. 2021;10:20. https://doi.org/10.12688/f1000research.27468.2

Galtier N, Belkhir K, Antoine PO, Bibal C, Boëte C, Delsuc F, Huchard E, Kéfi S, Maeder C, Paradis L, Puechmaille SJ, Queffelec A, Scornavacca C, Smadja CM. Time to Publish Responsibly: DAFNEE, a Database of Academia-Friendly Journals in Ecology and Evolutionary Biology. Journal of Evolutionary Biology. 2026;39(2):190–199.