Transitions between dry and wet hydrologic states are the defining characteristic of non-perennial rivers and streams, which constitute the majority of the global river network. Although past work has focused on stream drying characteristics, there has been less focus on how hydrology, ecology and biogeochemistry respond and interact during stream wetting. Wetting mechanisms are highly variable and can range from dramatic floods and debris flows to gradual saturation by upwelling groundwater. This variation in wetting affects ecological and biogeochemical functions, including nutrient processing, sediment transport and the assembly of biotic communities. Here we synthesize evidence describing the hydrological mechanisms underpinning different types of wetting regimes, the associated biogeochemical and organismal responses, and the potential scientific and management implications for downstream ecosystems. This combined multidisciplinary understanding of wetting dynamics in non-perennial streams will be key to predicting and managing for the effects of climate change on non-perennial ecosystems. This Perspective presents a wetting regime framework that is classified by dominant hydrologic mechanisms and highlights the resulting responses of stream biogeochemistry and community ecology.

Humans have exaggerated natural habitat fragmentation, negatively impacting species dispersal and reducing population connectivity. Habitat fragmentation can be especially detrimental in freshwater populations, whose dispersal is already constrained by the river network structure. Aquatic insects, for instance, are generally limited to two primary modes of dispersal: downstream drift in the aquatic juvenile life stages and flight during the terrestrial winged adult stage. Yet the impacts of large hydropower dams can make rivers uninhabitable for incoming (drifting) juvenile insects, with remaining refugia found only in tributaries. The ability of adult aquatic insects to traverse such river stretches in search of suitable tributary habitat likely depends on factors such as species-specific dispersal ability and distance between tributaries. To explore the intersection of natural and human-induced habitat fragmentation on aquatic insect dispersal ability, we quantified population genetics of three taxa with varying dispersal abilities, a caddisfly (Hydropsychidae, Hydropsyche oslari), a mayfly (Baetidae: Fallceon quilleri), and a water strider (Veliidae: Rhagovelia distincta), throughout tributaries of the Colorado River in the Grand Canyon, Arizona, USA. Using 2bRAD reduced genome sequencing and landscape genetics analyses, we revealed a strong pattern of isolation by distance among mayfly populations. This contrasts with caddisfly and water strider populations, which were largely panmictic. Analysis of thousands of informative single nucleotide polymorphisms showed that realized dispersal ability may not be accurately predicted by species traits for these widespread species. Principal components analysis revealed a strong division between caddisfly populations upstream and downstream of Havasu Creek (279 km through the 390 km study reach), suggesting that the geography of the Grand Canyon imposes a dispersal barrier for this species. Our use of genetic tools in the Grand Canyon to understand population structure has enabled us to elucidate dispersal barriers for aquatic insects. Ultimately, these data may be useful in informing effective conservation management plans for understudied organisms of conservation interest.

Ecological communities are shaped by biotic interactions as well as environmental forces, and both must be incorporated to obtain models capable of forecasting realistic community dynamics. Many community models first specify pairwise biotic interactions and then secondarily examine how extrinsic factors such as abiotic conditions affect species abundances. A disadvantage of this approach is that the species interactions themselves are often environment and context specific, making parameterization difficult. We propose an alternative approach, matrix community models (MCMs), which are sets of matrix population models linked by an assumption of aggregate density dependence. MCMs incorporate detailed species autecology but are neutral with respect to pairwise species interactions, instead allowing interactions to be revealed within the model structure. These model-revealed species interactions, including competitive exclusion, facilitation, and interference competition, shape the distribution and abundance of species within communities and generate empirically testable predictions about species interactions. We develop a framework for building MCMs using vital rates in a stochastic, multispecies framework. Single-species matrix population models are connected via an assumption of aggregate density dependence, pairwise species interactions are estimated with sensitivity analysis, and community trajectories are analyzed under different environmental regimes using standard statistical tools and network analysis. MCMs have the advantage that pairwise species interactions need not be specified a priori, and that mechanistic demographic-environment linkages permit forecasting of community dynamics under novel, non-stationary environmental regimes. A challenge is that species’ autecological vital rates, such as fecundity, growth and survivorship, must be measured under a diverse range of environmental conditions to parameterize the models. We illustrate the approach with examples and discuss prospects for future theoretical and empirical developments.

Accelerating the design and implementation of environmental flows (e-flows) is essential to curb the rapid, ongoing loss of freshwater biodiversity and the benefits it provides to people. However, the effectiveness of e-flow programs may be limited by a singular focus on ensuring adequate flow conditions at local sites, which overlooks the role of other ecological processes. Recent advances in metasystem ecology have shown that biodiversity patterns and ecosystem functions across river networks result from the interplay of local (environmental filtering and biotic interactions) and regional (dispersal) ecological processes. No guidelines currently exist to account for these processes in designing e-flows. We address this gap by providing a step-by-step operational framework that outlines how e-flows can be designed to conserve or restore metasystem dynamics. Our recommendations are relevant to diverse regulatory contexts and can improve e-flow outcomes even in basins with limited in situ data.

River biodiversity is threatened globally by hydropower dams, and there is a need to understand how dam management favors certain species while filtering out others. We examined aquatic invertebrate communities within the tailwaters 0-24 km downstream of seven large hydropower dams in the Colorado River Basin of the western United States. We quantified aquatic invertebrate dominance, richness, abundance, and biomass at multiple locations within individual tailwaters and across the basin and identified biological community responses associated with dam operations and distance from dam. We found that each tailwater was dominated by 3-7 invertebrate taxa, accounting for 95% of total abundance. Half of these dominant taxa were non-insect, non-flying species and thus were unavailable to terrestrial consumers. Consistent with previous studies, aquatic insects and sensitive taxa were negatively associated with hydropeaking intensity (magnitude of daily flow fluctuations associated with hydropower generation), which limits the composition and potentially the quality of the invertebrate food base. While total invertebrate abundance and biomass did not change with increasing distance downstream from dams, insect and sensitive taxa richness, abundance, and biomass all increased, suggesting that impacts of hydropeaking are most acute immediately downstream of dams. Our results demonstrate that tailwaters experiencing hydropeaking support high abundances of aquatic invertebrate, but the diversity of these communities is low.

Overcoming challenges of water scarcity necessitates creative flow management approaches that account for multiple, potentially competing water needs of plants and animals in river ecosystems. Mechanistic multispecies models can guide decision making by evaluating trade-offs associated with flow regimes designed for specific ecosystem outcomes before implementation. We investigated the cross-ecosystem effects of environmental flow regimes designed to benefit focal groups of riparian vegetation, fishes, and invertebrates. The models revealed trade-offs among different designer flow regimes with narrow taxonomic targets, which in some cases caused non-target taxa to become locally extirpated within short (decadal) timespans. By incorporating multiple flow frequencies - from intra-annual-scale pulses to large decadal-scale floods - the simulated natural flow regime enabled balanced, albeit smaller, population sizes across the three ecosystem components: 72% of that achieved by designer flow regimes, on average. Although returning to a natural flow regime may not be possible in highly flow-modified rivers, novel flow regimes must incorporate diverse flood and drought frequencies to accommodate the occasionally conflicting requirements of different taxa at different times.

Ecosystems are defined, studied, and managed according to boundaries constructed to conceptualize patterns of interest at a certain scale and scope. The distinction between ecosystems becomes obscured when resources from multiple origins cross porous boundaries and are assimilated into food webs through repeated trophic transfers. Ecosystem compartments can define bounded localities in a heterogeneous landscape that simultaneously retain and exchange energy in the form of organic matter. Here we developed and tested a framework to quantify reciprocal reliance on cross-boundary resource exchange and calculate the contribution of primary production from adjacent ecosystem compartments cycling through food webs to support consumers at different trophic levels. Under this framework, an integrated ecosystem can be measured and designated when the boundary between spatially distinct compartments is permeable and the bidirectional exchange of resources contributes significantly to sustaining both food webs. Using a desert river and riparian zone as a case study, we demonstrate that resources exchanged across the aquatic-riparian boundary cycle through multiple trophic levels. Furthermore, predators on both sides of the boundary were supported by externally produced resources to a similar extent, indicating this is a tightly integrated river-riparian ecosystem and that changes to either compartment will substantially impact the other. Using published data on lake ecosystems, we demonstrated that benthic and pelagic ecosystem compartments are likely not fully integrated, but differences between lakes could be used to test ecological hypotheses. Finally, we discuss how the integrated ecosystem framework could be applied in urban-preserve and field-forest ecosystems to address a broad range of ecological concepts. Because few systems function in complete isolation, this novel approach has application to research and management strategies globally as ecosystems continue to face novel pressures that precipitate cascading ecological repercussions well beyond a bounded system of focus.

Top predator foraging strategy and prey base community composition can influence food web structure and function. To investigate the role of functional trait diversity and taxonomic richness in determining food chain length and energy flow in high elevation desert streams, we examined aquatic invertebrate community data along with carbon and nitrogen stable isotope analysis of a top predator, Abedus herberti (giant water bug). We also examined isotopic niche differences across different levels of population structure and seasons. We hypothesized that communities with higher richness would have longer food chains. We found food chain length did not vary substantially across a wide taxonomic and functional richness gradient, which contradicts theoretical mechanisms stating that more resources or higher functional diversity should lead to longer food chains. The isotopic niche of A. herberti was conserved across seasons and sites, and the majority of carbon in tissues came from allochthonous materials. Stable isotopes suggested that A. herberti occupy similar feeding niches in spring and autumn, despite seasonal changes in stream conditions, leaf litter inputs, and invertebrate community structure. Due to the strong aquatic–terrestrial linkages we identified, human activities and climate-driven alterations to the adjacent terrestrial environment may affect the dynamics and integrity of the within-stream ecosystem.

10 Overcoming the physical limits of dam operations under nonstationarity will require cre11 ative approaches to ow management and modeling approaches that forecast the e ects of 12 management actions on multiple ecosystem components simultaneously. Using a novel mul13 tispecies modeling approach, we investigated the cross-ecosystem e ects of environmental 14 ow regimes designed for speci c ecosystem outcomes. We reveal tradeo s associated with 15 ow regimes targeting riparian vegetation, shes, and invertebrates. The di erent frequen16 cies associated with each ow regime in some cases caused non-target ecosystem components 17 to become locally extirpated within 50 years. By incorporating multiple ow frequencies, the 18 natural ow regime enabled a balanced but sub-optimal response of the three ecosystem com19 ponents (mean 72% of designer ow). Although returning to a natural ow regime may not be 20 possible in highly managed rivers, novel ow regimes must incorporate diverse frequencies 21 inherent to such a regime and accomodate the sometimes con icting requirements of di erent 22 taxa at di erent times. 23

Partial migration is a unique form of phenotypic diversity wherein migrant and non-migrant individuals coexist together in a population. Recent research has shown that the partial migration can be an evolutionarily stable strategy (ESS) and convergent stable strategy (CSS) if migrants and non-migrants experience density-dependent competition among individuals of the same type during reproduction. However, not all partially migratory species experience this particular form of competition during reproduction. In this paper, we investigate how various degrees of competition between migrants and non-migrants influence whether or not partial migration is an ESS and CSS. We find that the degree of competition influences the evolutionary outcome of partial migration and provides sharp thresholds relating these degrees of competition to the carrying capacities of both phenotypes.

Understanding how novel biological assemblages are structured in relation to dynamic environmental regimes remains a central challenge in ecology. Demographic approaches to modeling species assemblages show promise because they seek to represent fundamental relationships between population dynamics and environmental conditions. In dryland rivers, rapidly changing climate conditions have shifted drought and flooding regimes with implications for fish communities. Our goals were to (1) develop a mechanistic multispecies demographic model that links native and nonnative species with river flow regimes, and (2) evaluate demographic responses in population and community structure to changing flow regimes. Each fish species was represented by a stage-structured matrix, and species were coupled together into a multispecies framework through density-dependent relationships in reproduction. Then, community dynamics were simulated through time using annual flow events classified from gaged streamflow data. We parameterized the model with vital rates and flow-response relationships for a community of native and nonnative fishes using literature-derived values. We applied the simulation model to the Verde River (Arizona, USA), a major tributary within the Colorado River Basin, for the past half century (1%4-2017). Model validation revealed a match between model projections and relative abundance trends observed in a long-term fish monitoring dataset (1994-2008). At the beginning of the validation period (1994), model and survey observations showed that native species comprised approximately 80% of total abundance. Model projections beyond the survey data (2008-2017) predicted a shift from a native dominant to a normative dominant assemblage, coinciding with increasing drought frequency. Trade-offs between native and nonnative species dominance emerged from differences in mortality in response to the changing sequence of major flow events including spring floods, summer high flows, and droughts. In condusion, the demographic approach presented here provides a flexible modeling framework that is readily applied to other stream systems and species by adjusting or transferring, when appropriate, species vital rates and flow-event thresholds.

As the climate warms, we can’t restore waterways to pristine condition, but models can predict potential changes, argue Jonathan D. Tonkin, N. LeRoy Poff and colleagues. As the climate warms, we can’t restore waterways to pristine condition, but models can predict potential changes, argue Jonathan D. Tonkin, N. LeRoy Poff and colleagues.

That biodiversity declines with latitude is well known, but whether a metacommunity process is behind this gradient has received limited attention. We tested the hypothesis that dispersal limitation is progressively replaced by mass effects with increasing latitude, along with a series of related hypotheses. We explored these hypotheses by examining metacommunity structure in stream invertebrate metacommunities spanning the length of New Zealand’s two largest islands (∼1,300 km), further disentangling the role of dispersal by deconstructing assemblages into strong and weak dispersers. Given the highly dynamic nature of New Zealand streams, our alternative hypothesis was that these systems are so unpredictable (at different stages of post-flood succession) that metacommunity structure is highly context dependent from region to region. We rejected our primary hypotheses, pinning this lack of fit on the strong unpredictability of New Zealand’s dynamic stream ecosystems and fauna that has evolved to cope with these conditions. While local community structure turned over along this latitudinal gradient, metacommunity structure was highly context dependent and dispersal traits did not elucidate patterns. Moreover, the emergent metacommunity types exhibited no trends, nor did the important environmental variables. These results provide a cautionary tale for examining singular metacommunities. The considerable level of unexplained contingency suggests that any inferences drawn from one-off snapshot sampling may be misleading and further points to the need for more studies on temporal dynamics of metacommunity processes.

This code accompanies: Lytle, D. A., D. M. Merritt, J. D. Tonkin, J. D. Olden, and L. V. Reynolds. (2017). Linking river flow regimes to riparian plant guilds: a community-wide modeling approach. Ecological Applications. For code to run, it requires the accompanied 'Maybell.csv' file in the same directory.

We consider the phenomenon of partial migration which is exhibited by populations in which some individuals migrate between habitats during their lifetime, but others do not. First, using an adaptive dynamics approach, we show that partial migration can be explained on the basis of negative density dependence in the per capita fertilities alone, provided that this density dependence is attenuated for increasing abundances of the subtypes that make up the population. We present an exact formula for the optimal proportion of migrants which is expressed in terms of the vital rates of migrant and non-migrant subtypes only. We show that this allocation strategy is both an evolutionary stable strategy (ESS) as well as a convergence stable strategy (CSS). To establish the former, we generalize the classical notion of an ESS because it is based on invasion exponents obtained from linearization arguments, which fail to capture the stabilizing effects of the nonlinear density dependence. These results clarify precisely when the notion of a "weak ESS", as proposed in Lundberg (2013) for a related model, is a genuine ESS. Secondly, we use an evolutionary game theory approach, and confirm, once again, that partial migration can be attributed to negative density dependence alone. In this context, the result holds even when density dependence is not attenuated. In this case, the optimal allocation strategy towards migrants is the same as the ESS stemming from the analysis based on the adaptive dynamics. The key feature of the population models considered here is that they are monotone dynamical systems, which enables a rather comprehensive mathematical analysis.

Riverine ecosystems are governed by patterns of temporal variation in river flows. This dynamism will change due to climate change and the near-ubiquitous human control of river flows globally, which may have severe effects on species distributions and interactions. We employed a combination of population modelling and network theory to explore the consequences of possible flow regime futures on riparian plant communities, including scenarios of increased drought, flooding and flow homogenization (removal of flow variability). We found that even slight modifications to the historic natural flow regime had significant consequences for the structure of riparian plant networks. Networks of emergent interactions between plant guilds were most connected at the natural flow regime and became simplified with increasing flow alteration. The most influential component of flow alteration was flood reduction, with drought and flow homogenization both having greater simplifying community-wide consequences than increased flooding. These findings suggest that maintaining floods under future climates will be needed to overcome the negative long-term consequences of flow modification on riverine ecosystems.

Disturbances cause high mortality in populations while simultaneously enhancing population growth by improving habitats. These countervailing effects make it difficult to predict population dynamics following disturbance events. To address this challenge, we derived a novel form of the logistic growth equation that permits time-varying carrying capacity and growth rate. We combined this equation with concepts drawn from disturbance ecology to create a general model for population dynamics in disturbance-prone systems. A river flooding example using three insect species (a fast life-cycle mayfly, a slow life-cycle dragonfly and an ostracod) found optimal trade-offs between disturbance frequency vs. magnitude and a close fit to empirical data in 62% of cases. A savanna fire analysis identified fire frequencies of 3-4 years that maximised population size of a perennial grass. The model shows promise for predicting population dynamics after multiple disturbance events and for management of river flows and fire regimes.

Diversity of primary producer is often surprisingly high, despite few limiting factors such as nutrients and light to facilitate species coexistence. In theory, the presence of herbivores could increase the diversity of primary producers, resolving this "paradox of the plankton." Little experimental evidence supports this natural enemies hypothesis, but previous tests suffer from several deficiencies. Previous experiments often did not allow for multigeneration effects; utilized low diversity assemblages of herbivores; and limited opportunities for new primary producer and herbivore species to colonize and undergo species sorting that favors some species over others. Using pond plankton, we designed a mesocosm experiment that overcame these problems by allowing more time for interactions over multiple generations, openness to allow new colonists, and manipulated higher diversity of primary producers and grazers than have previous studies. With this design, the presence of zooplankton grazers doubled phytoplankton richness. The additional phytoplankton species in grazed mesocosms were larger, and therefore likely more grazer resistant. Furthermore, phytoplankton richness in grazed mesocosms was similar to that observed in natural ponds whereas it was much lower in mesocosms without grazers. However, stoichiometric imbalance caused by variation in nitrogen : phosphorus ratios and light supply did not alter phytoplankton richness. Therefore, grazers enhanced primary producer richness more strongly than ratios of nutrient supply (even though both grazing and ratios of resource supply altered composition of primary producer assemblages). Taken together, these experimental and field data show that grazing from a diverse assemblage of herbivores greatly elevated richness of phytoplankton producers in pond ecosystems.