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Abrupt changes in system states and dynamical behaviors are often observed in natural systems; such phenomena, named regime shifts, are explained as transitions between alternative steady states (more generally, attractors). Various methods have been proposed to detect regime shifts from time series data, but a generic detection method with theoretical linkage to underlying dynamics is lacking. Here, we provide a novel method named Nested-Library Analysis (NLA) to retrospectively detect regime shifts using empirical dynamic modeling (EDM) rooted in theory of attractor reconstruction. Specifically, NLA determines the time of regime shift as the cutting point at which sequential reduction of the library set (i.e., the time series data used to reconstruct the attractor for forecasting) optimizes the forecast skill of EDM. We illustrate this method on a chaotic model of which changing parameters present a critical transition. Our analysis shows that NLA detects the change point in the model system and outperforms existing approaches based on statistical characteristics. In addition, NLA empirically detected a real-world regime shift event revealing an abrupt change of Pacific Decadal Oscillation index around the mid-1970s. Importantly, our method can be easily generalized to various systems because NLA is equation-free and requires only a single time series.

ABSTRACT Trade-offs between competitive ability and resistance to top-down control manifest the “kill-the-winner” hypothesis that explains how mortality caused by protists and viruses can promote bacterial diversity. However, the existence of such trade-offs has rarely been investigated in natural marine bacterial communities. To address this question, we conducted on-board dilution experiments to manipulate top-down control pressure (protists only or protists plus viruses [protists+viruses] combined) and then applied 16S rRNA gene high-throughput sequencing techniques to assess the responses of each bacterial taxon. Dilution experiments enabled us to measure the top-down-control-free growth rate as the competitive ability and top-down-control-caused mortality as the reverse of resistance to top-down control. Overall, bacterial taxa with higher top-down-control-free growth rates were accompanied by lower top-down-control-caused resistance. Furthermore, competition-resistance trade-offs were stronger and more consistent when top-down control was caused by protists+viruses combined than by protists only. When protists+viruses were diluted, the bacterial rank abundance distribution became steepened and evenness and richness were decreased. However, when protists were diluted, only richness decreased. Our results indicate the existence of competition-resistance trade-offs in marine microbes and demonstrate the positive impacts of such trade-offs on bacterial diversity. Regardless, the strength of the competition-resistance trade-offs and the impacts on bacterial diversity were contingent on whether top-down control was caused by protists+viruses combined or protists only. IMPORTANCE We addressed the “kill-the-winner” hypothesis from the perspective of its principle (the competition-resistance trade-off) in marine bacterial communities incubated in situ. Our results supported the existence of competition-resistance trade-offs and the positive effect on bacterial community diversity. The study linked theoretical expectations and complex natural systems and provided new knowledge regarding how top-down controls and competition trade-offs shaped natural bacterial communities.

Disentangling causal interactions among biodiversity, ecosystem functioning and environmental factors is key to understanding how ecosystems respond to changing environment. This study presents a global scale analysis quantifying causal interactions and feedbacks among phytoplankton diversity, biomass and nutrients along environmental gradients of aquatic ecosystems.

ABSTRACT The presence of more species in the community of a sampling site (α diversity) typically increases ecosystem functions via nonrandom processes like resource partitioning. When considering multiple communities, we hypothesize that higher compositional difference (β diversity) increases overall functions of these communities. Further, we hypothesize that the β diversity effect is more positive when β diversity is increased by nonrandom assembly processes. To test these hypotheses, we collected bacterioplankton along a transect of 6 sampling sites in the southern East China Sea in 14 cruises. For any pairs of the 6 sites within a cruise, we calculated the Bray-Curtis index to represent β diversity and summed bacterial biomass as a proxy to indicate the overall function of the two communities. We then calculated deviation of observed mean pairwise phylogenetic similarities among species in two communities from random to represent the influences of nonrandom processes. The bacterial β diversity was found to positively affect the summed bacterial biomass; however, the effect varied among cruises. Cross-cruise comparison indicated that the β diversity effect increased with the nonrandom processes selecting for phylogenetically dissimilar species. This study extends biodiversity-ecosystem functioning research to the scale of multiple sites and enriches the framework by considering community assembly processes. IMPORTANCE The implications of our analyses are twofold. First, we emphasize the importance of studying β diversity. We expanded the current biodiversity-ecosystem functioning framework from single to multiple sampling sites and investigated the influences of species compositional differences among sites on the overall functioning of these sites. Since natural ecological communities never exist alone, our analyses allow us to more holistically perceive the role of biodiversity in natural ecosystems. Second, we took community assembly processes into account to attain a more mechanistic understanding of the impacts of biodiversity on ecosystem functioning.

Abstract 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‐dependent habitat selection. Population spatial variability elevates with increasing age truncation, and the response is stronger for populations with stronger age‐specific habitat preference. On a gradient landscape, reducing carrying capacity elevates the relative importance of density dependence in habitat selection, which weakens the response of spatial variability to age truncation for populations with strong age‐specific habitat preference. On a fragmented landscape, both populations with strong and weak age‐specific habitat preferences are restricted at local optimal habitats, and reducing carrying capacity weakens the responses of spatial variability to age truncation for both populations. Synthesis and applications. We demonstrate that to track and predict the changes in population spatial variability under exploitation, it is essential to consider the interactive effects of age‐specific habitat preference, carrying capacity, and landscape structure. To improve spatial management in fisheries, it is crucial to enhance empirical and theoretical developments in the methodology to quantify age‐specific habitat preference of marine fish, and to understand how climatic change influences carrying capacity and landscape continuity.

Abstract Plankton live in dynamic fluid environments. Their ability to change in response to different hydrodynamic cues is critical to their energy allocation and resource uptake. This study used a microfluidic device to evaluate the rheotactic behaviors of a model dinoflagellate species, Karlodinium veneficum, in different flow conditions. Although dinoflagellates experienced forced alignment in strong shear (i.e. “trapping”), fluid straining did not play a decisive role in their rheotactic movements. Moderate hydrodynamic magnitude (20

Extracting causality from time series on natural populations is challenging. Here the authors apply empirical dynamical modeling to 25 years of fish survey data from North Sea fisheries to quantify causal effects of age structure, abundance, and environment on population spatial variability, finding both common and species-specific patterns.

The Kuroshio is the western boundary current of the North Pacific Ocean. In the subtropical region of eastern Taiwan, a coastal uplift of the isotherms has occurred. To explore its impact on this oligotrophic ecosystem, hydrographic data along the transect line at 23.75°N were measured between September 2012 and September 2014. Results show that the intensity of coastal uplift was positively correlated to the flow volume transport of the Kuroshio. Significant dissolved inorganic nutrients were uplifted to the sunlit zone, especially in the onshore. For example, compared to the offshore, nitrate concentration increased 0.49 μM (or ∼178%) in the upper 100 m of the onshore. The increased nutrients thereafter enhanced the growth of phytoplankton; for instance, the Chl a concentration increased 88.3%, compared to offshore, in the upper 100 m of the onshore. Phytoplankton community was mostly composed of picophytoplankton (

Environmental and climatic changes are expected to redistribute species, altering the strengths of species interaction networks; however, long-term and large-scale evaluations remain elusive. One way to infer species interaction networks is by analyzing their geographical overlaps, which provides indices of species interdependence, such as mean spatial robustness (MSR), which represents the geographical impact of a species on other species, and mean spatial sensitivity (MSS), which indicates how a species is influenced by other species. Integrating MSR and MSS further allows us to assess community coexistence stability and structure, with a stronger negative relationship between MSR and MSS (i.e., species are unequally dependent on each other) within a community at a given time suggesting a more stable community. Here, we assessed multidecadal changes in adult marine fish communities using bottom trawl datasets across latitudes from 1982 to 2011 in the Eastern US Continental Shelf, North Sea, and Eastern Bering Sea. Consistent, significant long-term increasing temporal trends of MSR and MSS were found in all three large marine communities. MSR exhibited strong correlations with species’ range sizes, especially in high-latitude communities, while MSS was strongly positively correlated with species’ median proportion of overlap with interacting species. The relationships between MSR and MSS were generally negative, indicating stably coexisting fish communities. However, the negative relationships weakened over time, implying that the coexisting fish communities gradually became unstable. Our findings provide an assessment of changes in spatially geographical aspects of multiple species, for decades and at mid- to high latitudes, to allow the detection of global ecological changes in marine systems by alternative estimation of geographic overlaps of species interaction networks. Such species co-occurrence estimation can help stay vigilant of strategies for accelerating climate change mitigation particularly at coarser spatial scales.

Biological organic carbon production and consumption play a fundamental role in the understanding of organic carbon cycling in oceans. However, studies on them in the Kuroshio, the western boundary current in the North Pacific Ocean, are scarce. To better understand the variations of plankton community respiration (CR) and particulate organic carbon (POC), eight cruises. which covered four seasons over a 2-year period, were surveyed across the Kuroshio at the KTV1 transect east of Taiwan. Spatially, a coastal uplift of isotherms (i.e., onshore lifting and offshore deepening) was observed along the KTV1 transect. During the uplift, the cold and nutrient-rich deep waters shoal to shallow water and enhance phytoplankton growth, resulting in higher values of phytoplankton, POC, and plankton CR on the onshore side. In this study, phytoplankton was dominated by picophytoplankton including Prochlorococcus, Synechococcus, and picoeukaryotes. Plankton CR was low, and its mean depth-normalized integrated rate (the upper 100 m water depth) ranged from 7.07 to 22.27 mg C m−3 d−1, to which the picophytoplankton and heterotrophic bacteria contributed the most. The mean depth-normalized integrated value of POC ranged from 12.7 to 21.6 μg C L−1. POC is mainly associated with phytoplankton biomass with a mean carbon ratio of chlorophyll a/POC ≈ 1.03. All results suggest that plankton CR and POC variations may be associated with picoplankton dynamics in the Kuroshio.

Predator and prey α-diversities are often positively associated; yet, understandings of the underlying mechanisms require manipulative experiments and thus remain unclear. We attempt to address this issue by deciphering how α-diversity of predator and prey influences each other’s community assembly processes, which subsequently determine their α-diversity. The occurrence of assembly processes was indicated by the mean pairwise taxonomic index within a community (αMPTI), assuming assembly processes left traceable imprints on species’ phylogeny. Specifically, αMPTI quantifies deviations of observed phylogenetic distances from that of random, so that it can be used to hint at the occurrence of non-random/deterministic assembly processes. Larger αMPTI of a community implies the occurrence of weaker homogenizing deterministic assembly processes, which suggests that this community might be comprised of less similar species and thus has higher α-diversity. We hypothesize that higher predator and prey α-diversity would be positively associated with each other’s αMPTI, which would then be positively associated with their α-diversity. To test the hypothesis, we calculated Shannon diversity and αMPTI for heterotrophic nanoflagellates (HNF; predator) and bacteria (prey) communities in the East China Sea (ECS). The HNF Shannon diversity was found to be positively associated with αMPTI of bacteria, which was then positively associated with bacterial Shannon diversity. In contrast, bacterial Shannon diversity did not correlate with HNF’s αMPTI. We argue that top-down control is one of the explanations to the positive α-diversity association among trophic levels in microbes of the ECS.

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 highest positive relationships with larval fish density. Temperature, salinity, and chlorophyll-a concentration did not significantly explain larval fish density. Based on these findings, we demonstrate the importance of considering prey size when investigating prey availability for larval fishes.

ABSTRACT Performance of a bioreactor is affected by complex microbial consortia that regulate system functional processes. Studies so far, however, have mainly emphasized the selective pressures imposed by operational conditions (i.e., deterministic external physicochemical variables) on the microbial community as well as system performance, but have overlooked direct effects of the microbial community on system functioning. Here, using a bioreactor with ammonium as the sole substrate under controlled operational settings as a model system, we investigated succession of the bacterial community after a disturbance and its impact on nitrification and anammox (anaerobic ammonium oxidation) processes with fine-resolution time series data. System performance was quantified as the ratio of the fed ammonium converted to anammox-derived nitrogen gas (N2) versus nitrification-derived nitrate (npNO3−). After the disturbance, the N2/npNO3− ratio first decreased, then recovered, and finally stabilized until the end. Importantly, the dynamics of N2/npNO3− could not be fully explained by physicochemical variables of the system. In comparison, the proportion of variation that could be explained substantially increased (tripled) when the changes in bacterial composition were taken into account. Specifically, distinct bacterial taxa tended to dominate at different successional stages, and their relative abundances could explain up to 46% of the variation in nitrogen removal efficiency. These findings add baseline knowledge of microbial succession and emphasize the importance of monitoring the dynamics of microbial consortia for understanding the variability of system performance. IMPORTANCE 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 multiple bacterial taxa would account for more system variation than focusing on any particular taxon, highlighting the need to integrate microbial community ecology for understanding system functioning.

Many studies indicate that variation of marine bacterial beta diversity in the horizontal dimension is mainly attributable to environmental and spatial effects. However, whether and how these two effects drive bacterial beta diversity in the vertical dimension remains unclear, especially when considering seasonal variation in the strength of water stratification. Here, we used 78 paired bacterioplankton community samples from surface and deep chlorophyll maximum (DCM) layers along a transect in the Kuroshio region east of Taiwan across multiple seasons. Variance partitioning was used to evaluate the mechanisms driving the vertical beta diversity between surface-DCM bacterioplankton communities during weak stratification periods (i.e., spring and fall) versus strong stratification periods (i.e., summer). During strong periods of stratification, vertical beta diversity was shaped by both environmental and spatial effects; notably, the strength of stratification played an important role in enhancing environmental dissimilarity and creating a barrier to dispersal. In contrast, during periods of weak stratification, environmental effects dominate, with a non-significant spatial effect due to mixing. Variation of vertical beta diversity for bacterioplankton communities in the Kuroshio region east of Taiwan was structured by different mechanisms across seasons, and was further dependent on stratification strength of the water column.

In the California Current Ecosystem, El Niño acts as a natural phenomenon that is partially representative of climate change impacts on marine bacteria at timescales relevant to microbial communities. Between 2014–2016, the North Pacific warm anomaly (a.k.a., the “blob”) and an El Niño event resulted in prolonged ocean warming in the Southern California Bight (SCB). To determine whether this “marine heatwave” resulted in shifts in microbial populations, we sequenced the rpoC1 gene from the biogeochemically important picocyanobacteria Prochlorococcus and Synechococcus at 434 time points from 2009–2018 in the MICRO time series at Newport Beach, CA. Across the time series, we observed an increase in the abundance of Prochlorococcus relative to Synechococcus as well as elevated frequencies of ecotypes commonly associated with low-nutrient and high-temperature conditions. The relationships between environmental and ecotype trends appeared to operate on differing temporal scales. In contrast to ecotype trends, most microdiverse populations were static and possibly reflect local habitat conditions. The only exceptions were microdiversity from Prochlorococcous HLI and Synechococcus Clade II that shifted in response to the 2015 El Niño event. Overall, Prochlorococcus and Synechococcus populations did not return to their pre-heatwave composition by the end of this study. This research demonstrates that extended warming in the SCB can result in persistent changes in key microbial populations.

Abstract Size structure of fish stock plays an important role in maintaining sustainability of the population. Size distribution of an exploited stock is predicted to shift toward small individuals caused by size-selective fishing and/or warming; however, their relative contribution remains relatively unexplored. In addition, existing analyses on size structure have focused on univariate size-based indicators (SBIs), such as mean length, evenness of size classes, or the upper 95-percentile of the length frequency distribution; these approaches may not capture full information of size structure. To bridge the gap, we used the variation partitioning approach to examine how the size structure (composition of size classes) responded to fishing, warming and the interaction. We analyzed 28 exploited stocks in the West US, Alaska and North Sea. Our result shows fishing has the most prominent effect on the size structure of the exploited stocks. In addition, the fish stocks experienced higher variability in fishing is more responsive to the temperature effect in their size structure, suggesting that fishing may elevate the sensitivity of exploited stocks in responding to environmental effects. The variation partitioning approach provides complementary information to univariate SBIs in analyzing size structure.

Viral production (VP) and bacterial mortality by viral lysis critically influence the production and mortality of aquatic bacteria. Although bacterial production, mortality by viral lysis, and viral density have been found to exhibit diel variations, the diel change in viral production has rarely been investigated. In this study, we conducted two diel dilution incubation experiments in a semi-enclosed, nutrient-rich coastal region in northeastern Taiwan to estimate the diel viral production and the mortality by viral lysis. We also compared two methods (linear regression between viral density and time versus arithmetic mean of VP during incubation) of estimating viral production. We found that viral production estimated by linear regression and bacterial mortality by viral lysis were higher during the daytime than during the nighttime. A possible explanation for the high viral production at daytime is that the bacterial community was composed of cell types with higher burst sizes at daytime. We further argued that the classical linear regression method can be used only when viral density significantly linearly increases with time, which does not always occur in dilution incubations. This study offered observations of diel variation in viral dynamics and discussed the methods estimating viral production in a marine environment.

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 particulate organic matter (POM), and temperature. We found that the intensity of trophic cascades weakly decreased with the NBSS slope and increased with temperature; however, both relationships were not statistically significant. We did not find a clear relationship between the strength of the trophic cascades and the C:N ratio of POM. Our results do not support the hypothesis that the proportion of large phytoplankton, the stoichiometric quality of phytoplankton, and the temperature affect trophic cascades. Instead, we suggest that other critical factors, such as protist abundance, play a role in affecting trophic cascades in the plankton food web in the East China Sea. We further propose some issues which should be addressed when conducting in situ shipboard incubation.

Mammalian herbivores rely on microbial activities in an expanded gut chamber to convert plant biomass into absorbable nutrients. Distinct from ruminants, small herbivores typically have a simple stomach but an enlarged cecum to harbor symbiotic microbes; however, knowledge of this specialized gut structure and characteristics of its microbial contents is limited. Here, we used leaf-eating flying squirrels as a model to explore functional characteristics of the cecal microbiota adapted to a high-fiber, toxin-rich diet. Specifically, environmental conditions across gut regions were evaluated by measuring mass, pH, feed particle size, and metabolomes. Then, parallel metagenomes and metatranscriptomes were used to detect microbial functions corresponding to the cecal environment. Based on metabolomic profiles, >600 phytochemical compounds were detected, although many were present only in the foregut and probably degraded or transformed by gut microbes in the hindgut. Based on metagenomic (DNA) and metatranscriptomic (RNA) profiles, taxonomic compositions of the cecal microbiota were dominated by bacteria of the Firmicutes taxa; they contained major gene functions related to degradation and fermentation of leaf-derived compounds. Based on functional compositions, genes related to multidrug exporters were rich in microbial genomes, whereas genes involved in nutrient importers were rich in microbial transcriptomes. In addition, genes encoding chemotaxis-associated components and glycoside hydrolases specific for plant beta-glycosidic linkages were abundant in both DNA and RNA. This exploratory study provides findings which may help to form molecular-based hypotheses regarding functional contributions of symbiotic gut microbiota in small herbivores with folivorous dietary habits.

We have developed a modified FlowCAM procedure for efficiently quantifying the size distribution of zooplankton. The modified method offers the following new features: 1) prevents animals from settling and clogging with constant bubbling in the sample container; 2) prevents damage to sample animals and facilitates recycling by replacing the built-in peristaltic pump with an external syringe pump, in order to generate negative pressure, creates a steady flow by drawing air from the receiving conical flask (i.e. vacuum pump), and transfers plankton from the sample container toward the main flowcell of the imaging system and finally into the receiving flask; 3) aligns samples in advance of imaging and prevents clogging with an additional flowcell placed ahead of the main flowcell. These modifications were designed to overcome the difficulties applying the standard FlowCAM procedure to studies where the number of individuals per sample is small, and since the FlowCAM can only image a subset of a sample. Our effective recycling procedure allows users to pass the same sample through the FlowCAM many times (i.e. bootstrapping the sample) in order to generate a good size distribution. Although more advanced FlowCAM models are equipped with syringe pump and Field of View (FOV) flowcells which can image all particles passing through the flow field; we note that these advanced setups are very expensive, offer limited syringe and flowcell sizes, and do not guarantee recycling. In contrast, our modifications are inexpensive and flexible. Finally, we compared the biovolumes estimated by automated FlowCAM image analysis versus conventional manual measurements, and found that the size of an individual zooplankter can be estimated by the FlowCAM image system after ground truthing.

This study investigated the spatial variation in the components of a microbial food web (viruses, picoplankton, nanoflagellates, and ciliates) in different hydrographic environments in the Taiwan Strait during winter. Water temperature and salinity varied spatially, with lower temperatures (15.3−22.8 °C) and salinities (32.2−33.4 psu) in the northern part of the Taiwan Strait, largely affected by runoff from the coast of China. Concentrations of nutrients and Chl a were significantly higher in the northern part than that in the southern part of the study area. Synechococcus spp., nanoflagellate, and ciliate abundance also varied significantly, with the northern strait having higher abundances of these communities. In contrast, a higher abundance of bacteria was found in the southern part of the Taiwan Strait. The results of this study, which describes two different ecosystems in the Taiwan Strait, suggest that during winter, a “viral loop” might play an important role in controlling bacterial production in the southern part of the Taiwan Strait, while nanofalgellate grazing of picophytoplankton may contribute mainly to the flux of energy in the northern part.

The spatial structure of species richness is often characterized by the species-area relationship (SAR). However, the SAR approach rarely considers the spatial variability of individual plants that arises from species interactions and species' habitat associations. Here, we explored how the interactions of individual plants of target species influence SAR patterns at a range of neighborhood distances. We analyzed the data of 113,988 woody plants of 110 species from the Fushan Forest Dynamics Plot (25 ha), northern Taiwan, which is a subtropical rainforest heavily influenced by typhoons. We classified 34 dominant species into 3 species types (i.e., accumulator, repeller, or no effect) by testing how the individual species-area relationship (i.e., statistics describing how neighborhood species richness changes around individuals) of target species departs (i.e., positively, negatively, or with no obvious trend) from a null model that accounts for habitat association. Deviation from the null model suggests that the net effect of species' interactions increases (accumulate) or decreases (repel) neighborhood species richness. We found that (i) accumulators were dominant at small interaction distances (30 m); (iii) repellers were rarely detected; and (iv) large-sized and abundant species tended to be accumulators. The findings suggest that positive species interactions have the potential to accumulate neighborhood species richness, particularly through size- and density-dependent mechanisms. We hypothesized that the frequently disturbed environment of this subtropical rainforest (e.g., typhoon-driven natural disturbances such as landslides, soil erosion, flooding, and windthrow) might create the spatial heterogeneity of species richness and promote positive species interactions.

Theories and empirical evidence suggest that random dispersal of organisms promotes species coexistence in spatially structured environments. However, directed dispersal, where movement is adjusted with fitness-related cues, is less explored in studies of dispersal-mediated coexistence. Here, we present a metacommunity model of two consumers exhibiting directed dispersal and competing for a single resource. Our results indicated that directed dispersal promotes coexistence through two distinct mechanisms, depending on the adaptiveness of dispersal. Maladaptive directed dispersal may promote coexistence similar to random dispersal. More importantly, directed dispersal is adaptive when dispersers track patches of increased resources in fluctuating environments. Coexistence is promoted under increased adaptive dispersal ability of the inferior competitor relative to the superior competitor. This newly described dispersal-mediated coexistence mechanism is likely favored by natural selection under the trade-off between competitive and adaptive dispersal abilities.

Long-term (1967-2008) glass eel catches were used to investigate climatic effects on the annual recruitment of Japanese eel to Taiwan. Specifically, three prevailing hypotheses that potentially explain the annual recruitment were evaluated. Hypothesis 1: high precipitation shifts the salinity front northward, resulting in favorable spawning locations. Hypothesis 2: a southward shift of the position of the North Equatorial Current (NEC) bifurcation provides a favorable larval transport route. Hypothesis 3: ocean conditions (eddy activities and productivity) along the larval migration route influence larval survival. Results of time series regression and wavelet analyses suggest that Hypothesis 1 is not supported, as the glass eel catches exhibited a negative relationship with precipitation. Hypothesis 2 is plausible. However, the catches are correlated with the NEC bifurcation with a one-year lag. Considering the time needed for larval transport (only four to six months), the one-year lag correlation does not support the direct transport hypothesis. Hypothesis 3 is supported indirectly by the results. Significant correlations were found between catches and climate indices that affect ocean productivity and eddy activities, such as the Quasi Biennial Oscillation (QBO), North Pacific Gyre Oscillation (NPGO), Pacific Decadal Oscillation (PDO), and Western Pacific Oscillation (WPO). Wavelet analysis reveals three periodicities of eel catches: 2.7, 5.4, and 10.3 years. The interannual coherence with QBO and the Niño 3.4 region suggests that the shorter-term climate variability is modulated zonally by equatorial dynamics. The low-frequency coherence with WPO, PDO, and NPGO demonstrates the decadal modulation of meridional teleconnection via ocean-atmosphere interactions. Furthermore, WPO and QBO are linked to solar activities. These results imply that the Japanese eel recruitment may be influenced by multi-timescale climate variability. Our findings call for investigation of extra-tropical ocean dynamics that affect survival of eels during transport, in addition to the existing efforts to study the equatorial system.

Body size and environmental prey availability are both key factors determining feeding habits of gape-limited fish predators. However, our understanding of their interactive or relative effects is still limited. In this study, we performed quantitative dietary analysis of different body sizes of goby (Gymnogobius isaza) specimens collected from Lake Biwa between 1962 and 2004. First, we report that the diet was composed mainly of zooplankton (cladocerans and copepods) before the 1980s, and thereafter, shifted to zoobenthos (gammarids). This foraging shift coincided with, and thus can be linked to, known historical events in the lake at that time: decrease in zooplankton abundance with the alleviation of eutrophication, increase in fish body size resulting from fish population collapse, and increase in gammarid abundance due to reduced fish predation pressure. Supporting this view, our data analyses revealed how the long-term changes in the diet composition would be co-mediated by changes in fish body size and environmental prey availability. Specifically, while zoobenthos abundance strongly affected the fish diet composition, larger (smaller) fish preferred zoobenthos (zooplankton). Furthermore, the body size effects were stronger than those of prey availability. These results provide the best long-term evidence that fish feeding habits vary over decades with its body size and prey community due to anthropogenic disturbances.

Characterizing relationships between individual body size and trophic niche position is essential for understanding how population and food-web dynamics are mediated by size-dependent trophic interactions. However, whether (and how) intraspecific size-trophic relationships (i.e., trophic ontogeny pattern at the population level) vary with time remains poorly understood. Using archival specimens of a freshwater predatory fish Gymnogobius isaza (Tanaka 1916) from Lake Biwa, Japan, we assembled a long-term (>40 years) time-series of the size-dependence of trophic niche position by examining nitrogen stable isotope ratios (delta(15)N) of the fish specimens. The size-dependence of trophic niche position was defined as the slope of the relationship between delta(15)N and log body size. Our analyses showed that the slope was significantly positive in about 60% of years and null in other years, changing through time. This is the first quantitative (i.e., stable isotope) evidence of long-term variability in the size-trophic relationship in a predatory fish. This finding had implications for the fish trophic dynamics, despite that about 60% of the yearly values were not statistically different from the long-term average. We proposed hypotheses for the underlying mechanism of the time-varying size-trophic relationship.

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 Lévy flights) in the temporal structure of spontaneous flight maneuvers in tethered Drosophila fruit flies. Lévy-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.