Priority effects transcend scales and disciplines in biology

Trends in Ecology & Evolution, Journal Year: 2024, Volume and Issue: 39(7), P. 677 - 688

Published: March 19, 2024

Language: Английский

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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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Application of modern coexistence theory to rare plant restoration provides early indication of restoration trajectories

Ecological Applications, Journal Year: 2022, Volume and Issue: 32(7)

Published: May 13, 2022

Restoration ecology commonly seeks to re-establish species of interest in degraded habitats. Despite a rich understanding how succession influences re-establishment, there are several outstanding questions that remain unaddressed: short-term abundances sufficient determine long-term re-establishment success, and what factors contribute unpredictable restorations outcomes? In other words, when restoration fails, is it because the restored habitat substandard, strong competition with invasive species, or alternatively due changing environmental conditions would equally impact established populations? Here, we re-purpose tools developed from modern coexistence theory address these questions, apply them an effort restore endangered Contra Costa goldfields (Lasthenia conjugens) constructed ("restored") California vernal pools. Using 16 years data, construct population model L. conjugens, conservation concern primarily loss invasion exotic grasses. We show initial, appearances success misleading, as year-to-year fluctuations cause growth rates fall below zero. The failure pools driven by lower maximum compared reference ("natural") pools, coupled stronger negative sensitivity annual abiotic yield decreased rates. Nonetheless, our modeling shows (mainly grasses) benefit conjugens through periods competitive release, especially intermediate pool depth. therefore reductions invasives seed addition particular depths could change outcome for conjugens. By applying largely theoretical framework urgent goal ecological restoration, study provides blueprint predicting identifies future actions reverse loss.

Language: Английский

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Ecological and evolutionary consequences of temporal variation in dispersal

Ecography, Journal Year: 2023, Volume and Issue: 2024(2)

Published: Aug. 28, 2023

The importance of dispersal rates and distances has long been appreciated by ecologists evolutionary biologists. An emerging field research is revealing how temporal variation in can substantially influence ecological outcomes. We review temporally vary many ecosystems, a pattern that particularly well‐documented for aquatic organisms but likely pervasive terrestrial ecosystems as well. then synthesize the effects on five key processes: 1) metapopulation dynamics, 2) local adaptation, 3) range limits expansions, 4) species coexistence 5) metacommunity dynamics. Our demonstrates more than just statistical ‘noise' fact lead to different outcomes expected were constant. For example, increasing magnitude lower growth rates, permit greater facilitate accelerate expansion, increase regional coexistence, alter diversity. These inform conservation natural resource management decisions such prioritization spatial planning, spillover from domesticated or captive populations into native populations, design effective control strategies invasive species.

Language: Английский

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The assembly and dynamics of ecological communities in an ever‐changing world

Ecological Monographs, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 30, 2024

Abstract Alternative perspectives on the maintenance of biodiversity and assembly ecological communities suggest that both processes cannot be investigated simultaneously. In this concept synthesis, we challenge view by presenting major theoretical advances in structural stability permanence theory. These advances, which provide complementary views, allow studying short‐ long‐term dynamics as changes species richness, composition, abundance. Here, global attractor, technically named informational structure (IS), is central element to construct from information species' intrinsic growth rates their strength sign interactions. The attractor has four main properties: (1) It contains all limits what feasible unfeasible dynamical behavior an system, therefore, (2) it provides a thorough characterization combinations richness composition can coexist (i.e., stable equilibrium), (3) well connections (paths) between coexisting communities. Importantly, (4) such topology when environmental (abiotic biotic) variation affects ability grow interact with others. Overall, these properties switching traditional evaluation coexistence at equilibrium much more realistic nonequilibrium perspective where underlie transient dynamics. Several fields ecology benefit study IS. For instance, serve evaluate community responses after end perturbation, design restoration trajectories, consequences biological invasions persistence native within communities, or assess ecosystem health status. We illustrate latter possibility empirical observations 7 years Mediterranean annual grasslands. document extremely wet dry generate ISs supporting few paths. remaining distinguish winners losers ongoing climate change indicate future opportunities. A fully tractable operational framework readily available understand predict ever‐changing world.

Language: Английский

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Population Genetics Meets Ecology: A Guide to Individual‐Based Simulations in Continuous Landscapes

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT Individual‐based simulation has become an increasingly crucial tool for many fields of population biology. However, continuous geography is important to applications, and implementing realistic stable simulations in space presents a variety difficulties, from modeling choices computational efficiency. This paper aims be practical guide spatial simulation, helping researchers implement individual‐based avoid common pitfalls. To do this, we delve into mechanisms mating, reproduction, density‐dependent feedback, dispersal, all which may vary across the landscape, discuss how these affect dynamics, describe parameterize convenient ways (for instance, achieve desired density). We also demonstrate models using current version simulator, SLiM. additionally natural selection—in particular, genetic variation can demographic processes. Finally, provide four short vignettes: pikas that shift their range up mountain as temperatures rise; mosquitoes live rivers juveniles experience seasonally changing habitat; cane toads expand Australia, reaching 120 million individuals; monarch butterflies whose populations are regulated by explicitly modeled resource (milkweed).

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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Species occupancy is inflated by sink populations in productive environments but not unproductive environments

Ecology, Journal Year: 2025, Volume and Issue: 106(4)

Published: April 1, 2025

Abstract For decades, community ecologists have examined how diversity varies with ecosystem productivity. Despite this long history, tests of hypothesized mechanisms, namely the interplay between environmental filtering, biotic interactions, and dispersal, are lacking, largely due to intractability using traditional approaches. Across a productivity gradient in serpentine grassland (California, USA), for four annual plant species, we coupled local estimates, occupancy surveys, measures persistence tested on transplants under natural conditions when interactions neighbors were experimentally reduced. We found positive effect (i.e., proportion our focal species occupying location) despite strong competition limiting productive environments. Additionally, across community, mismatch versus persistence, dispersal excess causing sink populations negative growth rates. Our results suggest that diversity–productivity relationships can be driven by its interactive effects abiotic conditions.

Language: Английский

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Disturbance alters transience but nutrients determine equilibria during grassland succession with multiple global change drivers

Ecology Letters, Journal Year: 2023, Volume and Issue: 26(7), P. 1132 - 1144

Published: May 1, 2023

Abstract Disturbance and environmental change may cause communities to converge on a steady state, diverge towards multiple alternative states or remain in long‐term transience. Yet, empirical investigations of successional trajectories are rare, especially systems experiencing concurrent anthropogenic drivers change. We examined succession old field grassland subjected disturbance nitrogen fertilization using data from (22‐year) experiment. Regardless initial disturbance, after decade converged largely determined by resource availability, where species turnover declined as approached dynamic equilibria. Species favoured the were those that eventually came dominate highly fertilized plots. Furthermore, made pathways more direct revealing an important interaction effect between nutrients community Our results underscore dynamical nature succession, demonstrating how properties such diversity through transient equilibrium states.

Language: Английский

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