Chih-Hao Hsieh - Academia.edu (original) (raw)

Papers by Chih-Hao Hsieh

Nature Communications

The original version of this Article contained an error in the Acknowledgements, which incorrectl... more The original version of this Article contained an error in the Acknowledgements, which incorrectly read: "Data for Lake Võrtsjärv were provided by Estonian Environment Agency and by the Centre for Limnology at Estonian University of Life Sciences funded by the Estonian Research Council grants PRG 1167 and PRG709, and by the European Union's Horizon 2020 research and innovation programme under grant agreement No. 95196." The correct version replaces this sentence with "Data for Lake Võrtsjärv were provided by Estonian Environment Agency and by the Centre for Limnology at Estonian University of Life Sciences funded by the Estonian Research Council grants PRG 1167 and PRG709. This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 951963." This has now been corrected in both the HTML and the PDF versions of the Article.

Nature Communications, 2022

Untangling causal links and feedbacks among biodiversity, ecosystem functioning, and environmenta... more Untangling causal links and feedbacks among biodiversity, ecosystem functioning, and environmental factors is challenging due to their complex and context-dependent interactions (e.g., a nutrient-dependent relationship between diversity and biomass). Consequently, studies that only consider separable, unidirectional effects can produce divergent conclusions and equivocal ecological implications. To address this complexity, we use empirical dynamic modeling to assemble causal networks for 19 natural aquatic ecosystems (N24◦~N58◦) and quantified strengths of feedbacks among phytoplankton diversity, phytoplankton biomass, and environmental factors. Through a cross-system comparison, we identify macroecological patterns; in more diverse, oligotrophic ecosystems, biodiversity effects are more important than environmental effects (nutrients and temperature) as drivers of biomass. Furthermore, feedback strengths vary with productivity. In warm, productive systems, strong nitrate-mediated f...

Diversity, 2021

Copepods have been known to be able to cause an increase in phytoplankton through trophic cascade... more Copepods have been known to be able to cause an increase in phytoplankton through trophic cascades, as copepods consume heterotrophic protists that feed on phytoplankton. However, how the intensity of copepod-induced trophic cascades varies with environmental conditions remains elusive. We hypothesized that a higher proportion of large phytoplankton in the phytoplankton size distribution, a higher stoichiometric quality of phytoplankton, and a higher temperature could mitigate the intensity of a trophic cascade through increasing direct grazing on phytoplankton by copepods. To explore this issue, we quantified the intensity of a trophic cascade as the difference in phytoplankton concentration reduction by grazing using in situ incubations with and without copepods in the East China Sea. We then investigated the relationship between the intensity of trophic cascades versus the slope of the normalized biomass size spectrum (NBSS) of the phytoplankton community, the C:N ratio of partic...

mSystems, 2020

Dynamics of microbial communities are believed to be associated with system functional processes ... more Dynamics of microbial communities are believed to be associated with system functional processes in bioreactors. However, few studies have provided quantitative evidence. The difficulty of evaluating direct microbe-system relationships arises from the fact that system performance is affected by convolved effects of microbiota and bioreactor operational parameters (i.e., deterministic external physicochemical forcing). Here, using fine-resolution time series data (daily sampling for 2 months) under controlled operational settings, we performed an in-depth analysis of system performance as a function of the microbial community in the context of bioreactor physicochemical conditions. We obtained statistically evaluated results supporting the idea that monitoring microbial community dynamics could improve the ability to predict system functioning, beyond what could be explained by operational physicochemical variables. Moreover, our results suggested that considering the succession of m...

ABSTRACTClassic niche theory assumes that species-level functional traits affect species relative... more ABSTRACTClassic niche theory assumes that species-level functional traits affect species relative fitness and thus community structuring, but empirical tests of this assumption are scarce. Moreover, recent evidence shows increasing functional over-redundancy towards the tropics, suggesting that the extent to which functional traits confer species’ fitness and thus impact community structuring differs across latitudes. Here, we develop a new method: comparing the frequencies of trait categories in the species-rank abundance distributions of local communities versus their frequencies in the regional average species pool. We contrasted subarctic versus subtropical copepod communities for six important traits. In subarctic communities, medium-sized and cold-water species are selected to dominate, thus traits affect relative fitness as predicted by classic niche theory. In subtropical communities, most species are small and warm-water, but these categories are not selected to dominate, s...

Despite the consensus that warming will affect biodiversity, alter physicochemical environments, ... more Despite the consensus that warming will affect biodiversity, alter physicochemical environments, and disrupt biological interactions, the relative importance of these key processes and how they interact to determine overall ecosystem function is poorly understood. Here, we analyze long-term (16∼39 years) time series data from ten aquatic ecosystems and use convergent cross mapping (CCM) to quantify the hidden causal network linking species diversity, ecosystem function, and physicochemical factors. We observe that aquatic ecosystems subject to stronger warming exhibit decreased stability (larger fluctuations in phytoplankton biomass). We further show that this effect can be attributed to a weakening of stabilizing causal pathways between biodiversity, nutrient cycling, and phytoplankton biomass. Thus, rather than thinking in terms of separate factors, a more holistic view, that causally links biodiversity and the other ecosystem components, is required to understand and predict clim...

Oikos, 2019

Increases in phytoplankton biomass have been widely observed over the past decades, even in lakes... more Increases in phytoplankton biomass have been widely observed over the past decades, even in lakes experiencing nutrient reduction. However, the mechanisms giving rise to this trend remain unclear. Here, we unveil the potential mechanisms through quantifying the relative contribution of bottom-up versus top-down control in determining biomasses of phytoplankton assemblages in Lake Geneva. Specifically, we apply nonlinear time series analysis, convergent cross mapping (CCM), to decipher the degree of bottom-up versus top-down control among phytoplankton assemblages via quantifying 1) causal links between environmental factors and various phytoplankton assemblages and 2) the relative importance of bottom-up, top-down, and environmental effects. We show that the recent increase in total phytoplankton biomass, albeit with phosphorus reduction, was mainly caused by a particular phytoplankton assemblage which was better adapted to the re-oligotrophicated environment characterized by relatively low phosphorus concentrations and warm water temperature, and poorly controlled by zooplankton grazing. Our findings suggest that zooplankton act as a critical driver of phytoplankton biomass and strongly impact the dynamics of recovery from eutrophication. Therefore, our phytoplankton assemblage approach in combination with causal identification of top-down versus bottom-up controls provides insights into the reason why phytoplankton biomass may increase in lakes undergoing phosphorus reduction.

Ecological Research, 2017

Natural systems are often complex and dynamic (i.e. nonlinear), making them difficult to understa... more Natural systems are often complex and dynamic (i.e. nonlinear), making them difficult to understand using linear statistical approaches. Linear approaches are fundamentally based on correlation. Thus, they are illposed for dynamical systems, where correlation can occur without causation, and causation may also occur in the absence of correlation. ''Mirage correlation'' (i.e., the sign and magnitude of the correlation change with time) is a hallmark of nonlinear systems that results from state dependency. State dependency means that the relationships among interacting variables change with different states of the system. In recent decades, nonlinear methods that acknowledge state dependence have been developed. These nonlinear statistical methods are rooted in state space reconstruction, i.e. lagged coordinate embedding of time series data. These methods do not assume any set of equations governing the system but recover the dynamics from time series data, thus called empirical dynamic modeling (EDM). EDM bears a variety of utilities to investigating dynamical systems. Here, we provide a step-by-step tutorial for EDM applications with rEDM, a free software package written in the R language. Using model examples, we aim to guide users through several basic applications of EDM, including (1) determining the complexity (dimensionality) of a system, (2) distinguishing nonlinear dynamical systems from linear stochastic systems, and quantifying the nonlinearity (i.e. state dependence), (3) determining causal variables, (4) forecasting, (5) tracking the strength and sign of interaction, and (6) exploring the scenario of external perturbation. These methods and applications can be used to provide a mechanistic understanding of dynamical systems.

Journal of Plankton Research, 2016

Functional trait studies are proliferating in plankton ecology, especially studies analysing body... more Functional trait studies are proliferating in plankton ecology, especially studies analysing body size. Yet, empirical studies comparing species versus individual-size structuring are scarce. Here, we conducted a comparison of copepod species-based and individual-size-based community structuring in the East China Sea, and found that: (i) Species, species-based nominal-size and individual-size distributions exhibit very different patterns, and that juveniles (neglected in species counts due to limitation of recognition) tend to dominate in a certain size range. (ii) Species-based structuring is more strongly shaped by physical conditions, while individual-size-based structuring is more strongly shaped by food availability. (iii) Despite these differences, the congruence (i.e. degree of match) between species-based and individual-size-based structuring remains statistically significant. Finally, we tested intrinsic factors potentially explaining the degree of mismatch (i.e. species richness and proxies for: size partitioning of species without accounting for intraspecific variability, intraspecific variability without accounting for ontogeny and ontogeny). (iv) The frequency of juveniles (proxy for ontogeny) is the only intrinsic factor significantly explaining the mismatch between species and size structuring, highlighting the problem of the classic species-based analysis that unavoidably neglects juveniles in the species counts. These results support individual-size as a useful complementary descriptor to species-based studies.

Brains are usually described as input/output systems: they transform sensory input into motor out... more 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 Lé vy flights) in the temporal structure of spontaneous flight maneuvers in tethered Drosophila fruit flies. Lé vy-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.

Proceedings of the National Academy of Sciences, 2013

For many marine species and habitats, climate change and overfishing present a double threat. To ... more 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.

Nature, 2005

The prospect of rapid dynamic changes in the environment is a pressing concern that has profound ... more 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. Recent effort to characterize the decadal-scale behaviour of North Pacific physical and biological phenomena has centred on the concept of 'regime shifts' 18-21. These regime shifts appear as quasistationary states in measured parameters, separated by periods of rapid transition 20. Although attention has been focused on the qualitative phenomenology of these shifts (that is, documenting the appearance of distinct regimes with rapid shifts between them), nowhere in the discussion has their dynamical origin been directly assessed. True regime shifts are not random features of the time series, but are formally associated with the ideas of nonlinear amplification 7 , alternative basins of attraction 20,22 , multiple stable states 2 , hysteresis and fold catastrophe 1,23 , all of which require the underlying dynamics to be nonlinear in origin. For example, while it is quite clear that major changes occurred in the commonly measured North Pacific abiotic and biotic indices around 1976-77 (for example, patterns of sea surface temperature (SST), fisheries landings data, zooplankton abundance and community composition) 18,21 , the nature of such changes remains elusive. Are such changes indicative of the operation of nonlinear dynamics or are they features of the data that might arise stochastically? Some researchers (predominantly physical oceanographers) have suggested that apparent shifts observed in key physical variables are not singular (nonlinear transitional) events but instead represent normal statistical deviations 9,10. Insofar as similar features in marine physical observations can be reproduced stochastically as random

PLOS ONE, 2021

Prey availability plays an important role in determining larval fish survival. Numerous studies h... more Prey availability plays an important role in determining larval fish survival. Numerous studies have found close relationships between the density of mesozooplankton and larval fishes; however, emerging studies suggest that small-size zooplankton are more important prey for some larval fish species. One arising question is whether the size of zooplankton determines the relationship between zooplankton and larval fish community in natural environments. To address this question, we collected small-size (50–200 μm) zooplankton, mesozooplankton (> 330 μm), and larval fish using three different mesh-size (50, 330, 1000 μm, respectively) nets in the East China Sea, and examined their relationships in density. Both meso- and small-size zooplankton densities showed positive relationships with larval fish density, while the relationship is much stronger for the small-size zooplankton. Specifically, the smallest size classes (50–75 and 75–100 μm) of small-size zooplankton showed the highes...

Geophysical Research Letters, 2011

Microbial ecology, 2021

MArine STramenopiles (MASTs) have been recognized as parts of heterotrophic protists and contribu... more MArine STramenopiles (MASTs) have been recognized as parts of heterotrophic protists and contribute substantially to protist abundances in the ocean. However, little is known about their spatiotemporal variations with respect to environmental and biological factors. The objectives of this study are to use canonical correspondence analysis to investigate how MASTs communities are shaped by environmental variables, and co-occurrence networks to examine their potential interactions with prokaryotic communities. Our dataset came from the southern East China Sea (sECS) in the subtropical northwestern Pacific, and involved 14 cruises along a coastal-oceanic transect, each of which sampled surface water from 4 to 7 stations. MASTs communities were revealed by metabarcoding of 18S rDNA V4 region. Most notably, MAST-9 had a high representation in warm waters in terms of read number and diversity. Subclades of MAST-9C and -9D showed slightly different niches, with MAST-9D dominating in more c...

Understanding the mechanisms underlying spatial variability of exploited fish is critical for the... more Understanding the mechanisms underlying spatial variability of exploited fish is critical for the sustainable management of fish stocks. Empirical studies suggest that size‐selective fishing can elevate fish population spatial variability (i.e., more heterogeneous distribution) through age truncation, making the population less resilient to changing environment. However, species differ in how their spatial variability responds to age truncation and the underlying mechanisms remain unclear. We hypothesize that age‐specific habitat preference, together with environmental carrying capacity and landscape structure, determines the response of population spatial variability to fishing‐induced age truncation. To test these hypotheses, we design an individual‐based model of an age‐structured fish population on a two‐dimensional landscape under size‐selective fishing. Individual fish reproduces and survives, and moves between habitats according to age‐specific habitat preference and density‐...

and methods developed are appropriate. However the relatively high number of methods used by the ... more and methods developed are appropriate. However the relatively high number of methods used by the authors and the different initial matrices (obtained after the aggregation of original data), I suggest that the authors make a general schematic representation of their methodology (i.e., a global diagram showing all steps of the analyses and the connections between them). When the methodology will be clear and the options used at each step justiïňĄed (as mentioned in MM section) this will help the reader to capture the key messages from the methodological aspects.

Chih-Hao Hsieh, Tai-Sheng Chiu and Chang-tai Shih (2004) Copepod diversity and composition as ind... more Chih-Hao Hsieh, Tai-Sheng Chiu and Chang-tai Shih (2004) Copepod diversity and composition as indicators of the intrusion of the Kuroshio Branch Current into the northern Taiwan Strait in spring 2000. Zoological Studies 43(2): 393-403. This study was carried out during the waning of the northeastern monsoon, at which time the Kuroshio Branch Current intrudes into the northern Taiwan Strait. The Kuroshio Branch Current was characterized by high temperature and salinity in contrast to the low temperature and salinity of the China Coastal Current. A front was induced south of the Haitan Island, which resulted in a phytoplankton bloom when the China Coastal Current and Kuroshio Branch Current met. The front is marked by a temperature of 18 ± 2 ° C and a salinity of 33 ± 0.5 psu. The intrusion of the Kuroshio Branch Current apparently influenced the species diversity of copepods. Species richness and diversity were higher in the area affected by the Kuroshio Branch Current than that affe...