Beyond simple adaptation: Incorporating other evolutionary processes and concepts into eco-evolutionary dynamics.

Studies of eco-evolutionary dynamics have integrated evolution with ecological processes at multiple scales (populations, communities and ecosystems) and with multiple interspecific interactions (antagonistic, mutualistic and competitive). However, evolution has often been conceptualised as a simple process: short-term directional adaptation that increases population growth. Here we argue that diverse other evolutionary processes, well studied in population genetics and evolutionary ecology, should also be considered to explore the full spectrum of feedback between ecological and evolutionary processes. Relevant but underappreciated processes include (1) drift and mutation, (2) disruptive selection causing lineage diversification or speciation reversal and (3) evolution driven by relative fitness differences that may decrease population growth. Because eco-evolutionary dynamics have often been studied by population and community ecologists, it will be important to incorporate a variety of concepts in population genetics and evolutionary ecology to better understand and predict eco-evolutionary dynamics in nature.

Reversed evolution of grazer resistance to cyanobacteria.

Exploring the capability of organisms to cope with human-caused environmental change is crucial for assessing the risk of extinction and biodiversity loss. We study the consequences of changing nutrient pollution for the freshwater keystone grazer, Daphnia, in a large lake with a well-documented history of eutrophication and oligotrophication. Experiments using decades-old genotypes resurrected from the sediment egg bank revealed that nutrient enrichment in the middle of the 20th century, resulting in the proliferation of harmful cyanobacteria, led to the rapid evolution of grazer resistance to cyanobacteria. We show here that the subsequent reduction in nutrient input, accompanied by a decrease in cyanobacteria, resulted in the re-emergence of highly susceptible Daphnia genotypes. Expression and subsequent loss of grazer resistance occurred at high evolutionary rates, suggesting opposing selection and that maintaining resistance was costly. We provide a rare example of reversed evolution of a fitness-relevant trait in response to relaxed selection.

A unified framework for herbivore-to-producer biomass ratio reveals the relative influence of four ecological factors.

The biomass ratio of herbivores to primary producers reflects the structure of a community. Four primary factors have been proposed to affect this ratio, including production rate, defense traits and nutrient contents of producers, and predation by carnivores. However, identifying the joint effects of these factors across natural communities has been elusive, in part because of the lack of a framework for examining their effects simultaneously. Here, we develop a framework based on Lotka-Volterra equations for examining the effects of these factors on the biomass ratio. We then utilize it to test if these factors simultaneously affect the biomass ratio of freshwater plankton communities. We found that all four factors contributed significantly to the biomass ratio, with carnivore abundance having the greatest effect, followed by producer stoichiometric nutrient content. Thus, the present framework should be useful for examining the multiple factors shaping various types of communities, both aquatic and terrestrial.

Consumer-resource dynamics is an eco-evolutionary process in a natural plankton community.

When traits affecting species interactions evolve rapidly, ecological dynamics can be altered while they occur. These eco-evolutionary dynamics have been documented repeatedly in laboratory and mesocosm experiments. We show here that they are also important for understanding community functioning in a natural ecosystem. Daphnia is a major planktonic consumer influencing seasonal plankton dynamics in many lakes. It is also sensitive to succession in its phytoplankton food, from edible algae in spring to relatively inedible cyanobacteria in summer. We show for Daphnia mendotae in Oneida Lake, New York, United States, that within-year ecological change in phytoplankton (from spring diatoms, cryptophytes and greens to summer cyanobacteria) resulted in consumers evolving increasing tolerance to cyanobacteria over time. This evolution fed back on ecological seasonal changes in population abundance of this major phytoplankton consumer. Oneida Lake is typical of mesotrophic lakes broadly, suggesting that eco-evolutionary consumer-resource dynamics is probably common.

A shady phytoplankton paradox: when phytoplankton increases under low light.

Light is a fundamental driver of ecosystem dynamics, affecting the rate of photosynthesis and primary production. In spite of its importance, less is known about its community-scale effects on aquatic ecosystems compared with those of nutrient loading. Understanding light limitation is also important for ecosystem management, as human activities have been rapidly altering light availability to aquatic ecosystems. Here we show that decreasing light can paradoxically increase phytoplankton abundance in shallow lakes. Our results, based on field manipulation experiments, field observations and models, suggest that, under competition for light and nutrients between phytoplankton and submersed macrophytes, alternative stable states are possible under high-light supply. In a macrophyte-dominated state, as light decreases phytoplankton density increases, because macrophytes (which effectively compete for nutrients released from the sediment) are more severely affected by light reduction. Our results demonstrate how species interactions with spatial heterogeneity can cause an unexpected outcome in complex ecosystems. An implication of our findings is that partial surface shading for controlling harmful algal bloom may, counterintuitively, increase phytoplankton abundance by decreasing macrophytes. Therefore, to predict how shallow lake ecosystems respond to environmental perturbations, it is essential to consider effects of light on the interactions between pelagic and benthic producers.

Fasting or fear: disentangling the roles of predation risk and food deprivation in the nitrogen metabolism of consumers.

Predators can alter nutrient cycles simply by inducing stress in prey. This stress accelerates prey's protein catabolism, nitrogen waste production, and nitrogen cycling. Yet predators also reduce the feeding rates of their prey, inducing food deprivation that is expected to slow protein catabolism and nitrogen cycling. The physiology of prey under predation risk thus balances the influences of predation risk and food deprivation, and this balance is central to understanding the role of predators in nutrient cycles. We explored the separate and combined effects of predation risk and food deprivation on prey physiology and nutrient cycling by exposing guppies (Poecilia reticulata) to predation risk and food deprivation in a 2 × 2 design. We simulated predation risk using chemical cues from a natural predator of guppies, and we created food deprivation by rationing food availability. We measured guppy response as food consumption, growth, tissue energy density, tissue carbon:nitrogen, and nitrogen (N) excretion and assimilation. We found that N-linked physiological processes (N consumption, assimilation, excretion) were strongly affected by predation risk, independent of food consumption. Guppies excreted substantially less under predation risk than they did under food deprivation or control conditions. These results suggest that predation risk, per se, triggers physiological changes in guppies that increase N retention and decrease N excretion. We suggest that slower N metabolism under predation risk is an adaptive response that minimizes protein loss in the face of predictable, predator-induced food restriction. Notably, N metabolism shares common hormonal control with food seeking behavior, and we speculate that increased N retention is a direct and immediate result of reduced food seeking under predation risk. Contrary to predation-stress-based hypotheses for how predators affect nutrient cycling by prey, our result indicates that even short-term exposure to predators may decelerate, rather than accelerate, the speed of N cycling by suppressing N turnover by prey.

What genomic data can reveal about eco-evolutionary dynamics.

Recognition that evolution operates on the same timescale as ecological processes has motivated growing interest in eco-evolutionary dynamics. Nonetheless, generating sufficient data to test predictions about eco-evolutionary dynamics has proved challenging, particularly in natural contexts. Here we argue that genomic data can be integrated into the study of eco-evolutionary dynamics in ways that deepen our understanding of the interplay between ecology and evolution. Specifically, we outline five major questions in the study of eco-evolutionary dynamics for which genomic data may provide answers. Although genomic data alone will not be sufficient to resolve these challenges, integrating genomic data can provide a more mechanistic understanding of the causes of phenotypic change, help elucidate the mechanisms driving eco-evolutionary dynamics, and lead to more accurate evolutionary predictions of eco-evolutionary dynamics in nature.

Can Population Genetics Adapt to Rapid Evolution?

Population genetics largely rests on a 'standard model' in which random genetic drift is the dominant force, selective sweeps occur infrequently, and deleterious mutations are purged from the population by purifying selection. Studies of phenotypic evolution in nature reveal a very different picture, with strong selection and rapid heritable trait changes being common. The time-rate scaling of phenotypic evolution suggests that selection on phenotypes is often fluctuating in direction, allowing phenotypes to respond rapidly to environmental fluctuations while remaining within relatively constant bounds over longer periods. Whether such rapid phenotypic evolution undermines the standard model will depend on how many genomic loci typically contribute to strongly selected traits and how phenotypic evolution impacts the dynamics of genetic variation in a population. Population-level sequencing will allow us to dissect the genetic basis of phenotypic evolution and study the evolutionary dynamics of genetic variation through direct measurement of polymorphism trajectories over time.

Cryptic eco-evolutionary dynamics.

Natural systems harbor complex interactions that are fundamental parts of ecology and evolution. These interactions challenge our inclinations and training to seek the simplest explanations of patterns in nature. Not least is the likelihood that some complex processes might be missed when their patterns look similar to predictions for simpler mechanisms. Along these lines, theory and empirical evidence increasingly suggest that environmental, ecological, phenotypic, and genetic processes can be tightly intertwined, resulting in complex and sometimes surprising eco-evolutionary dynamics. The goal of this review is to temper inclinations to unquestioningly seek the simplest explanations in ecology and evolution, by recognizing that some eco-evolutionary outcomes may appear very similar to purely ecological, purely evolutionary, or even null expectations, and thus be cryptic. We provide theoretical and empirical evidence for observational biases and mechanisms that might operate among the various links in eco-evolutionary feedbacks to produce cryptic patterns. Recognition that cryptic dynamics can be associated with outcomes like stability, resilience, recovery, or coexistence in a dynamically changing world provides added impetus for finding ways to study them.

A newly discovered role of evolution in previously published consumer-resource dynamics.

Consumer-resource interactions are fundamental components of ecological communities. Classic features of consumer-resource models are that temporal dynamics are often cyclic, with a »-period lag between resource and consumer population peaks. However, there are few published empirical examples of this pattern. Here, we show that many published examples of consumer-resource cycling show instead patterns indicating eco-evolutionary dynamics. When prey evolve along a trade-off between defence and competitive ability, two-species consumer-resource cycles become longer and antiphase (half-period lag, so consumer maxima coincide with minima of the resource species). Using stringent criteria, we identified 21 two-species consumer-resource time series, published between 1934 and 1997, suitable to investigate for eco-evolutionary dynamics. We developed a statistical method to probe for a transition from classic to eco-evolutionary cycles, and find evidence for eco-evolutionary type cycles in about half of the studies. We show that rapid prey evolution is the most likely explanation for the observed patterns.

Modes and mechanisms of a Daphnia invasion.

Whether exotic species invade new habitats successfully depends on (i) a change in the invaded habitat that makes it suitable for the invader and (ii) a genetic change in the invading taxon that enhances its fitness in the new habitat, or both. We dissect the causes of invasions of Swiss lakes, north of the Alps, by Daphnia galeata (a zooplankter typical of eutrophic lakes, e.g. those south of the Alps, which are also warmer) by comparing the fitness performance of eight geographically distributed clones that were fed algal-food typical of oligotrophic versus eutrophic conditions at two temperatures. Daphnia longispina, native to oligotrophic Swiss lakes, served as a reference. Daphnia galeata requires eutrophic food to persist, whereas D. longispina survives and grows on oligotrophic food but does even better on eutrophic food. Invasion by D. galeata is further explained because invading clones from the north perform better on eutrophic food and at cooler temperatures than native clones from the south, suggesting a local response to countergradient selection. Our data support the hypothesis that populations of the invader in northern lakes are dominated by well-adapted genotypes. Our results illustrate how environmental change (i.e. eutrophication) and local adaptation can act together to drive a successful invasion.

The functional genomics of an eco-evolutionary feedback loop: linking gene expression, trait evolution, and community dynamics.

Feedbacks between ecological and evolutionary change may play important roles in community and ecosystem functioning, but a complete eco-evolutionary feedback loop has not been demonstrated at the community level, and we know little about molecular mechanisms underlying this kind of eco-evolutionary dynamics. In predator-prey (rotifer-alga) microcosms, cyclical changes in predator abundance generated fluctuating selection for a heritable prey defence trait, cell clumping. Predator population growth was affected more by prey evolution than by changes in prey abundance, and changes in predator abundance drove further prey evolution, completing the feedback loop. Within a predator-prey cycle, genes up-regulated as clumping declined were down-regulated as clumping increased, and vice-versa. Genes changing most in expression tended to be associated with defence or its cost. Expression patterns of individual genes differed greatly between consecutive cycles (often reversing direction), suggesting that a particular phenotype may be produced by several (perhaps many) different gene transcription pathways.

Linking genes to communities and ecosystems: Daphnia as an ecogenomic model.

How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances.

Does rapid evolution matter? Measuring the rate of contemporary evolution and its impacts on ecological dynamics.

Rapid contemporary evolution due to natural selection is common in the wild, but it remains uncertain whether its effects are an essential component of community and ecosystem structure and function. Previously we showed how to partition change in a population, community or ecosystem property into contributions from environmental and trait change, when trait change is entirely caused by evolution (Hairston et al. 2005). However, when substantial non-heritable trait change occurs (e.g. due to phenotypic plasticity or change in population structure) that approach can mis-estimate both contributions. Here, we demonstrate how to disentangle ecological impacts of evolution vs. non-heritable trait change by combining our previous approach with the Price Equation. This yields a three-way partitioning into effects of evolution, non-heritable phenotypic change and environment. We extend the approach to cases where ecological consequences of trait change are mediated through interspecific interactions. We analyse empirical examples involving fish, birds and zooplankton, finding that the proportional contribution of rapid evolution varies widely (even among different ecological properties affected by the same trait), and that rapid evolution can be important when it acts to oppose and mitigate phenotypic effects of environmental change. Paradoxically, rapid evolution may be most important when it is least evident.

Reduction of adaptive genetic diversity radically alters eco-evolutionary community dynamics.

Adaptive variation in the traits determining ecological interactions can lead to evolution so rapid that ecological dynamics change course while in progress (i.e., 'eco-evolutionary dynamics'). However, little is known about how the qualitative properties of eco-evolutionary dynamics (e.g., cycling, equilibrium, etc.) are affected by the amount of heritable variation present. Here, we show that a change in the range of variation in a heritable prey defense trait determines what dynamics are observed in an experimental predator-prey system. We combine modelling and laboratory experiments to show that initial defense trait variation determines whether populations exhibit eco-evolutionary cycles in which heritable variation is maintained, or converge to an equilibrium at which the prey population becomes monomorphic. Our results show how small changes in the amount of adaptive genetic variance initially present can radically alter eco-evolutionary dynamics, and can ultimately determine whether heritable variation is maintained or lost.

Rapid contemporary evolution and clonal food web dynamics.

Character evolution that affects ecological community interactions often occurs contemporaneously with temporal changes in population size, potentially altering the very nature of those dynamics. Such eco-evolutionary processes may be most readily explored in systems with short generations and simple genetics. Asexual and cyclically parthenogenetic organisms such as microalgae, cladocerans and rotifers, which frequently dominate freshwater plankton communities, meet these requirements. Multiple clonal lines can coexist within each species over extended periods, until either fixation occurs or a sexual phase reshuffles the genetic material. When clones differ in traits affecting interspecific interactions, within-species clonal dynamics can have major effects on the population dynamics. We first consider a simple predator-prey system with two prey genotypes, parametrized with data from a well-studied experimental system, and explore how the extent of differences in defence against predation within the prey population determine dynamic stability versus instability of the system. We then explore how increased potential for evolution affects the community dynamics in a more general community model with multiple predator and multiple prey genotypes. These examples illustrate how microevolutionary 'details' that enhance or limit the potential for heritable phenotypic change can have significant effects on contemporaneous community-level dynamics and the persistence and coexistence of species.

Cryptic population dynamics: rapid evolution masks trophic interactions.

Trophic relationships, such as those between predator and prey or between pathogen and host, are key interactions linking species in ecological food webs. The structure of these links and their strengths have major consequences for the dynamics and stability of food webs. The existence and strength of particular trophic links has often been assessed using observational data on changes in species abundance through time. Here we show that very strong links can be completely missed by these kinds of analyses when changes in population abundance are accompanied by contemporaneous rapid evolution in the prey or host species. Experimental observations, in rotifer-alga and phage-bacteria chemostats, show that the predator or pathogen can exhibit large-amplitude cycles while the abundance of the prey or host remains essentially constant. We know that the species are tightly linked in these experimental microcosms, but without this knowledge, we would infer from observed patterns in abundance that the species are weakly or not at all linked. Mathematical modeling shows that this kind of cryptic dynamics occurs when there is rapid prey or host evolution for traits conferring defense against attack, and the cost of defense (in terms of tradeoffs with other fitness components) is low. Several predictions of the theory that we developed to explain the rotifer-alga experiments are confirmed in the phage-bacteria experiments, where bacterial evolution could be tracked. Modeling suggests that rapid evolution may also confound experimental approaches to measuring interaction strength, but it identifies certain experimental designs as being more robust against potential confounding by rapid evolution.

Prey evolution on the time scale of predator-prey dynamics revealed by allele-specific quantitative PCR.

Using rotifer-algal microcosms, we tracked rapid evolution resulting from temporally changing natural selection in ecological predator-prey dynamics. We previously demonstrated that predator-prey oscillations in rotifer-algal laboratory microcosms are qualitatively altered by the presence of genetic variation within the prey. In that study, changes in algal gene frequencies were inferred from their effects on population dynamics but not observed directly. Here, we document rapid prey evolution in this system by directly observing changes in Chlorella vulgaris genotype frequencies as the abundances of these algae and their consumer, Brachionus calyciflorus, change through time. We isolated a group of algal clones that we could distinguish by using microsatellite-DNA markers, and developed an allele-specific quantitative PCR technique (AsQ-PCR) to quantify the frequencies of pairs of clones in mixed culture. We showed that two of these genotypes exhibited a fitness tradeoff in which one was more resistant to predation (more digestion-resistant), and the other had faster population growth under limiting nitrogen concentrations. A fully specified mathematical model for the rotifer-algal population and evolutionary dynamics predicted that these two clones would undergo a single oscillation in clonal frequencies followed by asymptotic fixation of the more resistant clone, rather than the recurrent oscillations previously observed with other algal clones. We used AsQ-PCR to confirm this prediction: the superior competitor dominated initially, but as rotifer densities increased, the more predator-resistant clone predominated.

Ecology: mechanisms for consumer diversity.

A variety of mechanisms can theoretically produce competitive coexistence in nature, making it hard to identify a single explanation for the maintenance of diversity in any particular system. Based on laboratory experiments with a consumer-resource system of crustacean Daphnia eating algae, Nelson et al. suggest that maintenance of genetic diversity in the consumer populations they studied depends only on the dynamics of the population structure of the consumer. We suggest that the differences in Daphnia genetic diversity that they find for different experimental treatments could equally be explained by a simple, well known mechanism: the number of coexisting competitors cannot exceed the number of shared resources. Here we confirm this possibility by using a simple mathematical model and suggest that more than one mechanism may account for the maintenance of genetic diversity observed by Nelson et al. in their system.

Evolutionary trade-off between defence against grazing and competitive ability in a simple unicellular alga, Chlorella vulgaris.

Trade-offs between defence and other fitness components are expected in principle, and can have major qualitative impacts on ecological dynamics. Here we show that such a trade-off exists even in the simple unicellular alga Chlorella vulgaris. We grew algal populations for multiple generations in either the presence ('grazed algae') or absence ('non-grazed algae') of the grazing rotifer Brachionus calyciflorus, and then evaluated their defence and competitive abilities. Grazed algae were better defended, yielding rotifer growth rate 32% below that of animals fed non-grazed algae, but they also had diminished competitive ability, with a growth rate under nutrient-limiting conditions 28% below that of non-grazed algae. Grazed algae also had a smaller cell size and were more concentrated in carbon and nitrogen. Thus, C. vulgaris genotypes vary phenotypically in their position along a trade-off curve between defence against grazing and competitive ability. This genetic variation underlies rapid algal evolution that significantly alters the ecological predator-prey cycles between rotifers and algae.