Widespread analytical pitfalls in empirical coexistence studies and a checklist for improving their statistical robustness

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(4), P. 594 - 611

Published: Feb. 28, 2024

Abstract Modern coexistence theory (MCT) offers a conceptually straightforward approach for connecting empirical observations with an elegant theoretical framework, gaining popularity rapidly over the past decade. However, beneath this surface‐level simplicity lie various assumptions and subjective choices made during data analysis. These can lead researchers to draw qualitatively different conclusions from same set of experiments. As predictions MCT studies are often treated as outcomes, many readers reviewers may not be familiar framework's assumptions, there is particular risk ‘researcher degrees freedom’ inflating confidence in results, thereby affecting reproducibility predictive power. To tackle these concerns, we introduce checklist consisting statistical best practices promote more robust applications MCT. Our recommendations organised into four categories: presentation sharing raw data, testing model fits, managing uncertainty associated coefficients incorporating predictions. We surveyed published 15 years discovered high degree variation level rigour adherence practices. present case illustrate dependence results on seemingly innocuous among competition structure error distributions, which some cases reversed predicted outcomes. demonstrate how analytical approaches profoundly alter interpretation experimental underscoring importance carefully considering thoroughly justifying each step taken analysis pathway. serves resource authors alike, providing guidance strengthen foundation analyses. field shifts descriptive, trailblazing phase stage consolidation, emphasise need caution when building upon findings earlier studies. ensure that progress ecological based reliable evidence, it crucial subject our predictions, generalisability rigorous assessment than currently trend.

Language: Английский

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Restoration ecology through the lens of coexistence theory

Trends in Ecology & Evolution, Journal Year: 2023, Volume and Issue: 38(11), P. 1085 - 1096

Published: July 17, 2023

Ecological restoration success can depend on environmental conditions and species interactions, initial trajectories may not reflect long-term outcomes.Coexistence theory help diagnose outcomes early by assessing whether focal increase when at low density.Partitioning the effect of environment competition low-density growth rates guide efforts. As human influence over Earth's ecosystems increases amount land available for traditional conservation dwindles, ecological is gaining traction as an essential tool biodiversity [1.Gann G.D. et al.International principles standards practice restoration.Restor. Ecol. 2019; 27: S1-S46Crossref Scopus (571) Google Scholar]. Despite enthusiasm, discipline ecology has struggled to become a predictive science capable consistently improving [2.Hobbs R.J. Norton D.A. Towards conceptual framework ecology.Restor. 1996; 4: 93-110Crossref Scholar,3.Suding K. Toward era in ecology: successes, failures, opportunities ahead.Annu. Rev. Evol. Syst. 2011; 42: 465-487Crossref (233) Over history ecology, frameworks often assumed monotonic recovery trajectory [4.Brudvig L.A. The biodiversity: where research been does it need go?.Am. J. Bot. 98: 549-558Crossref PubMed (202) Scholar] or aimed 'carbon copy' past site [5.Hilderbrand R.H. al.The myths ecology.Ecol. Soc. 2005; 10: 19Crossref (311) Scholar], drawing largely from theories succession community assembly [6.Wainwright C.E. al.Links between are rise.J. Appl. 2017; 55: 570-581Crossref (55) At same time, there long-standing appreciation that nonlinear [7.Young T.P. al.Community comparing, contrasting combining paradigms context restoration.Ecol. Restor. 2001; 19: 5-18Crossref Scholar,8.Suding K.N. Hobbs Threshold models conservation: developing framework.Trends 2009; 24: 271-279Abstract Full Text PDF (495) diverge due specific time period project implementation [9.Choi Y.D. Theories changing environment: toward 'futuristic' Res. 2004; 75-81Crossref (0) Scholar,10.Vaughn K.J. Young Contingent conclusions: year initiation influences field experiments, but temporal replication rare.Restor. 2010; 18: 59-64Crossref (65) Explicitly incorporating role variability important assess efforts variable world Scholar,9.Choi Within broader Modern Coexistence Theory (hereafter 'coexistence theory') [11.Chesson P. Mechanisms maintenance diversity.Annu. 2000; 31: 343-366Crossref (4341) Scholar,12.Barabás G. al.Chesson's coexistence theory.Ecol. Monogr. 2018; 88: 277-303Crossref (152) emerged delineate interactions how coexist, ultimately influencing composition diversity. emphasizes importance spatial dynamics provides analytical metrics relation average conditions. led advances numerous subfields, such [13.Bowler C.H. al.Accounting demographic uncertainty predictions coexistence: case study with annual plants.Ecol. Lett. 2022; 25: 1618-1628Crossref (5) Scholar, 14.Hallett L.M. al.Rainfall maintains grass-forb coexistence.Ecol. 22: 1658-1667Crossref (52) 15.Grainger T.N. Invasion Criterion: common currency research.Trends 34: 925-935Abstract (69) invasion biology [16.MacDougall A.S. al.Plant invasions niche.J. 97: 609-615Crossref (332) Scholar,17.Godoy O. understand biological interaction networks: Implications novel ecosystems.Funct. 33: 1190-1201Crossref (26) trait-based [18.Adler P.B. al.Trait-based tests mechanisms.Ecol. 2013; 16: 1294-1306Crossref (367) 19.Kraft N.J. functional traits multidimensional nature coexistence.Proc. Natl. Acad. Sci. U. S. A. 2015; 112: 797-802Crossref 20.Yu W. Li ecology.Biodivers. 2020; 28: 1362Crossref (6) Here, we unify improve goals, strategies, assessment increasingly (Figure 1). We concentrate restoring herbaceous plant communities, because they both frequent focus model system developments theory. However, our proposed approaches adaptable other systems. understanding delineating mechanisms (see Glossary) maintain These include classic niche partitioning well fluctuations. For example, formalized differences responses fluctuations lead able 'store' through bad years, seed banks adult stages, component commonly considered 'storage effect' mechanism [12.Barabás Scholar,21.Sears A.L. Chesson New methods quantifying storage effect: illustration desert annuals.Ecology. 2007; 2240-2247Crossref (100) Similarly, abiotic biotic greater benefits good years relative tend promote persistence [22.Chesson Quantifying testing arising recruitment fluctuations.Theor. Popul. Biol. 2003; 64: 345-357Crossref 23.Letten A.D. al.Species simultaneous fluctuation-dependent mechanisms.Proc. 115: 6745-6750Crossref (64) 24.Shoemaker L.G. al.Integrating underlying structure stochasticity into ecology.Ecology. 101e02922Crossref (67) A key contribution tools quantify contributing variability. How will persist go extinct time? Persistence assessed via criterion, whereby coexist if each density while experiencing surrounding resident Scholar,25.Chesson Updates diversity.J. 106: 1773-1794Crossref (128) criterion evaluated calculating rate (LDGR) species; positive LDGR indicates persist, negative cannot invade or, present, predicted eventually locally such, reflects joint intrinsic absence net impact Long-term averaging periods capture full range experiences [14.Hallett use helpful imperfect; one fails scenarios which depends presence conspecifics (e.g., Allee effects) generally realistic conditions, most populations experience rarity, especially within small sites and/or diverse communities [26.Maina G.G. Howe H.F. Inherent rarity restoration.Conserv. 14: 1335-1340Crossref (41) Does their risk extinction? addresses this question partitioning, accounts variation occurs [27.Chesson Multispecies environments.Theor. 1994; 45: 227-276Crossref (480) space [28.Chesson General competitive spatially-varying 58: 211-237Crossref (636) Different partitionings have developed target different Scholar,27.Chesson 28.Chesson 29.Adler al.A neutrality.Ecol. 95-104Crossref (780) 30.Ellner S.P. al.An expanded modern empirical applications.Ecol. 3-18Crossref (72) idea written sum terms, reflecting alters coexistence. Ellner al. [30.Ellner simulations conducted turned 'on' 'off' population (such coefficients), singly combination, parameter overall Scholar,23.Letten This scenarios, isolates versus experience. In similar vein, be partition consequence strategies modifying community) abundance (Box 1).Box 1Applying scenariosCoexistence used make about interventions. To realistic, these should describe performance IA,B). Site descriptions, including climate records, soil maps, vegetation monitoring, natural history, practitioner experience, inform include. approach fit under representative condition. done experimentally, creating manipulating densities them, observationally, using monitoring data sufficient scenarios. yield biomass fecundity) measured, community. While form vary system, measures allow species' (λ) neighboring (α) estimated condition IC,D).Once fit, calculated simulation introduced existing environments, parameters associated condition, weighted frequency occur. partitioned λ, α) either varies held constant, combination IE). interventions likewise simulated altering distribution calculate (to actions ameliorate conditions) reducing before reduce competitors) Finally, step observed targeted benefit only requires modeling species, improved reciprocally residents, substantially affects them. IC,D). Once Restoration goals centered achieving desired composition, historically comparing restored reference 1A [1]). after management, many still flux, transient indicative [31.Guerrant E.O. value propriety reintroduction rare plants.Botany. 91: v-xCrossref (21) Scholar,32.Shriver R.K. Transient impede ecosystem transformation disturbance.Ecol. 1357-1366Crossref (47) rather representing successional stages [33.del Moral R. al.Insights gained landscape function.in: Walker L.R. Linking Succession. Springer, 2007: 19-44Crossref actions, planting seeding [34.Aoyama L. al.Application indication trajectories.Ecol. 32e2649Crossref (2) dynamics, paired short windows projects [3.Suding limit ability link patterns [35.Zurell D. al.Spatially explicit decision-making animal restoration.Ecography. 4e05787Google reconcile discrepancies indicators [32.Shriver Scholar,36.Armstrong D.P. Seddon P.J. Directions biology.Trends 2008; 23: 20-25Abstract (756) clear goal: puts persistence, precluding abundance-based additional gauges (Table appropriate minimal its aligned ancillary undesirable resident. concern, single-population analyses [37.Albrecht M.A. al.Effects life reproduction lags reintroductions plants.Conserv. 601-611Crossref (24) Scholar,38.Vitt community-level grassland management non-target Agalinis auriculata.Biol. Conserv. 142: 798-805Crossref (19) deviates interest than reciprocal all community, greatly reduces requirements. could expected quantified separately [39.Bowler al.Positive effects exotic dampened neighborhood heterogeneity.Ecology. 103e3779Crossref so long primary concern interact another [19.Kraft Scholar,40.Van Dyke M.N. al.Small rainfall changes drive substantial coexistence.Nature. 611: 507-511Crossref (8) develop nondesired aiming nondesirable rates, leading local elimination.Table 1Information required apply situationsRestoration goalInformationSituationRefsIncrease cover/biomassSpecies-level cover/biomass bare patches coverAfter mining events, constructing roads entirely remove cover[90.Cobbaert al.Experimental fen peat mining.Appl. Veg. 7: 209-220Crossref (66) Scholar,91.Miao Z.-W. al.Ecological rebuilding reclamation surface mines Shanxi province, China.J. Environ. 12: 486-497Google Scholar]Increase keystone speciesVariation across grown alone itself speciesAfter loss fire, flooding strong perturbation, following introduction dramatically altered ecosystem[92.Layton C. al.Kelp forest Australia.Front. Mar. 74Crossref (84) Scholar,93.Koch J.M. Samsa G.P. Restoring jarrah trees bauxite Western Australia.Restor. 15: S17-S25Crossref Scholar]Remove undesired invasive event new indirectly allows invasion, disturbance nitrogen deposition[34.Aoyama Scholar,94.Flory S.L. Clay Invasive removal method determines native responses.J. 46: 434-442Crossref biodiversityVariation group Differences distinguish groups (including itself)After perturbation particularly affected some groups. perturbations pest outbreak, nutrient deposition, extreme heat waves[95.Gherardi Sala O.E. Enhanced interannual precipitation diversity turn ameliorates productivity.Ecol. 1293-1300Crossref (94) Scholar,96.Ostertag al.Using restore Hawaiian rainforest.J. 52: 805-809Crossref (96) richnessThe data-demanding goal account individual independent axes densitiesRestoration mitigate global change drivers biodiversity, change, intensity[97.Allan E. al.Interannual land-use intensity enhances multidiversity.Proc. 2014; 111: 308-313Crossref Scholar,98.Pakeman Functional indices reveal impacts intensification assembly.J. 99: 1143-1151Crossref (161) Open table tab date, setting relied historic ranges ecosystems, data-intensive exercise [41.Farrell H.L. preparation equal those dryland site: 6 development.Restor. 2021; 29e13482Crossref (4) Scholar]) explicitly variables. By contrast, focuses viability shifts environments Scholar,42.Mordecai E.A. al.Controls perennial grass exclusion California grasslands invaded 96: 2643-2652Crossref (15) Scholar,43.Bimler M.D. Accurate systems require inclusion facilitative dependency.J. 1839-1852Crossref (59) informing more quantifiable Usinowicz Levine [44.Usinowicz Species change: geographical scale problem.Ecol. 21: 1589-1603Crossref (22) mapped LDGRs along gradient forecast set current future Improving heart ideally helping address questions as: what potential [45.Wilson K.A. al.Optimal restoration: accounting space, uncertainty.J. 48: 715-725Crossref Scholar]? Is passive (i.e., simply ceasing causes degradation) sufficient, active necessary [46.Holl K.D. Aide T.M. When actively ecosystems?.For. Manag. 261: 1558-1563Crossref (420) If needed, site, [47.Hobbs al.Intervention applying twenty-first century.BioScience. 61: 442-450Crossref (303) degree influenced Scholar,34.Aoyama

Language: Английский

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Higher‐order species interactions cause time‐dependent niche and fitness differences: Experimental evidence in plant‐feeding arthropods

Ecology Letters, Journal Year: 2024, Volume and Issue: 27(5)

Published: April 29, 2024

Abstract Species interact in different ways, including competition, facilitation and predation. These interactions can be non‐linear or higher order may depend on time species densities. Although these higher‐order are virtually ubiquitous, they remain poorly understood, as challenging both theoretically empirically. We propose to adapt niche fitness differences from modern coexistence theory apply them over time. As such, not merely inform about coexistence, but provide a deeper understanding of how change. Here, we investigated the exploitation biotic resource (plant) by phytophagous arthropods affects their interactions. performed monoculture competition experiments fit generalized additive mixed model empirical data, which allowed us calculate differences. found that switch between types time, intra‐ interspecific facilitation, strong weak competition.

Language: Английский

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Accounting for demographic uncertainty increases predictions for species coexistence: A case study with annual plants

Ecology Letters, Journal Year: 2022, Volume and Issue: 25(7), P. 1618 - 1628

Published: May 28, 2022

Abstract Natural systems contain more complexity than is accounted for in models of modern coexistence theory. Coexistence modelling often disregards variation arising from stochasticity biological processes, heterogeneity among individuals and plasticity trait values. However, these unaccounted‐for sources uncertainty are likely to be ecologically important have the potential impact estimates coexistence. We applied a Bayesian framework data an annual plant community Western Australia propagate outcomes using invasion criterion ratio niche fitness differences. found accounting this altered predictions versus competitive exclusion 3 out 14 species pairs yielded probability priority effects additional pair. The propagation improves our ability predict accurately natural systems.

Language: Английский

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Building modern coexistence theory from the ground up: The role of community assembly

Ecology Letters, Journal Year: 2023, Volume and Issue: 26(11), P. 1840 - 1861

Published: Sept. 25, 2023

Abstract Modern coexistence theory (MCT) is one of the leading methods to understand species coexistence. It uses invasion growth rates—the average, per‐capita rate a rare species—to identify when and why coexist. Despite significant advances in dissecting mechanisms occurs, MCT relies on ‘mutual invasibility’ condition designed for two‐species communities but poorly defined species‐rich communities. Here, we review well‐known issues with this component propose solution based recent mathematical advances. We clear framework expanding understanding resistance as well coexistence, especially that could not be analysed so far. Using two data‐driven community models from literature, illustrate utility our highlight opportunities bridging fields assembly

Language: Английский

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Pathways to global-change effects on biodiversity: new opportunities for dynamically forecasting demography and species interactions

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2023, Volume and Issue: 290(1993)

Published: Feb. 22, 2023

In structured populations, persistence under environmental change may be particularly threatened when abiotic factors simultaneously negatively affect survival and reproduction of several life cycle stages, as opposed to a single stage. Such effects can then exacerbated species interactions generate reciprocal feedbacks between the demographic rates different species. Despite importance such feedbacks, forecasts that account for them are limited individual-based data on interacting perceived essential mechanistic forecasting—but rarely available. Here, we first review current shortcomings in assessing population community dynamics. We present an overview advances statistical tools provide opportunity leverage population-level abundances multiple infer stage-specific demography. Lastly, showcase state-of-the-art Bayesian method project Mediterranean shrub community. This case study shows climate threatens populations most strongly by changing interaction conspecific heterospecific neighbours both juvenile adult survival. Thus, repurposing multi-species abundance forecasting substantially improve our understanding emerging threats biodiversity.

Language: Английский

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A Continuum From Positive to Negative Interactions Drives Plant Species' Performance in a Diverse Community

Ecology Letters, Journal Year: 2025, Volume and Issue: 28(1)

Published: Jan. 1, 2025

ABSTRACT With many species interacting in nature, determining which interactions describe community dynamics is nontrivial. By applying a computational modeling approach to an extensive field survey, we assessed the importance of from plants (both inter‐ and intra‐specific), pollinators insect herbivores on plant performance (i.e., viable seed production). We compared inclusion interaction effects as aggregate guild‐level terms versus specific taxonomic groups. found that continuum positive negative interactions, containing mostly few strong taxonomic‐specific effects, was sufficient performance. While with intraspecific varied weakly positive, heterospecific mainly promoted competition facilitated plants. The consistency these empirical findings over 3 years suggests including groups rather than all pairwise high‐order can be for accurately describing variation across natural communities.

Language: Английский

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Uncertain competition coefficients undermine inferences about coexistence

Nature, Journal Year: 2024, Volume and Issue: 632(8027), P. E9 - E14

Published: Aug. 28, 2024

Language: Английский

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Assembly Graph as the Rosetta Stone of Ecological Assembly

Environmental Microbiology, Journal Year: 2025, Volume and Issue: 27(1)

Published: Jan. 1, 2025

Ecological assembly-the process of ecological community formation through species introductions-has recently seen exciting theoretical advancements across dynamical, informational, and probabilistic approaches. However, these theories often remain inaccessible to non-theoreticians, they lack a unifying lens. Here, I introduce the assembly graph as an integrative tool connect emerging theories. The visually represents dynamics, where nodes symbolise combinations edges represent transitions driven by introductions. Through lens graphs, review how processes reduce uncertainty in random arrivals (informational approach), identify graphical properties that guarantee coexistence examine class dynamical models constrain topology graphs (dynamical quantify transition probabilities with incomplete information (probabilistic approach). To facilitate empirical testing, also methods decompose complex into smaller, measurable components, well computational tools for deriving graphs. In sum, this math-light progress aims catalyse research towards predictive understanding assembly.

Language: Английский

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Changing environmental conditions impact the phenotypic plasticity of Carex acuta and Glyceria maxima, two common wet grassland species

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: April 28, 2025

Introduction Maintenance of species coexistence is an important and on-going subject plant ecology. Here, we aimed to determine how Carex acuta Glyceria maxima , two common, co-occurring in European wet grasslands, respond changing environmental conditions what these changes portend for species. Such studies are predicting modelling the effects management climate change on grassland composition maintaining ability grasslands provide their ecosystem services including carbon sequestration water purification. Based past studies, hypothesized that both would be affected by hydrologic but modified nutrient with fertilization having a more positive impact G. . Methods We established mesocosm distinguish effect hydrology nutrients biomass allocation patterns may life history traits species, which influence co-exist. Plants were grown pots from late May early September 2019 subjected three level treatments. Half plants harvested July while other half calculated. Univariable multivariable analyses conducted treatments measured parameters. In addition, determined phenotypic plasticity whether showed allometric relationships size. Results discussion C. was changes, growing better dry saturated conditions, had Both stressed when flooded, so than Contrary our predictions, produced ramets taller plastic responses only some related Our results indicate likely co-exist oligo- mesotrophic fluctuating levels.

Language: Английский

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