Publications

Publications


Authors: Type:

2015

  • Clark, Adam Thomas, Hao Ye, Forest Isbell, Ethan R. Deyle, Jane Cowles, Dave Tilman, and George Sugihara. 2015. Spatial ‘convergent cross mapping’ to detect causal relationships from short time-series. Ecology .
    [Source] [Abstract]
    Recent developments in complex systems analysis have led to new techniques for detecting causal relationships using relatively short time-series - on the order of thirty sequential observations. Although many ecological observation series are even shorter - perhaps fewer than ten sequential observations - these shorter time-series are often highly replicated in space (i.e. plot replication). Here, we combine the existing techniques of convergent cross-mapping (CCM) and dewdrop regression to build a novel test of causal relations that leverages spatial replication, which we call multispatial CCM. Using examples from simulated and real-world ecological data, we test the ability of multispatial CCM to detect causal relationships between processes. We find that multispatial CCM successfully detects causal relationships with as few as five sequential observations, even in the presence of process noise and observation error. Our results suggest that this technique may constitute a useful test for causality in systems where experiments are difficult to perform and long time-series are not available. This new technique is available in the multispatialCCM package for the R programming language.

  • Nes, Egbert Van H., Marten Scheffer, Victor Brovkin, Timothy M. Lenton, Hao Ye, Ethan Deyle, and George Sugihara. 2015. Causal feedbacks in climate change. Nature climate change .
    [Source] [Abstract]
    The statistical association between temperature and greenhouse gases over glacial cycles is well documented, but causality behind this correlation remains difficult to extract directly from the data. A time lag of CO2 behind Antarctic temperature—originally thought to hint at a driving role for temperature—is absent at the last deglaciation, but recently confirmed at the last ice age inception and the end of the earlier termination II. We show that such variable time lags are typical for complex nonlinear systems such as the climate, prohibiting straightforward use of correlation lags to infer causation. However, an insight from dynamical systems theory now allows us to circumvent the classical challenges of unravelling causation from multivariate time series. We build on this insight to demonstrate directly from ice-core data that, over glacial–interglacial timescales, climate dynamics are largely driven by internal Earth system mechanisms, including a marked positive feedback effect from temperature variability on greenhouse-gas concentrations.

  • Tsonis, Anastasio A., Ethan R. Deyle, Robert M. May, George Sugihara, Kyle Swanson, Joshua D. Verbeten, and Geli Wang. 2015. Dynamical evidence for causality between galactic cosmic rays and interannual variation in global temperature. Proceedings of the national academy of sciences .
    [Source] [Abstract]

  • Ye, Hao, Richard J. Beamish, Sarah M. Glaser, Sue C. H. Grant, Chih-hao Hsieh, Laura J. Richards, Jon T. Schnute, and George Sugihara. 2015. Equation-free mechanistic ecosystem forecasting using empirical dynamic modeling. Proceedings of the national academy of sciences 112 E1569-1576.
    [Source] [Abstract]
    It is well known that current equilibrium-based models fall short as predictive descriptions of natural ecosystems, and particularly of fisheries systems that exhibit nonlinear dynamics. For example, model parameters assumed to be fixed constants may actually vary in time, models may fit well to existing data but lack out-of-sample predictive skill, and key driving variables may be misidentified due to transient (mirage) correlations that are common in nonlinear systems. With these frailties, it is somewhat surprising that static equilibrium models continue to be widely used. Here, we examine empirical dynamic modeling (EDM) as an alternative to imposed model equations and that accommodates both nonequilibrium dynamics and nonlinearity. Using time series from nine stocks of sockeye salmon (Oncorhynchus nerka) from the Fraser River system in British Columbia, Canada, we perform, for the the first time to our knowledge, real-data comparison of contemporary fisheries models with equivalent EDM formulations that explicitly use spawning stock and environmental variables to forecast recruitment. We find that EDM models produce more accurate and precise forecasts, and unlike extensions of the classic Ricker spawner–recruit equation, they show significant improvements when environmental factors are included. Our analysis demonstrates the strategic utility of EDM for incorporating environmental influences into fisheries forecasts and, more generally, for providing insight into how environmental factors can operate in forecast models, thus paving the way for equation-free mechanistic forecasting to be applied in management contexts.

2014

  • Glaser, Sarah M., Michael J. Fogarty, Hui Liu, Irit Altman, Chih-Hao Hsieh, Les Kaufman, Alec D. MacCall, Andrew A. Rosenberg, Hao Ye, and George Sugihara. 2014. Complex dynamics may limit prediction in marine fisheries. Fish and fisheries 15 (4):616-633.
    [Source] [Abstract]
    Complex nonlinear dynamics in marine fisheries create challenges for prediction and management, yet the extent to which they occur in fisheries is not well known. Using nonlinear forecasting models, we analysed over 200 time series of survey abundance and landings from two distinct ecosystems for patterns of dynamic complexity (dimensionality and nonlinear dynamics) and predictability. Differences in system dimensionality and nonlinear dynamics were associated with time series that reflected human intervention via fishing effort, implying the coupling between human and natural systems generated dynamics distinct from those detected in the natural resource subsystem alone. Estimated dimensionality was highest for landings and higher in abundance indices of unfished species than fished species. Fished species were more likely to display nonlinear dynamics than unfished species, and landings were significantly less predictable than abundance indices. Results were robust to variation in life history characteristics. Dynamics were predictable over a 1-year time horizon in seventy percent of time series, but predictability declined exponentially over a 5-year horizon. The ability to make predictions in fisheries systems is therefore extremely limited. To our knowledge, this is the first cross-system comparative study, and the first at the scale of individual species, to analyse empirically the dynamic complexity observed in fisheries data and to quantify predictability broadly. We outline one application of short-term forecasts to a precautionary approach to fisheries management that could improve how uncertainty and forecast error are incorporated into assessment through catch limit buffers.

  • Glaser, S. M., H. Ye, and G. Sugihara. 2014. A nonlinear, low data requirement model for producing spatially explicit fishery forecasts. Fisheries oceanography 23 (1):45-53.
    [Source] [Abstract]
    Spatial variability can confound accurate estimates of catch per unit effort (CPUE), especially in highly migratory species. The incorporation of spatial structure into fishery stock assessment models should ultimately improve forecasts of stock biomass. Here, we describe a nonlinear time series model for producing spatially explicit forecasts of CPUE that does not require ancillary environmental or demographic data, or specification of a model functional form. We demonstrate this method using spatially resolved (1 degrees x1 degrees cells) CPUE time series of North Pacific albacore in the California Current System. The spatial model is highly significant (P<0.00001) and outperforms two spatial null models. We then create a spatial forecast map for years beyond the range of data. Such approaches can guide spatial management of resources and provide a complement to more data-intensive, highly parameterized population dynamics and ecosystem models currently in use.

  • Liu, H., M. J. Fogarty, J. A. Hare, C. H. Hsieh, S. M. Glaser, H. Ye, E. Deyle, and G. Sugihara. 2014. Modeling dynamic interactions and coherence between marine zooplankton and fishes linked to environmental variability. Journal of marine systems 131 120-129.
    [Source] [Abstract]
    The dynamics of marine fishes are closely related to lower trophic levels and the environment. Quantitatively understanding ecosystem dynamics linking environmental variability and prey resources to exploited fishes is crucial for ecosystem-based management of marine living resources. However, standard statistical models typically grounded in the concept of linear system may fail to capture the complexity of ecological processes. We have attempted to model ecosystem dynamics using a flexible, nonparametric class of nonlinear forecasting models. We analyzed annual time series of four environmental indices, 22 marine copepod taxa, and four ecologically and commercially important fish species during 1977 to 2009 on Georges Bank, a highly productive and intensively studied area of the northeast U.S. continental shelf ecosystem. We examined the underlying dynamic features of environmental indices and copepods, quantified the dynamic interactions and coherence with fishes, and explored the potential control mechanisms of ecosystem dynamics from a nonlinear perspective. We found: (I) the dynamics of marine copepods and environmental indices exhibiting clear nonlinearity; (2) little evidence of complex dynamics across taxonomic levels of copepods; (3) strong dynamic interactions and coherence between copepods and fishes; and (4) the bottom-up forcing of fishes and top-down control of copepods coexisting as target trophic levels vary. These findings highlight the nonlinear interactions among ecosystem components and the importance of marine zooplankton to fish populations which point to two forcing mechanisms likely interactively regulating the ecosystem dynamics on Georges Bank under a changing environment.

2013

  • Deyle, E. R., M. Fogarty, C. H. Hsieh, L. Kaufman, A. D. MacCall, S. B. Munch, C. T. Perretti, H. Ye, and G. Sugihara. 2013. Predicting climate effects on pacific sardine. Proceedings of the national academy of sciences of the united states of america 110 (16):6430-6435.
    [Source] [Abstract]
    For many marine species and habitats, climate change and overfishing present a double threat. To manage marine resources effectively, it is necessary to adapt management to changes in the physical environment. Simple relationships between environmental conditions and fish abundance have long been used in both fisheries and fishery management. In many cases, however, physical, biological, and human variables feed back on each other. For these systems, associations between variables can change as the system evolves in time. This can obscure relationships between population dynamics and environmental variability, undermining our ability to forecast changes in populations tied to physical processes. Here we present a methodology for identifying physical forcing variables based on nonlinear forecasting and show how the method provides a predictive understanding of the influence of physical forcing on Pacific sardine.

  • Perretti, C. T., S. B. Munch, and G. Sugihara. 2013. Reply to hartig and dormann: the true model myth. Proceedings of the national academy of sciences of the united states of america 110 (42):E3976-E3977.
    [Source] [Abstract]
    n/a

  • Perretti, C. T., S. B. Munch, and G. Sugihara. 2013. Model-free forecasting outperforms the correct mechanistic model for simulated and experimental data. Proceedings of the national academy of sciences of the united states of america 110 (13):5253-5257.
    [Source] [Abstract]
    Accurate predictions of species abundance remain one of the most vexing challenges in ecology. This observation is perhaps unsurprising, because population dynamics are often strongly forced and highly nonlinear. Recently, however, numerous statistical techniques have been proposed for fitting highly parameterized mechanistic models to complex time series, potentially providing the machinery necessary for generating useful predictions. Alternatively, there is a wide variety of comparatively simple model-free forecasting methods that could be used to predict abundance. Here wepose a rather conservative challenge and ask whether a correctly specified mechanistic model, fit with commonly used statistical techniques, can provide better forecasts than simple model-free methods for ecological systems with noisy nonlinear dynamics. Using four different control models and seven experimental time series of flour beetles, we found that Markov chain Monte Carlo procedures for fitting mechanistic models often converged on best-fit parameterizations far different from the known parameters. As a result, the correctly specified models provided inaccurate forecasts and incorrect inferences. In contrast, a model-free method based on state-space reconstruction gave the most accurate short-term forecasts, even while using only a single time series from the multivariate system. Considering the recent push for ecosystem-based management and the increasing call for ecological predictions, our results suggest that a flexible model-free approach may be the most promising way forward.

  • Perretti, C. T., G. Sugihara, and S. B. Munch. 2013. Nonparametric forecasting outperforms parametric methods for a simulated multispecies system. Ecology 94 (4):794-800.
    [Source] [Abstract]
    Ecosystem dynamics are often complex, nonlinear, and characterized by critical thresholds or phase shifts. To implement sustainable management plans, resource managers need to accurately forecast species abundance. Moreover, an ecosystem-based approach to management requires forecasting the dynamics of all relevant species and the ability to anticipate indirect effects of management decisions. It is therefore crucial to determine which forecasting methods are most robust to observational and structural uncertainty. Here we describe a nonparametric method for multispecies forecasting and evaluate its performance relative to a suite of parametric models. We found that, in the presence of noise, it is often possible to obtain more accurate forecasts from the nonparametric method than from the model that was used to generate the data. The inclusion of data from additional species yielded a large improvement for the nonparametric model, a smaller improvement for the control model, and only a slight improvement for the alternative parametric models. These results suggest that flexible nonparametric modeling should be considered for ecosystem management.

2012

  • Liu, H., M. J. Fogarty, S. M. Glaser, I. Altman, C. H. Hsieh, L. Kaufman, A. A. Rosenberg, and G. Sugihara. 2012. Nonlinear dynamic features and co-predictability of the georges bank fish community. Marine ecology progress series 464 195-207.
    [Source] [Abstract]
    We examined evidence for nonlinear dynamics in fishery-independent survey data for an assemblage of 26 fish species on Georges Bank spanning the period 1963 to 2008. We used nonlinear time series analysis to determine (1) the presence of nonlinear dynamics in fish populations on Georges Bank, (2) the minimum number of dimensions required to effectively describe system dynamics, (3) the strength of patterns of co-predictability among all possible pairs of fish species, and (4) identification of groups of species characterized by similar dynamics. Here, nonlinear behavior refers to non-equilibrium dynamics, including chaos. The population trajectories of all 26 species exhibited strong density-dependent feedback as indicated by a Partial Rate Correlation Function analysis. Significant evidence of complex dynamical behavior was found for approximately 1 in 5 species. Low dimensionality for many of the individual series was identified, suggesting that for a given level of predictability, this system can be represented by a relatively small number of critically important ecological variables. Further, we found high levels of co-predictability among pairwise combinations of individual species. We identified 4 major species groups sharing similar dynamic features on the basis of patterns of co-predictability, and explored potential mechanisms for interpreting the groupings in terms of trophic interactions and life history characteristics.

  • Sugihara, G., R. May, H. Ye, C. H. Hsieh, E. Deyle, M. Fogarty, and S. Munch. 2012. Detecting causality in complex ecosystems. Science 338 (6106):496-500.
    [Source] [Abstract]
    Identifying causal networks is important for effective policy and management recommendations on climate, epidemiology, financial regulation, and much else. We introduce a method, based on nonlinear state space reconstruction, that can distinguish causality from correlation. It extends to nonseparable weakly connected dynamic systems (cases not covered by the current Granger causality paradigm). The approach is illustrated both by simple models (where, in contrast to the real world, we know the underlying equations/relations and so can check the validity of our method) and by application to real ecological systems, including the controversial sardine-anchovy-temperature problem.

2011

  • Deyle, E. R. and G. Sugihara. 2011. Generalized theorems for nonlinear state space reconstruction. Plos one 6 (3):.
    [Source] [Abstract]
    Takens' theorem (1981) shows how lagged variables of a single time series can be used as proxy variables to reconstruct an attractor for an underlying dynamic process. State space reconstruction (SSR) from single time series has been a powerful approach for the analysis of the complex, non-linear systems that appear ubiquitous in the natural and human world. The main shortcoming of these methods is the phenomenological nature of attractor reconstructions. Moreover, applied studies show that these single time series reconstructions can often be improved ad hoc by including multiple dynamically coupled time series in the reconstructions, to provide a more mechanistic model. Here we provide three analytical proofs that add to the growing literature to generalize Takens' work and that demonstrate how multiple time series can be used in attractor reconstructions. These expanded results (Takens' theorem is a special case) apply to a wide variety of natural systems having parallel time series observations for variables believed to be related to the same dynamic manifold. The potential information leverage provided by multiple embeddings created from different combinations of variables (and their lags) can pave the way for new applied techniques to exploit the time-limited, but parallel observations of natural systems, such as coupled ecological systems, geophysical systems, and financial systems. This paper aims to justify and help open this potential growth area for SSR applications in the natural sciences.

  • Glaser, S. M., H. Ye, M. Maunder, A. MacCall, M. Fogarty, and G. Sugihara. 2011. Detecting and forecasting complex nonlinear dynamics in spatially structured catch-per-unit-effort time series for north pacific albacore (thunnus alalunga). Canadian journal of fisheries and aquatic sciences 68 (3):400-412.
    [Source] [Abstract]
    The presence of complex, nonlinear dynamics in fish populations, and uncertainty in the structure (functional form) of those dynamics, pose challenges to the accuracy of forecasts produced by traditional stock assessment models. We describe two nonlinear forecasting models that test for the hallmarks of complex behavior, avoid problems of structural uncertainty, and produce good forecasts of catch-per-unit-effort (CPUE) time series in both standardized and nominal (unprocessed) form. We analyze a spatially extensive, 40-year-long data set of annual CPUE time series of North Pacific albacore (Thunnus alalunga) from 1 degrees x 1 degrees cells from the eastern North Pacific Ocean. The use of spatially structured data in compositing techniques improves out-of-sample forecasts of CPUE and overcomes difficulties commonly encountered when using short, incomplete time series. These CPUE series display low-dimensional, nonlinear structure and significant predictability. Such characteristics have important implications for industry efficiency in terms of future planning and can inform formal stock assessments used for the management of fisheries.

  • Sugihara, G., J. Beddington, C. H. Hsieh, E. Deyle, M. Fogarty, S. M. Glaser, R. Hewitt, A. Hollowed, R. M. May, S. B. Munch, C. Perretti, A. A. Rosenberg, S. Sandin, and H. Ye. 2011. Are exploited fish populations stable?. Proceedings of the national academy of sciences of the united states of america 108 (48):E1224-E1225.
    [Source] [Abstract]
    n/a

2010

  • Tsonis, A. A., K. L. Swanson, G. Sugihara, and P. A. Tsonis. 2010. Climate change and the demise of minoan civilization. Climate of the past 6 (4):525-530.
    [Source] [Abstract]
    Climate change has been implicated in the success and downfall of several ancient civilizations. Here we present a synthesis of historical, climatic, and geological evidence that supports the hypothesis that climate change may have been responsible for the slow demise of Minoan civilization. Using proxy ENSO and precipitation reconstruction data in the period 1650-1980 we present empirical and quantitative evidence that El Nino causes drier conditions in the area of Crete. This result is supported by modern data analysis as well as by model simulations. Though not very strong, the ENSO-Mediterranean drying signal appears to be robust, and its overall effect was accentuated by a series of unusually strong and long-lasting El Nino events during the time of the Minoan decline. Indeed, a change in the dynamics of the El Nino/Southern Oscillation (ENSO) system occurred around 3000 BC, which culminated in a series of strong and frequent El Nino events starting at about 1450 BC and lasting for several centuries. This stressful climatic trend, associated with the gradual demise of the Minoans, is argued to be an important force acting in the downfall of this classic and long-lived civilization.

2009

  • Fagre, D. B., C. W. Charles, C. D. Allen, C. Birkeland, F. S. Chapin, P. M. Groffman, G. R. Guntenspergen, A. K. Knapp, A. D. McGuire, P. J. Mulholland, D. P. C. Peters, D. D. Roby, and G. Sugihara. 2009. Thresholds of climate change in ecosystems final report (synthesis and assessment product, 4.2). .
    [Source] [Abstract]
    n/a

  • Hsieh, C. H., H. J. Kim, W. Watson, E. Di Lorenzo, and G. Sugihara. 2009. Climate-driven changes in abundance and distribution of larvae of oceanic fishes in the southern california region. Global change biology 15 (9):2137-2152.
    [Source] [Abstract]
    We examined climatic effects on the geographic distribution and abundance of 34 dominant oceanic fishes in the southern California region using larval fish data collected from the 50-year long California Cooperative Oceanic Fisheries Investigations (CalCOFI) surveys. The oceanic species responses to environmental changes in their geographic distributions were not very pronounced, perhaps because they lived in the deep layer where temperature change was relatively small or because the environmental variation of the CalCOFI region is not strong enough (with an average temperature gradient of the upper 100 m around 91 km degrees C(-1)). Among the 34 taxa, 16 showed a significant distributional shift (median latitude or boundaries) in relation to environmental variables, and eight species significantly shifted their geographic distribution from the 1951-1976 cold period to the 1977-1998 warm period. Interestingly, the vertically migrating taxa more often showed a significant response to environmental variables than the nonmigrating mesopelagic taxa, reflecting the more significant increase in heat content of the upper ocean (< 200 m), compared with the deeper zone (300-500 m) where the mesopelagic fishes typically remain. Climate change has significant effects on the abundances of oceanic fishes. Twenty-four taxa exhibited a significant change in abundance in relation to environmental variables, and 25 taxa, including both warm and cold-water taxa, showed a significant increase in abundance from the cold to warm period. Analysis of physical data indicated that the surface-layer (20-200 m) warmed significantly and the isotherms approached shoreward from the cold to the warm period. We further show that the spatial distribution of coastal-neritic fish retreated shoreward and oceanic fish extended shoreward from the cold to warm period. Our results suggest intensified stratification of the southern California region during the warm period may create a suitable habitat for the oceanic species. Moreover, such an unfavorable condition (e.g. changes in food habitat) for coastal-neritic species might result in competitive release for the oceanic fishes to flourish.

  • Kilcik, A., C. N. K. Anderson, J. P. Rozelot, H. Ye, G. Sugihara, and A. Ozguc. 2009. Nonlinear prediction of solar cycle 24. Astrophysical journal 693 (2):1173-1177.
    [Source] [Abstract]
    Sunspot activity is highly variable and challenging to forecast. Yet forecasts are important, since peak activity has profound effects on major geophysical phenomena including space weather (satellite drag, telecommunications outages) and has even been correlated speculatively with changes in global weather patterns. This paper investigates trends in sunspot activity, using new techniques for decadal-scale prediction of the present solar cycle (cycle 24). First, Hurst exponent H analysis is used to investigate the autocorrelation structure of the putative dynamics; then the Sugihara-May algorithm is used to predict the ascension time and the maximum intensity of the current sunspot cycle. Here we report H = 0.86 for the complete sunspot number data set (1700-2007) and H = 0.88 for the reliable sunspot data set (1848-2007). Using the Sugihara-May algorithm analysis, we forecast that cycle 24 will reach its maximum in 2012 December at approximately 87 sunspot units.

  • Scheffer, M., J. Bascompte, W. A. Brock, V. Brovkin, S. R. Carpenter, V. Dakos, H. Held, E. H. van Nes, M. Rietkerk, and G. Sugihara. 2009. Early-warning signals for critical transitions. Nature 461 (7260):53-59.
    [Source] [Abstract]
    Complex dynamical systems, ranging from ecosystems to financial markets and the climate, can have tipping points at which a sudden shift to a contrasting dynamical regime may occur. Although predicting such critical points before they are reached is extremely difficult, work in different scientific fields is now suggesting the existence of generic early-warning signals that may indicate for a wide class of systems if a critical threshold is approaching.

  • Sugihara, G., J. Gruver, K. Haeflinger, and H. Ye. 2009. Reducing chinook salmon bycatch with market-based incentives: individual tradable encounter credits (itec). .
    [Source] [Abstract]
    A market based bycatch credits-trading plan, using individual (vessel-level) tradable encounter credits (ITEC), is examined that addresses the incentive requirements of the C-2 Motion PPA. This recommended approach for an Industry Market Incentive Plan is shown to provide robust vessel-level incentives to reduce Chinook salmon bycatch under all levels of Chinook and Pollock abundance and can act cumulatively through time to further reduce overall fleet Chinook encounter rates. Sectors are given fixed annual allocations of salmon encounter(bycatch) credits (1 ITEC = 1 Chinook) in amounts as describedin the C-2 motion document underthe industry-wide hardcap of68,392. These are then distributedto individual vessels via the coopsaccording to a specificallydesigned uniform allocation rule(the Legacy Allocation Rule) thatprovides vessel-level incentives toavoid Chinook salmon encountersand explicitly addresses each of the C-2 motion requirements. Vesselscan use or trade credits within andacross sectors to offset salmonbycatch encounters and thesetransfers of ITEC are moderated byrules (currently under discussion) that further strengthen C-2 incentives and prevent potential abuses (eg. Dynamic Salmon Savings).

  • Swanson, K. L., G. Sugihara, and A. A. Tsonis. 2009. Long-term natural variability and 20th century climate change. Proceedings of the national academy of sciences of the united states of america 106 (38):16120-16123.
    [Source] [Abstract]
    Global mean temperature at the Earth's surface responds both to externally imposed forcings, such as those arising from anthropogenic greenhouse gases, as well as to natural modes of variability internal to the climate system. Variability associated with these latter processes, generally referred to as natural long-term climate variability, arises primarily from changes in oceanic circulation. Here we present a technique that objectively identifies the component of inter-decadal global mean surface temperature attributable to natural long-term climate variability. Removal of that hidden variability from the actual observed global mean surface temperature record delineates the externally forced climate signal, which is monotonic, accelerating warming during the 20th century.

2008

  • Anderson, C. N. K., C. H. Hsieh, S. A. Sandin, R. Hewitt, A. Hollowed, J. Beddington, R. M. May, and G. Sugihara. 2008. Why fishing magnifies fluctuations in fish abundance. Nature 452 (7189):835-839.
    [Source] [Abstract]
    It is now clear that fished populations can fluctuate more than unharvested stocks. However, it is not clear why. Here we distinguish among three major competing mechanisms for this phenomenon, by using the 50- year California Cooperative Oceanic Fisheries Investigations ( CalCOFI) larval fish record. First, variable fishing pressure directly increases variability in exploited populations. Second, commercial fishing can decrease the average body size and age of a stock, causing the truncated population to track environmental fluctuations directly. Third, age- truncated or juvenescent populations have increasingly unstable population dynamics because of changing demographic parameters such as intrinsic growth rates. We find no evidence for the first hypothesis, limited evidence for the second and strong evidence for the third. Therefore, in California Current fisheries, increased temporal variability in the population does not arise from variable exploitation, nor does it reflect direct environmental tracking. More fundamentally, it arises from increased instability in dynamics. This finding has implications for resource management as an empirical example of how selective harvesting can alter the basic dynamics of exploited populations, and lead to unstable booms and busts that can precede systematic declines in stock levels.

  • Hsieh, C. H., C. Anderson, and G. Sugihara. 2008. Extending nonlinear analysis to short ecological time series. American naturalist 171 (1):71-80.
    [Source] [Abstract]
    Nonlinearity is important and ubiquitous in ecology. Though detectable in principle, nonlinear behavior is often difficult to characterize, analyze, and incorporate mechanistically into models of ecosystem function. One obvious reason is that quantitative nonlinear analysis tools are data intensive (require long time series), and time series in ecology are generally short. Here we demonstrate a useful method that circumvents data limitation and reduces sampling error by combining ecologically similar multispecies time series into one long time series. With this technique, individual ecological time series containing as few as 20 data points can be mined for such important information as (1) significantly improved forecast ability, (2) the presence and location of nonlinearity, and (3) the effective dimensionality ( the number of relevant variables) of an ecological system.

  • Hsieh, C. H., C. S. Reiss, R. P. Hewitt, and G. Sugihara. 2008. Spatial analysis shows that fishing enhances the climatic sensitivity of marine fishes. Canadian journal of fisheries and aquatic sciences 65 (5):947-961.
    [Source] [Abstract]
    We compare the changes in geographic distribution of exploited fish species versus unexploited ones living in the same environment. For this comparative study, we use the 50- year larval fish time series from the California Cooperative Oceanic Fisheries Investigations, which allows us to view fishing as a treatment effect in a long-term ecological experiment. Our results indicate that exploited species show a clearer distributional shift in response to environmental change than unexploited species, even after accounting for life history and ecological traits and phylogeny. The enhanced response (improved signal- noise ratio) to environmental change in exploited species may be a consequence of reduced spatial heterogeneity caused by fishery- induced age (size) truncation and the constriction of geographic distribution that accompanies fishing pressure. We suggest that reduced spatial heterogeneity can cause exploited populations to be more vulnerable to climate variability, an effect that could have considerable importance in the management of fish stocks. This is the first study to compare the geographic distributions of a large suite of exploited and unexploited fish species from the northeastern Pacific in response to climate variability.

  • May, Robert M., Simon A. Levin, and George Sugihara. 2008. Ecology for bankers. Nature 451 (21):893-895.
    [Source] [Abstract]
    n/a

2007

  • Maye, A., C. H. Hsieh, G. Sugihara, and B. Brembs. 2007. Order in spontaneous behavior. Plos one 2 (5):.
    [Source] [Abstract]
    Brains are usually described as input/output systems: they transform sensory input into motor output. However, the motor output of brains (behavior) is notoriously variable, even under identical sensory conditions. The question of whether this behavioral variability merely reflects residual deviations due to extrinsic random noise in such otherwise deterministic systems or an intrinsic, adaptive indeterminacy trait is central for the basic understanding of brain function. Instead of random noise, we find a fractal order (resembling Levy flights) in the temporal structure of spontaneous flight maneuvers in tethered Drosophila fruit flies. Levy-like probabilistic behavior patterns are evolutionarily conserved, suggesting a general neural mechanism underlying spontaneous behavior. Drosophila can produce these patterns endogenously, without any external cues. The fly's behavior is controlled by brain circuits which operate as a nonlinear system with unstable dynamics far from equilibrium. These findings suggest that both general models of brain function and autonomous agents ought to include biologically relevant nonlinear, endogenous behavior-initiating mechanisms if they strive to realistically simulate biological brains or out-compete other agents.

  • Sugihara, G.. 2007. Tradable bycatch credits create new markets that reward careful fishing. Conservation magazine 8 (3):29-30.
    [Source] [Abstract]
    n/a

2006

  • Hsieh, C. H., C. S. Reiss, J. R. Hunter, J. R. Beddington, R. M. May, and G. Sugihara. 2006. Fishing elevates variability in the abundance of exploited species. Nature 443 (7113):859-862.
    [Source] [Abstract]
    The separation of the effects of environmental variability from the impacts of fishing has been elusive, but is essential for sound fisheries management. We distinguish environmental effects from fishing effects by comparing the temporal variability of exploited versus unexploited fish stocks living in the same environments. Using the unique suite of 50-year-long larval fish surveys from the California Cooperative Oceanic Fisheries Investigations we analyse fishing as a treatment effect in a long-term ecological experiment. Here we present evidence from the marine environment that exploited species exhibit higher temporal variability in abundance than unexploited species. This remains true after accounting for life-history effects, abundance, ecological traits and phylogeny. The increased variability of exploited populations is probably caused by fishery-induced truncation of the age structure, which reduces the capacity of populations to buffer environmental events. Therefore, to avoid collapse, fisheries must be managed not only to sustain the total viable biomass but also to prevent the significant truncation of age structure. The double jeopardy of fishing to potentially deplete stock sizes and, more immediately, to amplify the peaks and valleys of population variability, calls for a precautionary management approach.

  • Southwood, T. R. E., R. M. May, and G. Sugihara. 2006. Observations on related ecological exponents. Proceedings of the national academy of sciences of the united states of america 103 (18):6931-6933.
    [Source] [Abstract]
    We observe a relationship among three independently derived power laws in ecology: (i) total number of species versus area, (ii) species frequency versus species length, and (iii) maximal body size versus area. Aside from showing how these historically disparate phenomena are connected, we show how recent empirical results relating the maximal body size of top terrestrial vertebrates to the square root of land area conform to a prior theoretical expectation given by two of the above power laws. Of particular interest is the observation that the exponent relating species length to species frequency suggests a dimension for niche space for terrestrial vertebrate assemblages of D approximate to 3/2. This value, along with power law for maximal body size, versus area, gives rise to the canonical species area exponent z approximate to 1/4.

2005

  • Hsieh, C. H., S. M. Glaser, A. J. Lucas, and G. Sugihara. 2005. Distinguishing random environmental fluctuations from ecological catastrophes for the north pacific ocean. Nature 435 (7040):336-340.
    [Source] [Abstract]
    The prospect of rapid dynamic changes in the environment is a pressing concern that has profound management and public policy implications(1,2). Worries over sudden climate change and irreversible changes in ecosystems are rooted in the potential that nonlinear systems have for complex and 'pathological' behaviours(1,2). Nonlinear behaviours have been shown in model systems(3) and in some natural systems(1,4-8), but their occurrence in large-scale marine environments remains controversial(9,10). Here we show that time series observations of key physical variables(11-14) for the North Pacific Ocean that seem to show these behaviours are not deterministically nonlinear, and are best described as linear stochastic. In contrast, we find that time series for biological variables(5,15-17) having similar properties exhibit a low-dimensional nonlinear signature. To our knowledge, this is the first direct test for nonlinearity in large-scale physical and biological data for the marine environment. These results address a continuing debate over the origin of rapid shifts in certain key marine observations as coming from essentially stochastic processes or from dominant nonlinear mechanisms(1,9,10,18-20). Our measurements suggest that large-scale marine ecosystems are dynamically nonlinear, and as such have the capacity for dramatic change in response to stochastic fluctuations in basin-scale physical states.

  • Hsieh, C. H., C. Reiss, W. Watson, M. J. Allen, J. R. Hunter, R. N. Lea, R. H. Rosenblatt, P. E. Smith, and G. Sugihara. 2005. A comparison of long-term trends and variability in populations of larvae of exploited and unexploited fishes in the southern california region: a community approach. Progress in oceanography 67 (1-2):160-185.
    [Source] [Abstract]
    We have constructed an 'expert-knowledge classification system' to categorize 309 fish taxa in the California Cooperative Oceanic Fisheries Investigations ichthyoplankton database into primary (coastal, coastal-oceanic, and oceanic) assemblages based on their principal ecological domains and subsequently, secondary assemblages according to the habitat affinities of adults. We examined effects of fishing, climate, adult habitat, and age-at-maturation on long-term variation of fish populations. We tested the hypothesis that populations of unexploited taxa, track climatic trends more closely than those of exploited taxa insofar as climatic signals may be confounded by fishing effects. Most oceanic taxa (23/34) showed a significant relationship with environmental variables and followed the trend of the Pacific Decadal Oscillation. Very few coastal (3/10) and coastal-oceanic (3/23) taxa exhibited a significant relationship with environmental signals; however, several fluctuated coherently, and age-at-maturation is an important factor. The lack of close correlation between fish populations and environmental signals in the coastal and coastal-oceanic assemblages indicates that these species might show nonlinear biological responses to external forcing rather than a simple linear tracking of environmental variables. We did not find a systematic pattern indicating that fishing influenced population fluctuation of exploited species. Constrained comparisons of exploited to unexploited species living in the same habitat and reaching maturity at the same age revealed evidence of overexploitation for some species but not for all. Our results suggest that considering life history and ecological characteristics of fish species and applying a community approach are important in understanding fishing effects on fish populations in the context of a changing environment.

2003

  • Sugihara, G., L. F. Bersier, T. R. E. Southwood, S. L. Pimm, and R. M. May. 2003. Predicted correspondence between species abundances and dendrograms of niche similarities. Proceedings of the national academy of sciences of the united states of america 100 (9):5246-5251.
    [Source] [Abstract]
    We examine a hypothesized relationship between two descriptions of community structure: the niche-overlap dendrogram that describes the ecological similarities of species and the pattern of relative abundances. Specifically, we examine the way in. which this relationship follows from the niche hierarchy model, whose fundamental assumption is a direct connection between abundances and underlying hierarchical community organization. We test three important, although correlated, predictions of the niche hierarchy model and show that they are upheld in a set of 11 communities (encompassing fishes, amphibians, lizards, and birds) where both abundances and dendrograms were reported. First, species that are highly nested in the dendrogram are on average less abundant than species from branches less subdivided. Second, and more significantly, more equitable community abundances are associated with more evenly branched dendrogram structures, whereas less equitable abundances are associated with less even dendrograms. This relationship shows that abundance patterns can give insight into less visible aspects of community organization. Third, one can recover the distribution of proportional abundances seen in assemblages containing two species by treating each branch point in the dendrogram as a two-species case. This reconstruction cannot be achieved if abundances and the dendrogram are unrelated and suggests a method for hierarchically decomposing systems. To our knowledge, this is the first test of a species abundance model based on nontrivial predictions as to the origins and causes of abundance patterns, and not simply on the goodness-of-fit of distributions.

2000

  • Courchamp, F., M. Langlais, and G. Sugihara. 2000. Rabbits killing birds: modelling the hyperpredation process. Journal of animal ecology 69 (1):154-164.
    [Source] [Abstract]
    1. Introduced rabbits are known to have catastrophic effects on oceanic islands, either by direct destruction of the vegetative cover, or by the resulting disturbance of indigenous vertebrates. 2. Another dramatic effect, less well known, but potentially of major importance, is the hyperpredation process. This process, related to apparent competition, predicts that an introduced prey species, well adapted to high predation pressure, could induce the extinction of an indigenous prey, through the sudden increased population size of an introduced predator. In many island ecosystems, the simultaneous presence of introduced feral cats and rabbits is thus potentially a further threat for small vertebrates endemic of these islands. 3. Through a mathematical model, we tested this hypothesis, using a tri-trophic system comprising an indigenous prey (birds), an introduced prey (rabbits) and an introduced predator (cats), and we demonstrated the theoretical existence of the hyperpredation process. 4. In addition, the numerical analysis of the model allowed a quantification of this process. It shows that the conditions required for an indigenous species to cope with the hyperpredation process imply very high intrinsic growth rates and/or carrying capacity, as well as behavioural anti-predator response to the introduced predator. Since these conditions are unlikely to be met, this process is a further potential threat to most indigenous vertebrate prey. 5. Finally, our model shows that, although it can be induced by both types of adaptation together or alone, behavioural adaptations alone are more powerful in generating the hyperpredation process, than are life history traits adaptations.

1999

  • Bersier, L. F., P. Dixon, and G. Sugihara. 1999. Scale-invariant or scale-dependent behavior of the link density property in food webs: a matter of sampling effort?. American naturalist 153 (6):676-682.
    [Source] [Abstract]
    n/a

  • Courchamp, F., M. Langlais, and G. Sugihara. 1999. Cats protecting birds: modelling the mesopredator release effect. Journal of animal ecology 68 (2):282-292.
    [Source] [Abstract]
    1. Introduced predators account for a large part of the extinction of endemic insular species, which constitutes a major component of the loss of biodiversity among vertebrates. Eradication of alien predators from these ecosystems is often considered the best solution. 2. In some ecosystems, however, it can generate a greater threat for endemic prey through what is called the 'mesopredator release'. This process predicts that, once superpredators are suppressed, a burst of mesopredators may follow which leads their shared prey to extinction. 3. This process is studied through a mathematical model describing a three species system (prey-mesopredator-superpredator). Analysis of the modal, with and without control of meso- and superpredators, shows that this process does indeed exist and can drive shared prey to rapid extinction. 4. This work emphasizes that, although counter-intuitive, eradication of introduced superpredators, such as feral domestic cats, is not always the best solution to protect endemic prey when introduced mesopredators, such as rats, are also present.

  • Courchamp, F., M. Langlais, and G. Sugihara. 1999. Control of rabbits to protect island birds from cat predation. Biological conservation 89 (2):219-225.
    [Source] [Abstract]
    Both introduced predators (e.g. domestic cats) and introduced small grazers (e.g. rabbits) are harmful to many island vertebrate species. The effects of cats on indigenous species are direct (predation), whereas the most obvious effects of rabbits are often indirect and in the longer term. Thus, in situations where both cats and rabbits are present, priority is frequently given to control of cats. However, the presence of rabbits can allow an increased predator population which can lead to extinction of the indigenous and less well adapted prey species, and increase the difficulty of predator control. Through a mathematical model, we show that control of introduced prey facilitates the control of the introduced predator population. Moreover, predator control may fail to protect the indigenous prey if control of the introduced prey is not undertaken simultaneously. Therefore, control of both introduced species is the best strategy.

  • Courchamp, F. and G. Sugihara. 1999. Modeling the biological control of an alien predator to protect island species from extinction. Ecological applications 9 (1):112-123.
    [Source] [Abstract]
    Introduced feral cat (Felis catus) populations are an important threat to many island vertebrate populations and to bird species in particular. Elimination of feral cat populations is desirable in most of these ecosystems. Release of a parasite species in these mostly immune-naive populations is thought to be an efficient eradication measure. Such an approach is theoretically investigated here, using a mathematical model that describes the effects of introducing a virus into the cat population on population dynamics of both the cat and its prey. We studied the effects of two types of introduced feline viruses: Feline Immunodeficiency Virus and Feline Leukemia Virus, both of which are good candidates for eradicating a cat population. Results show that eradication is possible with Feline Leukemia Virus, if natural immunity is sufficiently low. Feline Immunodeficiency Virus cannot fully eradicate cat populations, but can be an effective agent for long-term control of cat populations on islands where total cat eradication is not possible (e.g., there is a high likelihood of continued introduction of cats) or not desirable (e.g., when rats are present). Culling, which by itself would require a very prolonged and logistically demanding effort to eliminate cat populations, may be more efficient when applied simultaneously with virus introduction.

  • Dixon, P. A., M. J. Milicich, and G. Sugihara. 1999. Episodic fluctuations in larval supply. Science 283 (5407):1528-1530.
    [Source] [Abstract]
    The lack of a clear relationship between spawning output and recruitment success continues to confound attempts to understand and manage temporally variable fish populations. This relationship for a common reef fish is shown to be obscured by nonlinear processes in operation during the larval phase. Non-linear responses of larval fish to their noisy physical environment may offer a general explanation for the erratic, often episodic, replenishment of open marine populations.

  • Sugihara, G., M. Casdagli, E. Habjan, D. Hess, P. Dixon, and G. Holland. 1999. Residual delay maps unveil global patterns of atmospheric nonlinearity and produce improved local forecasts. Proceedings of the national academy of sciences of the united states of america 96 (25):14210-14215.
    [Source] [Abstract]
    We use residual-delay maps of observational field date for barometric pressure to demonstrate the structure of latitudinal gradients in nonlinearity in the atmosphere. Nonlinearity is weak and largely lacking in tropical and subtropical sites and increases rapidly into the temperate regions where the time series also appear lo be much noisier. The degree of nonlinearity closely follows the meridional variation of midlatitude storm track frequency. We extract the specific functional form of this nonlinearity, a V shape in the lagged residuals that appears to be a basic feature of midlatitude synoptic weather systems associated with frontal passages. We present evidence that this form arises from the relative time scales of high-pressure versus low-pressure events. Finally, we show that this nonlinear feature is weaker in a well regarded numerical forecast model (European Centre for Medium-Range Forecasts) because small-scale temporal and spatial variation is smoothed out in the grided inputs. This is significant, in that it allows us to demonstrate how application of statistical corrections based on the residual-delay map may provide marked increases in local forecast accuracy, especially for severe weather systems.

1998

  • Segundo, J. P., G. Sugihara, P. Dixon, M. Stiber, and L. F. Bersier. 1998. The spike trains of inhibited pacemaker neurons seen through the magnifying glass of nonlinear analyses. Neuroscience 87 (4):741-766.
    [Source] [Abstract]
    This communication describes the new information that may be obtained by applying nonlinear analytical techniques to neurobiological time-series. Specifically, we consider the sequence of interspike intervals T-i (the 'timing') of trains recorded from synaptically inhibited crayfish pacemaker neurons. As reported earlier, different postsynaptic spike train forms (sets of timings with shared properties) are generated by varying the average rate and/or pattern (implying interval dispersions and sequences) of presynaptic spike trains. When the presynaptic train is Poisson (independent exponentially distributed intervals), the form is 'Poisson-driven' (unperturbed and lengthened intervals succeed each other irregularly). When presynaptic trains are pacemaker (intervals practically equal), forms are either 'p:q locked' (intervals repeat periodically), 'intermittent' (mostly almost locked but disrupted irregularly), 'phase walk throughs' (intermittencies with briefer regular portions), or 'messy' (difficult to predict or describe succinctly). Messy trains are either 'erratic' (some intervals natural and others lengthened irregularly) or 'stammerings' (intervals are integral multiples of presynaptic intervals). The individual spike train forms were analysed using attractor reconstruction methods based on the lagged coordinates provided by successive intervals from the time-series T-i. Numerous models were evaluated in terms of their predictive performance by a trial-and-error procedure: the most successful model was taken as best reflecting the true nature of the system's attractor. Each form was characterized in terms of its dimensionality, nonlinearity and predictability. (1) The dimensionality of the underlying dynamical attractor was estimated by the minimum number of variables (coordinates T-i) required to model acceptably the system's dynamics, i.e. by the system's degrees of freedom. Each model tested was based on a different number of T-i; the smallest number whose predictions were judged successful provided the best integer approximation of the attractor's true dimension (not necessarily an integer). Dimensionalities from three to five provided acceptable fits. (2) The degree of nonlinearity was estimated by: (i) comparing the correlations between experimental results and data from linear and nonlinear models, and (ii) tuning model nonlinearity via a distance-weighting function and identifying the either local or global neighborhood size. Lockings were compatible with linear models and stammerings were marginal; nonlinear models were best for Poisson-driven, intermittent and erratic forms. (3) Finally, prediction accuracy was plotted against increasingly long sequences of intervals forecast: the accuracies for Poisson-driven, locked and stammering forms were invariant, revealing irregularities due to uncorrelated noise, but those of intermittent and messy erratic forms decayed rapidly, indicating an underlying deterministic process. The excellent reconstructions possible for messy erratic and for some intermittent forms are especially significant because of their relatively low dimensionality (around 4), high degree of nonlinearity and prediction decay with time. This is characteristic of chaotic systems, and provides evidence that nonlinear couplings between relatively few variables are the major source of the apparent complexity seen in these cases. This demonstration of different dimensions. degrees of nonlinearity and predictabilities provides rigorous support for the categorization of different synaptically driven discharge forms proposed earlier on the basis of more heuristic criteria. This has significant implications. (1) It demonstrates that heterogeneous postsynaptic forms can indeed be induced by manipulating a few presynaptic variables. (2) Each presynaptic timing induces a form with characteristic dimensionality, thus breaking up the preparation into subsystems such that the physical variables in each operate as one formal parameter or degree of freedom. A system's partitions differ because of component subsystems and/or dynamics: the set of all partitions is probably large and continuous. Driver-induced partitions have general theoretical interest, and provide guidelines for identifying the responsible physical variables. (3) Because forms tolerate changing conditions and are encountered widely (e.g., along transients), it is hypothesized that they are elementary building blocks for many synaptic codings. Codings are linear if postsynaptic forms have the same spectral components as the presynaptic pacemaker, or nonlinear if novel components arise as with, respectively, 1:1 locked or erratic trains. This is relevant to network operations where regularity and irregularity are often vital. (4) Rigorously identifying spike train forms in experimental data from living preparations allowed matchings with available theoretical computations and considerations. Relevant models are based either on iterations of maps derived from rhythm resettings by isolated arrivals or on Bonhoeffer-van der Pol formulations: such models generate, respectively, only periodic locking and phase walk throughs, or all forms. This precise and broad conceptual context explains and predicts outcomes, recognizes data/theory discrepancies, and identifies their reasons (e.g., after-effects, noise). (5) Accordingly, forms pertain to universal behavior categories called 'noisy', 'periodic', 'intermittent', 'quasiperiodic' or 'chaotic' whose available theories provide valuable contexts For genuinely physiological issues. Thus, experimental design and thinking benefit from significant insights about the dynamics of pacemaker-driven pacemakers, the simplest of all synaptic codings.

1997

  • Bersier, L. F. and G. Sugihara. 1997. Scaling regions for food web properties. Proceedings of the national academy of sciences of the united states of america 94 (4):1247-1251.
    [Source] [Abstract]
    The robustness of eight common food web properties is examined with respect to web size. We show that the current controversy concerning the scale dependence or scale invariance of these properties can be resolved by acting for scaling constraints introduced by webs of very small size. We demonstrate statistically that the most robust way to view these properties is not to lump webs of all sizes, but to divide them Into two distinct categories. For the present data set, small webs containing 12 or fewer species exhibit scale dependence, and larger webs containing more than 12 species exhibit scale invariance.

  • Bersier, L. F. and G. Sugihara. 1997. Species abundance patterns: the problem of testing stochastic models. Journal of animal ecology 66 (5):769-774.
    [Source] [Abstract]
    1. Tokeshi (1990) proposed a goodness-of-fit test to distinguish among a general class of stochastic species abundance models using field data. This test is a good first step, but it is impaired by some shortcomings: there is no adjustment for the number of species (the rejection rate increases with the number of species in a data set); the variance of the generated abundance distributions are not taken into account (data sets with higher variance than a model are not rejected). 2. We propose an alternative Monte Carlo test that overcomes these problems. This is a versatile test that can be used with any stochastic model generating distributions.

  • Sugihara, G., L. F. Bersier, and K. Schoenly. 1997. Effects of taxonomic and trophic aggregation on food web properties. Oecologia 112 (2):272-284.
    [Source] [Abstract]
    Historically, ecologists have been more interested in organisms feeding at the tops of food chains than in organisms feeding at or near the bottom. The problem of taxonomic and trophic inconsistency within and among described food webs is central to criticisms of contemporary food web research. To study the effects of taxonomic and trophic aggregation on food web properties, 38 published food webs, each containing a large fraction of investigator-defined biological species, were systematically aggregated by taxonomy and trophic (functional) group similarity. During each step of taxonomic and trophic aggregation, eight food web properties (MIN, MAX. mean chain lengths; the fractions of basal, intermediate and top species; the ratio of all links by the total number of species, L/S; and rigid circuits) were calculated and their departures from the original, unaggregated version were recorded. We found only two properties showing wide systematic departure from initial values after both taxonomic and trophic group aggregation: the fraction of basal species and L/S. One reason for the relative 'constancy' of the six other properties was due in part to large numbers of trophically equivalent species (species with identical sets of prey and predators) found in these and other published webs. In the 38 webs. the average number of trophically equivalent species was 45% and ranged from a low of 13% in aquatic webs to a high of 71% in certain terrestrial systems (i.e., carrion webs). Six of the eight properties (MIN, MAX and mean chain lengths, the fractions of top and basal species, and the L/S ratio) were found to be more sensitive to taxonomic than to trophic aggregation. The relatively smaller variations observed in trophically lumped versions suggest that food web properties more aptly reflect functional, rather than taxonomic, attributes of real food webs. These findings parallel earlier trophic-based results, and bolster the conclusion that uneven lumping of taxonomic and trophic groups in published food web reports do not modify markedly the scaling behaviour of most of their descriptive properties.

1996

  • Bersier, L. F. and G. Sugihara. 1996. Scale invariance versus size dependence in food web properties. Rev. suisse zool. 103 799.
    [Source] [Abstract]
    n/a

  • Bersier, L. F. and G. Sugihara. 1996. A correspondence between two classical notions of community structure. Rev. suisse zool. 102 855.
    [Source] [Abstract]
    n/a

  • Sugihara, G., W. Allan, D. Sobel, and K. D. Allan. 1996. Nonlinear control of heart rate variability in human infants. Proceedings of the national academy of sciences of the united states of america 93 (6):2608-2613.
    [Source] [Abstract]
    Nonlinear analyses of infant heart rhythms reveal a marked rise in the complexity of the electrocardiogram with maturation, We find that normal mature infants (gestation greater than or equal to 35 weeks) have complex and distinctly nonlinear heart rhythms (consistent with recent reports for healthy adults) but that such nonlinearity is lacking in preterm infants (gestation less than or equal to 27 weeks) where parasympathetic-sympathetic interaction and function are presumed to be less well developed. Our study further shows that infants with clinical brain death and those treated with atropine exhibit a similar lack of nonlinear feedback control, These three lines of evidence support the hypothesis championed by Goldberger et al, [Goldberger, A. L., Rigney, D. R. & West, B. J. (1990) Sci, Am, 262, 43-49] that autonomic nervous system control underlies the nonlinearity and possible chaos of normal heart rhythms. This report demonstrates the acquisition of nonlinear heart rate dynamics and possible chaos in developing human infants and its loss in brain death and with the administration of atropine. It parallels earlier work documenting changes in the variability of heart rhythms in each of these cases and suggests that nonlinearity may provide additional power in characterizing physiological states.

1995

  • Dixon, Paul, Alistair Hobday, and George Sugihara. 1995. Review of ‘fractals in science’, armin bunde, shlomo havlin (eds.). springer-verlag, oxford (1994). Bulletin of mathematical biology 57 (6):939-941.
    [Source] [Abstract]
    n/a

  • Sugihara, George and Alistair Hobday. 1995. One thousand words = one millipicture; review of ‘fractals in biology and medicine’ by t. f. nonnenmacker, g. a. losa, e. r. weibel (eds.), birkhauser (1994). Trends in ecology & evolution 10 (2):89-90.
    [Source] [Abstract]
    n/a

1994

  • Sugihara, G.. 1994. Nonlinear forecasting for the classification of natural time series. Philosophical transactions of the royal society of london series a-mathematical physical and engineering sciences 348 (1688):477-495.
    [Source] [Abstract]
    There is a growing trend in the natural sciences to view time series as products of dynamical systems. This viewpoint has proven to be particularly useful in stimulating debate and insight into the nature of the underlying generating mechanisms. Here I review some of the issues concerning the use of forecasting in the detection of nonlinearities and possible chaos, particularly with regard to stochastic chaos. Moreover, it is shown how recent attempts to measure meaningful Lyapunov exponents for ecological data are fundamentally flawed, and that when observational noise is convolved with process noise, computing Lyapunov exponents for the real system will be difficult. Such problems pave the way for more operational definitions of dynamic complexity (cf. Yao and Tong, this volume). Aside from its use in the characterization of chaos, nonlinear forecasting can be used more broadly in pragmatic classification problems. Here I review a recent example of nonlinear forecasting as it is applied to classify human heart rhythms. In particular, it is shown how forecast nonlinearity can be a good discriminator of the physiological effects of age, and how prediction-decay may discriminate heart-disease. In so doing, I introduce a method for characterizing nonlinearity using 'S-maps' and a method for analysing multiple short time series with composite attractors.

1993

  • Yamazaki, H., G. Sugihara, G. J. Kirkpatrick, and D. Kamykowski. 1993. Is the photosynthetic process nonlinear?. Journal of plankton research 15 (11):1297-1308.
    [Source] [Abstract]
    We applied two non-linear time series analysis methods to photosynthetic data obtained from a single-species population of Thalassiosira pseudonana incubated in situ in order to identify whether the time series were generated predominantly by linear or non-linear processes. The tests used to make these distinctions involved a comparison of the predictability of the observed data under a non-linear hypothesis versus a linear hypothesis. Two records were analyzed. For the first data segment taken in the morning, the linear method performed as well or better than the nonlinear methods. Although a weak non-linearity was detected in the second data set observed in the afternoon, the time series is dominantly linear. The best embedding dimension, whose value suggests the number of participating independent parameters in the system, is 2 for the morning data and 7 for the afternoon data. These results are true for aggregate productivity measures (1.8 x 10^8 cells) on a time scale of 1-5 min.

1990

  • Sugihara, G., B. Grenfell, and R. M. May. 1990. Distinguishing error from chaos in ecological time series. Philosophical transactions of the royal society of london series b-biological sciences 330 (1257):235-251.
    [Source] [Abstract]
    Over the years, there has been much discussion about the relative importance of environmental and biological factors in regulating natural populations. Often it is thought that environmental factors are associated with stochastic fluctuations in population density, and biological ones with deterministic regulation. We revisit these ideas in the light of recent work on chaos and nonlinear systems. We show that completely deterministic regulatory factors can lead to apparently random fluctuations in population density, and we then develop a new method (that can be applied to limited data sets) to make practical distinctions between apparently noisy dynamics produced by low-dimensional chaos and population variation that in fact derives from random (high-dimensional)noise, such as environmental stochasticity or sampling error. To show its practical use, the method is first applied to models where the dynamics are known. We then apply the method to several sets of real data, including newly analysed data on the incidence of measles in the United Kingdom. Here the additional problems of secular trends and spatial effects are explored. In particular, we find that on a city-by-city scale measles exhibits low-dimensional chaos (as has previously been found for measles in New York City), whereas on a larger, country-wide scale the dynamics appear as a noisy two-year cycle. In addition to shedding light on the basic dynamics of some nonlinear biological systems, this work dramatizes how the scale on which data is collected and analysed can affect the conclusions drawn.

  • Sugihara, G. and R. M. May. 1990. Applications of fractals in ecology. Trends in ecology & evolution 5 (3):79-86.
    [Source] [Abstract]
    Fractal models describe the geometry of a wide variety of natural objects such as coastlines, island chains, coral reefs, satellite ocean-color images and patches of vegetation. Cast in the form of modified diffusion models, they can mimic natural and artificial landscapes having different types of complexity of shape. This article provides a brief introduction to fractals and reports on how they can be used by ecologists to answer a variety of basic questions, about scale, measurement and hierarchy in, ecological systems.

  • Sugihara, G. and R. M. May. 1990. Nonlinear forecasting as a way of distinguishing chaos from measurement error in time series. Nature 344 (6268):734-741.
    [Source] [Abstract]
    An approach is presented for making short-term predictions about the trajectories of chaotic dynamical systems. The method is applied to data on measles, chickenpox, and marine phytoplankton populations, to show how apparent noise associated with deterministic chaos can be distinguished from sampling error and other sources of externally induced environmental noise.

1989

  • Sugihara, G.. 1989. How do species divide resources?. American naturalist 133 (3):458-463.
    [Source] [Abstract]
    n/a

  • Sugihara, G., K. Schoenly, and A. Trombla. 1989. Scale invariance in food web properties. Science 245 (4913):48-52.
    [Source] [Abstract]
    The robustness of five common food web properties is examined by varying the resolution of the data through aggregation of trophic groupings. A surprising constancy in each of these properties is revealed as webs are collapsed down to approximately half their original size. This analysis of 60 invertebrate-dominated community food webs confirms the existence of all but one of these properties in such webs and addresses a common concern held by critics of food web theory that observed food web properties may be sensitive to trophic aggregation. The food web statistics (chain length; predator/prey ratio; fraction of top, intermediate, and bottom species; and rigid circuits) are scaling in the sense that they remain roughly invariant over a wide range of data resolution. As such, within present standards of reporting food web data, these statistics may be used to compare systems whose trophic data are resolved differently within a factor of 2.

1988

  • O’Neill, R. V., J. R. Krummel, R. H. Gardner, G. Sugihara, B. Jackson, D. L. DeAngelis, B. T. Milne, M. G. Turner, B. Zygmunt, S. W. Christensen, V. H. Dale, and R. L. Graham. 1988. Indices of landscape pattern. Landscape ecology 1 (3):153-162.
    [Source] [Abstract]
    Landscape ecology deals with the patterning of ecosystems in space. Methods are needed to quantify aspects of spatial pattern that can be correlated with ecological processes. The present paper develops three indices of pattern derived from information theory and fractal geometry. Using digitized maps, the indices are calculated for 94 quadrangles covering most of the eastern United States. The indices are shown to be reasonably independent of each other and to capture major features of landscape pattern. One of the indices, the fractal dimension, is shown to be correlated with the degree of human manipulation of the landscape.

1987

  • Krummel, J. R., R. H. Gardner, G. Sugihara, R. V. Oneill, and P. R. Coleman. 1987. Landscape patterns in a disturbed environment. Oikos 48 (3):321-324.
    [Source] [Abstract]
    Deciduous forest patterns were evaluated, using fractal analysis, in the U. S. Geological Survey 1: 250,000 Natchez Quadrangle, a region that has experienced relatively recent conversion of forest cover to cropland. A perimeter-area method was used to determine the fractal dimension; the results show a different dimension for small compared with large forest patches. This result is probably related to differences in the scale of human versus natural processes that affect this particular forest pattern. By identifying transition zones in the scale at which landscape patterns change this technique shows promise for use in developing hypotheses related to scale-dependent processes and as a simple metric to evaluate changes on the earth's surface using remotely sensed data.

  • Sugihara, G.. 1987. Hirata’s stability analysis defended. International journal of systems science 18 (7):1391-1393.
    [Source] [Abstract]
    Recent correspondence (Loehle 1985) claiming to {\textquoteleft}refute' Hirata's (1980) model of material cycling in a closed ecosystem is shown to be in error owing to a fundamental misunderstanding of the model and its aims.

1986

  • Sugihara, G.. 1986. Shuffled sticks: on calculating nonrandom niche overlaps. American naturalist 127 (4):554-560.
    [Source] [Abstract]
    An analytical method is presented for detecting nonrandom niche displacement that might result from competition by examining the degree to which niche overlap is minimized along a single niche dimension. Species' utilization spectra for different resources are viewed as intervals, or 'sticks,' arranged over a finite linear resource continuum. The method tests the actual extent to which the observed configuration of sticks overlaps less than would be expected if the sticks were cast down at random. Data previously analyzed to refute the importance of niche displacement (Poole and Rathke 1980) have been found to support it when reanalyzed with a computer simulation of the shuffled-sticks model (Cole 1981).

1984

  • Livdahl, T. P. and G. Sugihara. 1984. Non-linear interactions of populations and the importance of estimating per-capita rates of change. Journal of animal ecology 53 (2):573-580.
    [Source] [Abstract]
    (1) We derive a computational formula for estimating the per capita rate of change in experimental cohorts when detailed schedules for reproduction and survival during the reproductive period are impractical to obtain. For experiments that manipulate densities, this calculation can provide estimates for the unlimited population growth rate (rm), the equilibrium carrying capacity (K), and the intensity of interspecific interactions. (2) These methods are applied to life history data for treehole mosquitoes to underscore the potential shortcomings of analysing separate life-history features in testing the adequacy of simple linear models of population growth. We demonstrate that non-linearities which arise when survivorship and fecundity are treated separately may cancel when gathered into a well-behaved estimate of population growth.

1983

  • Siegel, A. F. and G. Sugihara. 1983. Moments of particle size distributions under sequential breakage with applications to species abundance. Journal of applied probability 20 (1):158-164.
    [Source] [Abstract]
    The sequential broken stick model has appeared in numerous contexts, including biology, physics, engineering and geology. Kolmogorov showed that under appropriate conditions, sequential breakage processes often yield a lognormal distribution of particle sizes. Of particular interest to ecologists is the observed variance of the logarithms of the sizes, which characterizes the evenness of an assemblage of species. We derive the first two moments for the logarithms of the sizes in terms of the underlying distribution used to determine the successive breakages. In particular, for a process yielding n pieces, the expected sample variance behaves asymptotically as log(n ). These results also yield a new identity for moments of path lengths in random binary trees.

1982

  • Sugihara, G.. 1982. Diversity as a concept and its measurement: comment. Journal of the american statistical association 77 (379):564-565.
    [Source] [Abstract]
    n/a

1981

  • Sugihara, G.. 1981. S = CA<sup>z</sup>. American naturalist 117 (5):790-793.
    [Source] [Abstract]
    n/a

  • Sugihara, G. and K. Heston. 1981. Field notes on winter flocks of the ocellated turkey (agriocharis ocellata). Auk 98 (2):396-398.
    [Source] [Abstract]
    n/a

1980

  • Sugihara, G.. 1980. Minimal community structure: an explanation of species abundance patterns. American naturalist 116 (6):770-787.
    [Source] [Abstract]
    Recent proposals that the canonical lognormal distribution and the resulting species-area constant, z 1/4, are artifacts of the general lognormal curve and regression techniques, are shown to be inadequate. An alternative hypothesis is suggested which accounts for these regularities in terms of a hierarchical community structure represented by a sequentially divided niche space. This hierarchical pattern, which can be considered to be a minimal form of community structure, derives from evolutionary and ecological considerations for generating species diversity, and is shown to account for the observed abundance structures of small ensembles as well as large natural communities. Evidence is presented which implies that niche apportionment between species may involve the random division of more than one resource, and an interesting invariance in the pattern of apportionment is observed for assemblages with three species. The possibility that the canonical lognormal distribution is a conceptual artifact resulting from arbitrary systems of classification is considered and shown to be false. Aside from its intuitive appeal, the model presented should be of interest because it offers explanations of two ubiquitous patterns in nature: the canonical lognormal and the resulting species-area constant.