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A central goal in evolutionary biology is to understand how different evolutionary processes cause trait change in wild populations. However, quantifying evolutionary change in the wild requires linking trait change to shifts in allele frequencies at causal loci. Nevertheless, datasets that allow for such tests are extremely rare and existing theoretical approaches poorly account for the evolutionary dynamics that likely occur in ecological settings. Using a decade-long integrative phenome-to-genome time-series dataset on wild threespine stickleback (Gasterosteus aculeatus), we identified how different modes of selection (directional, episodic, and balancing) drive microevolutionary change in correlated traits over time. Most strikingly, we show that feeding traits changed by as much 25% across 10 generations which was driven by changes in the genetic architecture (i.e., in both genomic breeding values and allele frequencies at genetic loci for feeding traits). Importantly, allele frequencies at genetic loci related to feeding traits changed at a rate greater than expected under drift, suggesting that the observed change was a result of directional selection. Allele frequency dynamics of loci related to swimming traits appeared to be under fluctuating selection evident in periodic population crashes in this system. Our results show that microevolutionary change in a wild population is characterized by different modes of selection acting simultaneously on different traits, which likely has important consequences for the evolution of correlated traits. Our study provides one of the most thorough descriptions to date of how microevolutionary processes result in trait change in a natural population. [ABSTRACT FROM AUTHOR]

The scaling exponent relating the mean and variance of the density of individual organisms in space (i.e., Taylor's slope: zspace) is well studied in ecology, but the analogous scaling exponent for temporal datasets (ztime) is underdeveloped. Previous theory suggests the narrow distribution of ztime (e.g., typically 1–2) could be due to interspecific competition. Here, using 1694 communities time series, we show that ztime can exceed 2, and reaffirm how this can affect our inference about the stabilizing effect of biodiversity. We also develop a new theory, based on temporal change in the ranks of species abundances, to help account for the observed ztime distribution. Specifically, we find that communities with minimal turnover in species' rank abundances are more likely to have higher ztime. Our analysis shows how species‐level variability affects our inference about the stability of ecological communities. [ABSTRACT FROM AUTHOR]

There is growing concern about the dire socioecological consequences of abrupt transitions between alternative ecosystem states in response to environmental changes. At the same time, environmental change can trigger evolutionary responses that could stabilize or destabilize ecosystem dynamics. However, we know little about how coupled ecological and evolutionary processes affect the risk of transition between alternative ecosystem states. Using shallow lakes as a model ecosystem, we investigate how trait evolution of a key species affects ecosystem resilience under environmental stress. We find that adaptive evolution of macrophytes can increase ecosystem resilience by shifting the critical threshold, which marks the transition from a clear-water state to a turbid-water state to a higher level of environmental stress. However, following the transition, adaptation to the turbid-water state can delay the ecosystem recovery back to the clear-water state. This implies that restoration could be more effective when implemented early enough after a transition occurs and before organisms adapt to the alternative state. Our findings provide new insights into how to prevent and mitigate the occurrence of regime shifts in ecosystems and highlight the need to understand ecosystem responses to environmental change in the context of coupled ecological and evolutionary processes. [ABSTRACT FROM AUTHOR]

Developmental plasticity is ubiquitous in natural populations, but the underlying causes and fitness consequences are poorly understood. For consumers, nutritional variation of juvenile diets is probably associated with plasticity in developmental rates, but little is known about how diet quality can affect phenotypic trajectories in ways that might influence survival to maturity and lifetime reproductive output. Here, we tested how the diet quality of a freshwater detritivorous isopod (Asellus aquaticus), in terms of elemental ratios of diet (i.e. carbon : nitrogen : phosphorus; C : N : P), can affect (i) developmental rates of body size and pigmentation and (ii) variation in juvenile survival. We reared 1047 individuals, in a full-sib split-family design (29 families), on either a high- (low C : P, C : N) or low-quality (high C : P, C : N) diet, and quantified developmental trajectories of body size and pigmentation for every individual over 12 weeks. Our diet contrast caused strong divergence in the developmental rates of pigmentation but not growth, culminating in a distribution of adult pigmentation spanning the broad range of phenotypes observed both within and among natural populations. Under low-quality diet, we found highest survival at intermediate growth and pigmentation rates. By contrast, survival under high-quality diet survival increased continuously with pigmentation rate, with longest lifespans at intermediate growth rates and high pigmentation rates. Building on previous work which suggests that visual predation mediates the evolution of cryptic pigmentation in A. aquaticus, our study shows how diet quality and composition can generate substantial phenotypic variation by affecting rates of growth and pigmentation during development in the absence of predation. [ABSTRACT FROM AUTHOR]

Phytoplankton play a key role in biogeochemical cycles, impacting atmospheric and aquatic chemistry, food webs, and water quality. However, it remains challenging to reconstruct changes in algal community composition throughout the geologic past, as existing proxies are suitable only for a subset of taxa and/or influenced by degradation. Here, we investigate if compound-specific hydrogen isotope ratios (δ2H values) of common algal lipids can serve as (paleo)ecological indicators. First, we grew 20 species of algae – representing cyanobacteria, diatoms, dinoflagellates, green algae, and cryptomonads – in batch cultures under identical conditions and measured δ2H values of their lipids. Despite identical source water δ2H values, lipid δ2H values ranged from −455 ‰ to −52 ‰, incorporating variability associated with chemical compound classes and taxonomic groups. In particular, green algae synthesized fatty acids with higher δ2H values than other taxa, cyanobacteria synthesized phytol with relatively low δ2H values, and diatoms synthesized sterols with higher δ2H values than other eukaryotes. Second, we assessed how changes in algal community composition can affect net δ2H values of common algal lipids in 20 experimental outdoor ponds, which were manipulated via nutrient loading, and the addition of macrophytes and mussels. High algal biomass in the ponds, which was mainly caused by cyanobacterial and green algal blooms, was associated with higher δ2H values for generic fatty acids, relatively stable δ2H values for phytol and the dinoflagellate biomarker dinostanol, and lower δ2H values for the more cosmopolitan sterol stigmasterol. These results are consistent with expectations from our culture-based analyses, with both datasets indicating large taxon-specific changes that are unlikely to be driven by bacterial heterotrophy. This suggests that measuring δ2H values of multiple lipids from sediment and calculating 2H-offsets between them can resolve changes in algal community composition from changes in source water isotopes. With an appropriate availability of sedimentary lipids, this approach could permit the reconstruction of both taxonomic variability and hydroclimate from diverse sedimentary systems. [ABSTRACT FROM AUTHOR]

Biological systems consist of elements that interact within and across hierarchical levels. For example, interactions among genes determine traits of individuals, competitive and cooperative interactions among individuals influence population dynamics, and interactions among species affect the dynamics of communities and ecosystem processes. Such systems can be represented as hierarchical networks, but can have complex dynamics when interdependencies among levels of the hierarchy occur. We propose integrating ecological and evolutionary processes in hierarchical networks to explore interdependencies in biological systems. We connect gene networks underlying predator–prey trait distributions to food webs. Our approach addresses longstanding questions about how complex traits and intraspecific trait variation affect the interdependencies among biological levels and the stability of meta-ecosystems. [ABSTRACT FROM AUTHOR]

Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics. We propose new ways to help link research on functional genomic diversity with (reciprocal) interactions between phenotypic evolution and ecosystem change. Despite numerous challenges, we anticipate that the wealth of genomic data being collected on natural populations will improve our understanding of ecosystems. [ABSTRACT FROM AUTHOR]

The presence of predators can impact a variety of organisms within the ecosystem, including microorganisms. Because the effects of fish predators and their phenotypic differences on microbial communities have not received much attention, we tested how the presence/absence, genotype, and plasticity of the predatory three-spine stickleback ( Gasterosteus aculeatus) influence aquatic microbes in outdoor mesocosms. We reared lake and stream stickleback genotypes on contrasting food resources to adulthood, and then added them to aquatic mesocosm ecosystems to assess their impact on the planktonic bacterial community. We also investigated whether the effects of fish persisted following the removal of adults, and the subsequent addition of a homogenous juvenile fish population. The presence of adult stickleback increased the number of bacterial OTUs and altered the size structure of the microbial community, whereas their phenotype affected bacterial community composition. Some of these effects were detectable after adult fish were removed from the mesocosms, and after juvenile fish were placed in the tanks, most of these effects disappeared. Our results suggest that fish can have strong short-term effects on microbial communities that are partially mediated by phenotypic variation of fish. [ABSTRACT FROM AUTHOR]

The composition and dynamics of plankton communities are critically affected by human-induced environmental changes. We analysed 33 years of phytoplankton monthly data collected in Lake Zurich (Switzerland), assigning organisms (genus level) to taxonomic groups (class, family), Reynolds associations and size categories. The aim was to understand how eutrophication and climate change have influenced taxa co-occurrence patterns within and between groups over the lake water column (14 depths, 0-135 m), using null-models to test for non-random spatial (depth) assembly. We found that the whole community showed high taxa co-occurrence levels, significantly deviating over time from random assembly concurrently with lake warming and reduced nutrient loading. This pattern was driven mostly by the depth structure of metalimnetic assemblages during summer and autumn. The prevalence of non-random spatial patterns changed for different taxonomic and functional groups, with only few significant deviations from null-model expectations. Within taxonomic and functional groups (particularly Classes and size categories), the frequency of spatial overdispersion of taxa decreased over time while the frequency of clustering increased. Our data suggest that the relative importance of mechanisms determining phytoplankton metacommunity dynamics have changed along with environmental gradients shaping water column structure. [ABSTRACT FROM AUTHOR]

Consumers can have strong effects on the biotic and abiotic dynamics of spatially-structured ecosystems. In metacommunities, dispersing consumers can alter local assembly dynamics either directly through trophic interactions or indirectly by modifying local environmental conditions. In aquatic systems, very little is known about how key grazers, such as Daphnia, structure the microbial diversity of metacommunities and influence bacterial-mediated ecosystem functions. In an outdoor mesocosm experiment with replicate metacommunities (two 300 L mesocosms), we tested how the presence and absence of Daphnia and the initial density of the microbial community (manipulated via dilution) influenced the diversity and community structure of algae and bacteria, and several ecosystem properties (e.g., pH, dissolved substances) and functions (e.g., enzyme activity, respiration). We found that Daphnia strongly affected the local and regional diversity of both phytoplankton and bacteria, the taxonomic composition of bacterial communities, the biomass of algae, and ecosystem metabolism (i.e., respiration). Diluting the microbial inoculum (0.2-5 μm size fraction) to the metacommunities increased local phytoplankton diversity, decreased bacteria beta-diversity, and changed the relative abundance of bacterial classes. Changes in the rank abundance of different bacterial groups exhibited phylogenetic signal, implying that closely related bacteria species might share similar responses to the presence of Daphnia. [ABSTRACT FROM AUTHOR]

Summary Differences in how organisms modify their environment can evolve rapidly and might influence adaptive population divergence [ 1, 2 ]. In a common garden experiment in aquatic mesocosms, we found that adult stickleback from a recently diverged pair of lake and stream populations had contrasting effects on ecosystem metrics. These modifications were caused by both genetic and plastic differences between populations and were sometimes comparable in magnitude to those caused by the presence/absence of stickleback. Lake and stream fish differentially affected the biomass of zooplankton and phytoplankton, the concentration of phosphorus, and the abundance of several prey (e.g., copepods) and non-prey (e.g., cyanobacteria) species. The adult-mediated effects on mesocosm ecosystems influenced the survival and growth of a subsequent generation of juvenile stickleback reared in the same mesocosms. The prior presence of adults decreased the overall growth rate of juveniles, and the prior presence of stream adults lowered overall juvenile survival. Among the survivors, lake juveniles grew faster than co-occurring stream juveniles, except in mesocosm ecosystems previously modified by adult lake fish that were reared on plankton. Overall, our results provide evidence for reciprocal interactions between ecosystem dynamics and evolutionary change (i.e., eco-evolutionary feedbacks) in the early stages of adaptive population divergence. [ABSTRACT FROM AUTHOR]

A major question in ecology is how often competing species evolve to reduce competitive interactions and facilitate coexistence. One untested route for a reduction in competitive interactions is through ontogenetic changes in the trophic niche of one or more of the interacting species. In such cases, theory predicts that two species can coexist if the weaker competitor changes its resource niche to a greater degree with increased body size than the superior competitor.We tested this prediction using stable isotopes that yield information about the trophic position (δ15N) and carbon source (δ13C) of two coexisting fish species: Trinidadian guppies Poecilia reticulata and killifish Rivulus hartii.We examined fish from locations representing three natural community types: (1) where killifish and guppies live with predators, (2) where killifish and guppies live without predators and (3) where killifish are the only fish species. We also examined killifish from communities in which we had introduced guppies, providing a temporal sequence of the community changes following the transition from a killifish only to a killifish–guppy community.We found that killifish, which are the weaker competitor, had a much larger ontogenetic niche shift in trophic position than guppies in the community where competition is most intense (killifish–guppy only). This result is consistent with theory for size‐structured populations, which predicts that these results should lead to stable coexistence of the two species. Comparisons with other communities containing guppies, killifish and predators and ones where killifish live by themselves revealed that these results are caused primarily by a loss of ontogenetic niche changes in guppies, even though they are the stronger competitor. Comparisons of these natural communities with communities in which guppies were translocated into sites containing only killifish showed that the experimental communities were intermediate between the natural killifish–guppy community and the killifish–guppy–predator community, suggesting contemporary evolution in these ontogenetic trophic differences.These results provide comparative evidence for ontogenetic niche shifts in contributing to species coexistence and comparative and experimental evidence for evolutionary or plastic changes in ontogenetic niche shifts following the formation of new communities. [ABSTRACT FROM AUTHOR]

Phenotypic differences among closely related populations and species can cause contrasting effects on ecosystems; however, it is unknown whether such effects result from genetic divergence, phenotypic plasticity, or both. To test this, we reared sympatric limnetic and benthic species of whitefish from a young adaptive radiation in a common garden, where the benthic species was raised on two distinct food types. We then used these fish in a mesocosm experiment to test for contrasting ecosystem effects of closely related species and of plastically induced differences within a species. We found that strong contrasting ecosystem effects resulted more frequently from genetic divergence, although they were not stronger overall than those resulting from phenotypic plasticity. Overall, our results provide evidence that genetically based differences among closely related species that evolved during a young adaptive radiation can affect ecosystems, and that phenotypic plasticity can modify the ecosystem effects of such species. [ABSTRACT FROM AUTHOR]

Summary: The role of natural selection in the maintenance of genetic variation in wild populations remains a major problem in evolution. The influence of disruptive natural selection on genetic variation is especially interesting because it might lead to the evolution of assortative mating or dominance [1, 2]. In theory, variation can persist at a gene under disruptive natural selection, but the process is little studied and there are few examples [3, 4]. We report a stable polymorphism in the bony armor of threespine stickleback maintained with a deficit of heterozygotes at the major underlying gene, Ectodysplasin (Eda) [5]. The deficit vanishes at the embryo life stage only to re-emerge in adults, indicating that disruptive natural selection, rather than nonrandom mating, is the cause. The mechanism enabling long-term persistence of the polymorphism is unknown, but disruptive selection is predicted to be frequency dependent, favoring homozygous genotypes when they become rare. Further research on the ecological and evolutionary processes affecting individual genes will ultimately lead to a better understanding of the causes of genetic variation in populations. [Copyright &y& Elsevier]

All living organisms modify their biotic and abiotic environment. Niche construction theory posits that organism-mediated modifications to the environment can change selection pressures and influence the evolutionary trajectories of natural populations. While there is broad support for this proposition in general, there is considerable uncertainty about how niche construction is related to other similar concepts in ecology and evolution. Comparative studies dealing with certain aspects of niche construction are increasingly common, but there is a troubling lack of experimental tests of the core concepts of niche construction theory. Here, we propose an operational framework to evaluate comparative and experimental evidence of the evolutionary consequences of niche construction, and suggest how such research can improve our understanding of ecological and evolutionary dynamics in ecosystems. We advocate for a shift toward explicit experimental tests of how organism-mediated environmental change can influence the selection pressures underlying evolutionary responses, as well as targeted field-based comparative research to identify the mode of evolution by niche construction and assess its importance in natural populations. [ABSTRACT FROM AUTHOR]

We investigated the influence of environmental parameters and spatial distance on bacterial, archaeal and viral community composition from 13 sites along a 3200-km long voyage from Halifax to Kugluktuk (Canada) through the Labrador Sea, Baffin Bay and the Arctic Archipelago. Variation partitioning was used to disentangle the effects of environmental parameters, spatial distance and spatially correlated environmental parameters on prokaryotic and viral communities. Viral and prokaryotic community composition were related in the Labrador Sea, but were independent of each other in Baffin Bay and the Arctic Archipelago. In oceans, the dominant dispersal mechanism for prokaryotes and viruses is the movement of water masses, thus, dispersal for both groups is passive and similar. Nevertheless, spatial distance explained 7-19% of the variation in viral community composition in the Arctic Archipelago, but was not a significant predictor of bacterial or archaeal community composition in either sampling area, suggesting a decoupling of the processes regulating community composition within these taxonomic groups. According to the metacommunity theory, patterns in bacterial and archaeal community composition suggest a role for species sorting, while patterns of virus community composition are consistent with species sorting in the Labrador Sea and suggest a potential role of mass effects in the Arctic Archipelago. Given that, a specific prokaryotic taxon may be infected by multiple viruses with high reproductive potential, our results suggest that viral community composition was subject to a high turnover relative to prokaryotic community composition in the Arctic Archipelago. [ABSTRACT FROM AUTHOR]

Lakes are recipients of allochthonous organic matter and nutrients. However, the importance of these subsidies for food webs and how they vary with lake trophic status remains unclear, especially for large lakes.We assessed the source and fate of organic matter and nutrients in seven perialpine lakes across a gradient of trophic status. We measured carbon and nitrogen stable isotopes of amino acids of lake‐residing Atlantic trout, Salmo trutta, to determine the source of primary production (i.e., how carbon is fixed in the ecosystem) and how it is transferred through food webs, respectively. Based on essential amino acid carbon fingerprinting, we estimated the probability of organic carbon originating from autochthonous (algal), allochthonous (terrestrial plant), and recycled (bacterial) sources. In addition, we used amino acid δ15N to track how this primary production is transferred to consumers in general, and by using different trophic amino acids (glutamic acid and alanine), identify the trophic pathways involving either metazoan or protozoans.We found a high likelihood of autochthonous origin of organic carbon (86 ± 9%) in trout that contrasted with allochthonous origins of particulate organic matter and some sediments. We showed that those estimates are good proxies of source reliance. Our results also highlighted the importance of bacterial origin of organic carbon in fish (12%). The likely autochthonous origin of this carbon was supported by trophic markers (Ala δ15N) that suggest the role of protists in transferring recycled organic carbon up the food web. While the sources of nitrogen sustaining food webs varied among lakes, we found a conserved carbon fingerprinting of fish. Overall, this suggests an uncoupling between the source of nutrients and organic carbon in large perialpine lakes.Across a wide range of trophic status (c. 2 orders of magnitude range of phosphorus concentration), several lines of evidence suggested that perialpine lake food webs shared a common reliance on autochthonous and bacterial production.Our study is the first to quantify the dependence on allochthonous organic carbon in lake food webs based on new amino acid stable isotope markers (carbon fingerprinting and Ala δ15N) and shows promise for estimating the source of carbon fixation in ecosystems. Our results support previous suggestions that terrestrial organic carbon is a relatively minor source for aquatic consumers despite contributing to the pool of organic matter, and more importantly, its contribution does not vary substantially with trophic status in perialpine lakes. [ABSTRACT FROM AUTHOR]

Negative relationships between species richness and the rate of compositional turnover are common, suggesting that diverse communities have greater stability than depauperate ones; however, the mechanistic basis for this pattern is still widely debated. Species richness and turnover can covary either because they are mechanistically linked or because they share common environmental drivers. Few empirical studies have combined long-term changes in community composition with multiple drivers of environmental change, and so little is known about how the underlying mechanisms of species coexistence interact with changes in the mean and variability of environmental conditions. Here, we use a 33 year long time series (1976-2008) of phytoplankton community composition from Lake Zurich, to examine how environmental variation influences the relationship between richness and annual turnover. We find that the relationship between richness and annual turnover reverses midway through the time series (1992-1993), leading to a hump-shaped relationship between species richness and annual turnover. Using structural equation modeling we show that annual turnover and diversity are independently associated with different drivers of environmental change. Furthermore, we find that the observed annual sequences of community assembly give rise to rates of species accumulation that are more heterogeneous through time than expected by chance, likely owing to a high proportion of species showing significant autocorrelation and to strong positive covariation in the occurrences of species. [ABSTRACT FROM AUTHOR]

We studied the effects of re-oligotrophication and climate warming on plankton richness and community stability over a period of 30 years in the deep mesotrophic Lake Zurich (Switzerland). We assembled monthly time-series of phytoplankton and zooplankton taxonomic richness, phytoplankton functional groups (species with similar functional traits) and physico-chemical environmental descriptors (temperature, conductivity, pH, P-PO43−, N-NO3−, light absorption). We used multiple linear regression to test: 1) the effect of environmental variability over time and depth on the accrual of plankton richness; and 2) the relative effect of richness and environmental variability on the stability of plankton. Environmental change was characterised by increase in temperature, decrease in phosphorus levels, reduced temporal variability of both, and higher heterogeneity of phosphorus over depth (spatial heterogeneity). These conditions occurred concurrently with accrual in plankton taxonomic and functional richness. Increase in temperature and spatial heterogeneity were the best predictors of phytoplankton richness, while phytoplankton richness and spatial heterogeneity had the strongest effects on zooplankton richness. Temporal stability in phytoplankton biovolume was mainly affected by variability in phosphorus and temperature, while zooplankton abundance levels were more strongly linked to fluctuations in nitrogen, temperature and phytoplankton biovolumes. Our analysis highlights that climate warming and re-oligotrophication may favour an increase in spatial (depth) heterogeneity in the water column of deep lakes, enhancing the potential for phytoplankton species co-existence and an increase in plankton richness. Our analysis also suggests that the intensity of fluctuations in key environmental variables can be a better predictor of plankton community stability then average richness. [ABSTRACT FROM AUTHOR]

Organisms alter the biotic and abiotic conditions of ecosystems. They can modulate the availability of resources to other species (ecosystem engineering) and shape selection pressures on other organisms (niche construction). Very little is known about how the engineering effects of organisms vary among and within species, and, as a result, the ecosystem consequences of species diversification and phenotypic evolution are poorly understood. Here, using a common gardening experiment, we test whether morphologically similar species and populations of Diaptomidae copepods (Leptodiaptomus ashlandi, Hesperodiaptomus franciscanus, Skistodiaptomus oregonensis) have similar or different effects on the structure and function of freshwater ecosystems. We found that copepod species had contrasting effects on algal biomass, ammonium concentrations, and sedimentation rates, and that copepod populations had contrasting effects on prokaryote abundance, sedimentation rates, and gross primary productivity. The average size of ecosystem-effect contrasts between species was similar to those between populations, and was comparable to those between fish species and populations measured in previous common gardening experiments. Our results suggest that subtle morphological variation among and within species can cause multifarious and divergent ecosystem-effects. We conclude that using morphological trait variation to assess the functional similarity of organisms may underestimate the importance of species and population diversity for ecosystem functioning. [ABSTRACT FROM AUTHOR]

Parasites can strongly affect the evolution of their hosts, but their effects on host diversification are less clear. In theory, contrasting parasite communities in different foraging habitats could generate divergent selection on hosts and promote ecological speciation. Immune systems are costly to maintain, adaptable, and an important component of individual fitness. As a result, immune system genes, such as those of the Major Histocompatability Complex (MHC), can change rapidly in response to parasite-mediated selection. In threespine stickleback (Gasterosteus aculeatus), as well as in other vertebrates, MHC genes have been linked with female mating preference, suggesting that divergent selection acting on MHC genes might influence speciation. Here, we examined genetic variation at MHC Class II loci of sticklebacks from two lakes with a limnetic and benthic species pair, and two lakes with a single species. In both lakes with species pairs, limnetics and benthics differed in their composition of MHC alleles, and limnetics had fewer MHC alleles per individual than benthics. Similar to the limnetics, the allopatric population with a pelagic phenotype had few MHC alleles per individual, suggesting a correlation between MHC genotype and foraging habitat. Using a simulation model we show that the diversity and composition of MHC alleles in a sympatric species pair depends on the amount of assortative mating and on the strength of parasite-mediated selection in adjacent foraging habitats. Our results indicate parallel divergence in the number of MHC alleles between sympatric stickleback species, possibly resulting from the contrasting parasite communities in littoral and pelagic habitats of lakes. [ABSTRACT FROM AUTHOR]

Divergence in habitat use among closely related species is a common characteristic of adaptive radiations. Large differences in the size structure of prey between habitats could strengthen disruptive selection on generalist predators and lead to a divergence in trophic position among species in an adaptive radiation. Using threespine stickleback (Gasterosteus aculeatus) in freshwater lakes as a model system, we examined whether divergence in habitat use coincides with shifts in trophic position. We examined the habitat use and trophic position of individual sticklebacks from divergent lake environments that have only one stickleback species (allopatric lakes) and from lakes that have a pair of benthic and limnetic stickleback species (sympatric lakes). In two sympatric lakes, the limnetic species had a higher trophic position than the benthic species, and in both allopatric and sympatric lakes, sticklebacks specializing on pelagic prey had a higher trophic position for a given size than sticklebacks specializing on benthic prey. Furthermore, the trophic position of pelagic specialists was correlated with individual variation in their gill raker length. Our results indicate that gill raker length is an important trait that underlies differentiation in both habitat use and trophic position among stickleback species, populations, and individuals. [ABSTRACT FROM AUTHOR]

Explaining the ecological causes of evolutionary diversification is a major focus of biology, but surprisingly little has been said about the effects of evolutionary diversification on ecosystems. The number of species in an ecosystem and their traits are key predictors of many ecosystem-level processes, such as rates of productivity, biomass sequestration and decomposition. Here we demonstrate short-term ecosystem-level effects of adaptive radiation in the threespine stickleback (Gasterosteus aculeatus) over the past 10,000 years. These fish have undergone recent parallel diversification in several lakes in coastal British Columbia, resulting in the formation of two specialized species (benthic and limnetic) from a generalist ancestor. Using a mesocosm experiment, we demonstrate that this diversification has strong effects on ecosystems, affecting prey community structure, total primary production, and the nature of dissolved organic materials that regulate the spectral properties of light transmission in the system. However, these ecosystem effects do not simply increase in their relative strength with increasing specialization and species richness; instead, they reflect the complex and indirect consequences of ecosystem engineering by sticklebacks. It is well known that ecological factors influence adaptive radiation. We demonstrate that adaptive radiation, even over short timescales, can have profound effects on ecosystems. [ABSTRACT FROM AUTHOR]

1. Stable isotopes of nitrogen are useful for quantifying the trophic structure of food webs, but only if the variation in trophic enrichment (ΔN), which is the difference in δ15N between a consumer and its food, is small relative to the value of ΔN itself. 2. We examined the sources of variation in zooplankton ΔN by measuring the trophic enrichment (ΔN) of seven species of freshwater cladocerans, and by testing for an effect of age and temperature on the ΔN of Daphnia pulicaria. 3. We found that ΔN was similar among Cladocera and was not correlated with body size. Overall, the ΔN for D. pulicaria was 1.4‰ (SE = 0.69, n = 57), as was expected for the detritus diet that we used in our experiments. We found no effect of temperature (15–25 °C) on ΔN, but found that ΔN of D. pulicaria increased with increasing age (10–30 days). 4. We developed a new method to test for trophic-level variation in a group of consumers that explicitly accounts for the uncertainty in ΔN. Using this approach, we confirmed that natural assemblages of zooplankton feed at several trophic levels in lake food webs. [ABSTRACT FROM AUTHOR]

We measured the δ15N of particulate organic matter (POM), Daphnia pulex (D), Holopedium gibberum (H), Leptodiaptomus tyrelli (LT), Epischura nevadensis (E), and Chaoborus trivittatus (C) over an annual cycle in Council Lake, a pristine, oligotrophic, fishless lake. Annual averages of the δ15N of plankton (C, LT, E > D, H > POM) matched expected differences in trophic position, but seasonal patterns differed among species. During midsummer, the δ15N of D, H, and LT increased above the δ15N of E and C, despite little temporal or spatial variation in the δ15N of POM (<41 µm). Larger size fractions of POM (41–200 µm) helped explain some of the temporal variability of zooplankton δ15N. Body size of zooplankton was correlated with δ15N for D, C, and E, which could indicate size-based, trophic-level variation; selective feeding; or physiological differences in 15N enrichment. We propose that detailed time series of δ15N for multiple zooplankton species can help determine the seasonal variability of trophic structure in zooplankton assemblages. [ABSTRACT FROM AUTHOR]

The significance of spatial subsidies depends on consumer resource interactions in the recipient habitat. Lakes are subsidized by terrestrial carbon sources, but the pathways of allochthonous carbon through lake food webs are complex and not well understood. Zooplankton vertically partition resources within stratified lakes in response to life history trade-offs that are governed by predators, the quantity and quality of food, and abiotic conditions (e.g., UV, temperature, and viscosity). We measured habitat specialization of zooplankton in an oligotrophic lake where allochthonous and autochthonous resources varied with depth. During stratification, the quantity and quality of zooplankton food was highest in the hypolimnion. We used a yearlong time series of the δ13C of zooplankton and particulate organic matter (POM) to determine which zooplankton species exploited, hypolimnetic rather than epilimnetic resources. Because the δ13C of POM decreased with depth, we used the δ13C of zooplankton to detect inter- and intraspecific variation in habitat selection. We incubated Daphnia pulex at discrete depths in the water column to confirm that the δ13C of zooplankton can indicate habitat specialization. Zooplankton that specialized in the epilimnion relied more on allochthonous carbon sources than those that specialized in the hypolimnion. Therefore, the fate of allochthonous carbon subsidies to lakes depends on spatially explicit consumer-resource interactions. [ABSTRACT FROM AUTHOR]

We use a temporal integration model (TIM) to determine how estimates of trophic variation, using δ15N, depend on consumer growth dynamics and temporal isotopic variation (δ15N) of food sources. Consumers are rarely in isotopic equilibrium with their food sources, so instantaneous comparisons between the δ15N of a consumer and its diet provide little information about trophic variation, even if the trophic positions of the diet are known. In this paper, we focus on the trophic link between zooplankton and planktivorous fish. We first review the extent of temporal variability of zooplankton δ15N, then examine the consequences of this variability for understanding the isotopic composition of planktivorous fish communities. We use time series of δ15N for Daphnia, calanoid copepods, and particulate organic matter (>200 µm) to generate theoretical diets for a model juvenile sockeye over a typical growing season. We use a TIM to predict the isotopic trajectory of individual juveniles feeding on these diets and explore how variance in growth rate and isotopic enrichment (ΔδN) can affect estimates of trophic position and intrapopulation isotopic variability. In general, we found that using a seasonal average of Daphnia δ15N to estimate the trophic position of planktivorous fish is nearly equivalent to using a TIM. However, temporal variation in the δ15N of food sources, coupled with individual differences in the growth rate of consumers, can contribute to intrapopulation isotopic variation of consumers and lead to correlations between consumer size and δ15N. [ABSTRACT FROM AUTHOR]

1. The stable carbon isotope ratioδ13C is a useful tracer of energy flow in lake food webs, and the zooplankton signature is commonly used to establish a baseline for the pelagic habitat. However, sources of temporal variability in theδ13C of different zooplankton taxa are rarely considered.2. Here, we investigate to what extent temporal variation in theδ13C of particulate organic matter (POM) (<41 μm) and the C : N of zooplankton can explain the temporal variability inδ13C of freshwater zooplankton. We compare temporal patterns ofδ13C and C : N forDaphnia,Hesperodiaptomus franciscanusandLeptodiaptomus tyrelliover a 6-month period at four sites in two oligotrophic lakes.3. In all three taxa, seasonal variation in zooplankton C : N explained more of the variation in zooplanktonδ13C than did theδ13C of POM. This suggests that variation in the lipid content of zooplankton can strongly influence temporal variation ofδ13C in zooplankton.4. Using these data, we evaluate procedures that estimate theδ13C of only the non-lipid component of zooplankton. If zooplankton lipids are primarily dietary in origin, than extracting lipids or‘normalising’ δ13C based on C : N will exclude a major dietary source, and therefore may be inappropriate.5. We conclude that temporal variation in body composition (C : N) of zooplankton can significantly influence the temporal variation of zooplanktonδ13C signatures. [ABSTRACT FROM AUTHOR]

Individual variation in the diet of consumers is common in many ecological systems and has important implications for the study of population dynamics, animal behavior, and evolutionary or ecological interactions. Ecologists frequently quantify the niche of a population by intensive analyses of gut contents and feeding behaviors of consumers. Inter-individual differences in δ13C signature can indicate long term differences in feeding behavior, often unattainable by a single snapshot analysis of gut contents. If a consumer’s food sources have unique δ13C signatures, then the intrapopulation variation in δ13C may be useful for quantifying diet variation and detecting isotopic evidence of individual specialization. However, intrapopulation variation in δ13C can underestimate or overestimate dietary variation, and therefore is not directly equivalent to a dietary based niche. In this paper we show that intrapopulation variability of δ13C in consumers critically depends on the isotopic range and distribution of food sources. Our analyses fundamentally challenge how we interpret the intrapopulation isotopic variance of δ13C, and how we evaluate isotopic evidence of individual specialization. [ABSTRACT FROM AUTHOR]

Zooplankton are commonly used to establish a baseline isotopic signature for pelagic production in lakes. Our objective was to evaluate this approach by quantifying among-lake and within-lake variability of δ[sup13]C and δ[sup15]N for different taxa of pelagic zooplankton. We measured the δ[sup13]C and δ[sup15]N of Daphnia, Holopedium, and calanoid copepods from four lakes sampled from June to November 2001 and from eight additional lakes sampled once in midsummer. In the four lakes with temporal sampling, within-lake differences due to taxonomic grouping accounted for 36.7% of the variance in δ[sup15]N and 41.7% of the variance in δ[sup13]C. Among all lakes, the δ[sup15]N of calanoid copepods was on average 2.55‰ and 2.44‰ higher than Daphnia or Holopedium, respectively, whereas the δ[sup13]C of calanoid copepods was 2.19‰ and 2.23‰ lower than Daphnia or Holopedium, respectively. If [sup15]N fractionation is similar among species, the differences in δ[sup15]N suggest that calanoid copepods either feed at a higher trophic position in the food web or they have a consistently higher baseline δ[sup15]N signature than Daphnia or Holopedium among lakes. Differences in δ[sup13]C suggest that zooplankton taxa in the pelagia of lakes have different food sources. We conclude that species composition and feeding behaviors of the zooplankton community should be considered before making among-lake comparisons of food web structure. We show that Daphnia is a useful isotopic baseline for organisms that rely on primary production in lakes. [ABSTRACT FROM AUTHOR]

The adaptation of marine fish to freshwater environments includes prodigious examples of rapid evolution.Given the scarcity of ω‐3 long‐chain polyunsaturated fatty acids (LC‐PUFA) in freshwater, we expect selection to be strong on fish transitioning to freshwater habitats and yet the underlying ecological causes of genomic and phenotypic differentiation are poorly understood for traits associated with lipid content and composition. Threespine stickleback Gasterosteus aculeatus have repeatedly colonized, and adapted to, freshwater habitats across the Northern Hemisphere. These freshwater populations often show elevated copy number of the fatty acid desaturase 2 gene (FADS2), which increases the biosynthetic capacity of LC‐PUFA. The starkly lower content of LC‐PUFA in freshwater compared to marine prey, especially docosahexaenoic acid (DHA), likely imposes strong positive selection on freshwater fish for either increased biosynthesis or greater dietary acquisition of LC‐PUFA. The recently colonized and relatively undisturbed threespine stickleback populations in postglacial coastal lakes of southern Greenland offer an exceptional opportunity to study how variation in the copy number of FADS2 is related to abiotic and biotic conditions of lakes and their morphometry. As expected, given its position on the stickleback X chromosome, we found strong sexual dimorphism in FADS2 copy number in all populations (19 freshwater, 1 marine and 1 brackish), and an increased dimorphism in some freshwater populations. We also found that FADS2 copy number was negatively correlated, for both males and females, with the abundance of copepods, which are a DHA‐rich food source in the zooplankton community. Overall, our results suggest that the prey community context of lakes might influence the process of metabolic adaptation of marine fish colonizing freshwater ecosystems. [ABSTRACT FROM AUTHOR]

Climate change is creating phenological mismatches between consumers and their resources. However, while the importance of nutritional quality in ecological interactions is widely appreciated, most studies of phenological mismatch focus on energy content alone. We argue that mismatches in terms of phenology and nutrition will increase with climate change. [ABSTRACT FROM AUTHOR]

Drawing insights from multiple disciplines is essential for finding integrative solutions that are required to tackle complex environmental problems. Human activities are causing unprecedented influence on global ecosystems, culminating in the loss of species and fundamental changes in the selective environments of organisms across the tree of life. Our collective understanding about biological evolution can help identify and mitigate many of the environmental problems in the Anthropocene. To this end, we propose a stronger integration of environmental sciences with evolutionary biology. Unlabelled Image • Evolutionary theory is not widely used to address environmental problems. • Evolutionary processes can both ameliorate and exacerbate environmental problems. • Evolution can be informative about disease dynamics, biofuel production, adaptation to pollution, and harmful algal blooms. • We propose a stronger integration of evolutionary biology with environmental sciences to help solve environmental problems. [ABSTRACT FROM AUTHOR]

Human land-use intensification threatens arthropod (for example, insect and spider) biodiversity across aquatic and terrestrial ecosystems. Insects and spiders play critical roles in ecosystems by accumulating and synthesizing organic nutrients such as polyunsaturated fatty acids (PUFAs). However, links between biodiversity and nutrient content of insect and spider communities have yet to be quantified. We relate insect and spider richness to biomass and PUFA-mass from stream and terrestrial communities encompassing nine land uses. PUFA-mass and biomass relate positively to biodiversity across ecosystems. In terrestrial systems, human-dominated areas have lower biomass and PUFA-mass than more natural areas, even at equivalent levels of richness. Aquatic ecosystems have consistently higher PUFA-mass than terrestrial ecosystems. Our findings reinforce the importance of conserving biodiversity and highlight the distinctive benefits of aquatic biodiversity. [ABSTRACT FROM AUTHOR]

In a warming world, the input of glacier meltwater to inland water ecosystems is predicted to change, potentially affecting their productivity. Meta-ecosystem theory, which posits that the nutrient availability in the recipient ecosystem can determine the extent of cross-ecosystem boundary utilization, can be useful for studying landscape-scale influences of glacier meltwater on inland waters. Here, we investigate how the input of glacier meltwater in a river system in Southern Greenland influences the utilization of marine subsidies in freshwater fish. Our study system comprised four sites, with controls for glacial meltwater and marine subsidies, harboring a partially migrating population of arctic char, meaning that some individuals migrate to the ocean and others remain in freshwaters, and two fully resident populations as a freshwater reference. We assessed the incorporation of marine carbon in freshwater resident char using both bulk and amino acid stable isotope analysis of muscle tissue. In the population with partial migration, marine subsidies were a significant resource for resident char individuals, and estimates of trophic position suggest that egg cannibalism is an important mechanism underlying the assimilation of these marine subsidies. In proglacial streams, namely those with high glacial meltwater, the total dependence on marine subsidies increased and reached 83% because char become cannibals at smaller sizes. In the configuration of our focal meta-ecosystem, our results suggest that the importance of marine subsidies to freshwater fish strengthens within increasing meltwater flux from upstream glaciers. [ABSTRACT FROM AUTHOR]

Discerning ecosystem change and food web dynamics underlying anthropogenic eutrophication and the introduction of non-native species is necessary for ensuring the long-term sustainability of fisheries and lake biodiversity. Previous studies of eutrophication in Lake Victoria, eastern Africa, have focused on the loss of endemic fish biodiversity over the past several decades, but changes in the plankton communities over this same time remain unclear. To fill this gap, we examined sediment cores from a eutrophic embayment, Mwanza Gulf, to determine the timing and magnitude of changes in the phytoplankton and zooplankton assemblages over the past century. Biogeochemical proxies indicate nutrient enrichment began around ~ 1920 CE and led to rapid increases in primary production, and our analysis of photosynthetic pigments revealed three zones: pre-eutrophication (prior to 1920 CE), onset of eutrophication with increases in all pigments (1920–1990 CE), and sustained eutrophication with cyanobacterial dominance (1990 CE–present). Cladoceran remains indicate an abrupt decline in biomass in ~ 1960 CE, in response to the cumulative effects of eutrophication and lake-level rise, preceding the collapse of haplochromine cichlids in the 1980s. Alona and Chydorus, typically benthic littoral taxa, have remained at relatively low abundances since the 1960s, whereas the abundance of Bosmina, typically a planktonic taxon, increased in the 1990s concurrently with the biomass recovery of haplochromine cichlid fishes. Overall, our results demonstrate substantial changes over the past century in the biomass structure and taxonomic composition of Mwanza Gulf phytoplankton and zooplankton communities, providing a historical food web perspective that can help understand the recent changes and inform future resource management decisions in the Lake Victoria ecosystem. [ABSTRACT FROM AUTHOR]

Preserved assemblages of invertebrate remains in lacustrine sediment reveal temporal variations of community composition and environmental conditions. However, records for large tropical lakes are scarce. Lake Victoria, the largest tropical lake, has a dynamic history of changes in water level, biogeochemistry and fish community composition over the past ~17,000 cal yr BP.In order to quantify changes in the invertebrate assemblage of Lake Victoria from the late Pleistocene throughout the Holocene, we examined chitinous remains of Cladocera and larval dipterans (Chironomidae and Chaoboridae) from a sediment core (37 m water depth) dated from ~13,700 cal yr BP to present.We identified four major phases in the invertebrate assemblage throughout this period of lake history. Firstly, Chironomidae and Chaoboridae appeared at low abundances during the earliest stages of lake inundation in the late Pleistocene, at a time when Cladocera were notably absent. Secondly, chaoborids and chironomids increased in abundance during the mid‐Holocene, which coincided with high diatom production toward the end of the Holocene African Humid Period. Thirdly, starting ~4,700 cal yr BP, Alona, a predominantly littoral cladoceran genus, consistently appeared in the invertebrate assemblage alongside changes in mixing regimes and persisted throughout the late Holocene to the present. Fourthly, the arrival of both Chydorus and Bosmina longirostris marked the establishment of an abundant cladoceran assemblage at ~1,350 cal yr BP. The assemblage then gradually shifted toward the increasing dominance of B. longirostris, a planktonic cladoceran.Several of the observed changes in the invertebrate assemblage occurred concurrently with changes in climatic conditions in East Africa and diatom productivity that have been previously recorded in Lake Victoria. This multi‐millennial record of sedimentary invertebrate assemblages in Lake Victoria elucidates some of the temporal development of these communities throughout most of the dynamic modern history of the ecosystem. [ABSTRACT FROM AUTHOR]

Differentiation of foraging traits among predator populations may help explain observed variation in the structure of prey communities. However, few studies have investigated the phenotypic effects of predators on their prey in natural communities. Here, we use a comparative analysis of 78 Greenlandic lakes to examine how foraging trait variation among threespine stickleback populations can help explain variation in zooplankton community composition among lakes. We find that landscape‐scale variation in zooplankton composition was jointly explained by lake properties, such as size and water chemistry, and the presence and absence of both stickleback and arctic char. Additional variation in zooplankton community structure can be explained by stickleback jaw protrusion, a trait with known utility for foraging on zooplankton, but only in lakes where stickleback co‐occur with arctic char. Overall, our results illustrate how trait variation of predators, alongside other ecosystem properties, can influence the composition of prey communities in nature. [ABSTRACT FROM AUTHOR]

Hybridization following secondary contact of genetically divergent populations can influence the range expansion of invasive species, though specific outcomes depend on the environmental dependence of hybrid fitness. Here, using two genetically and ecologically divergent threespine stickleback lineages that differ in their history of freshwater colonization, we estimate fitness variation of parental lineages and hybrids in semi‐natural freshwater ponds with contrasting histories of nutrient loading. In our experiment, we found that fish from the older freshwater lineage (Lake Geneva) and hybrids outperformed fish from the younger freshwater lineage (Lake Constance) in terms of both growth and survival, regardless of the environmental context of our ponds. Across all ponds, hybrids exhibited the highest survival. Although wild‐caught adult populations differed in their functional and defence morphology, it is unclear which of these traits underlie the fitness differences observed among juveniles in our experiment. Overall, our work suggests that when hybrid fitness is insensitive to environmental conditions, as observed here, introgression may promote population expansion into unoccupied habitats and accelerate invasion success. [ABSTRACT FROM AUTHOR]

Host resistance to parasites is a rapidly evolving trait that can influence how hosts modify ecosystems. Eco-evolutionary feedbacks may develop if the ecosystem effects of host resistance influence selection on subsequent host generations. In a mesocosm experiment, using a recently diverged (<100 generations) pair of lake and stream three-spined sticklebacks, we tested how experimental exposure to a common fish parasite (Gyrodactylus spp.) affects interactions between hosts and their ecosystems in two environmental conditions (low and high nutrients). In both environments, we found that stream sticklebacks were more resistant to Gyrodactylus and had different gene expression profiles than lake sticklebacks. This differential infection led to contrasting effects of sticklebacks on a broad range of ecosystem properties, including zooplankton community structure and nutrient cycling. These ecosystem modifications affected the survival, body condition, and gene expression profiles of a subsequent fish generation. In particular, lake juvenile fish suffered increased mortality in ecosystems previously modified by lake adults, whereas stream fish showed decreased body condition in stream fish-modified ecosystems. Parasites reinforced selection against lake juveniles in lake fish-modified ecosystems, but only under oligotrophic conditions. Overall, our results highlight the overlapping timescales and the interplay of host-parasite and host-ecosystem interactions. We provide experimental evidence that parasites influence host-mediated effects on ecosystems and, thereby, change the likelihood and strength of eco-evolutionary feedbacks. [ABSTRACT FROM AUTHOR]

Ecological stoichiometry has generated new insights into how the balance of elements affects ecological interactions and ecosystem processes, but little is known about the ecological and evolutionary dynamics of stoichiometric traits. Understanding the origins and drivers of stoichiometric trait variation between and within species will improve our understanding about the ecological responses of communities to environmental change and the ecosystem effects of organisms. In addition, studying the plasticity, heritability, and genetic basis of stoichiometric traits might improve predictions about how organisms adapt to changing environmental conditions, and help to identify interactions and feedbacks between phenotypic evolution and ecosystem processes. [ABSTRACT FROM AUTHOR]

Lineages with independent evolutionary histories often differ in both their morphology and diet. Experimental work has improved our understanding of the links between the biomechanics of morphological traits and foraging performance (trait utility). However, because the expression of foraging-relevant traits and their utility can be highly context-specific, it is often unclear how dietary divergence arises from evolved phenotypic differences. Here, we explore the phenotypic causes of dietary divergence between two genetically and phenotypically divergent lineages of threespine stickleback (Gasterosteus aculeatus) with independent evolutionary histories of freshwater colonization and adaptation. First, using individuals from a line-cross breeding design, we conducted 150 common-garden foraging trials with a community of multiple prey species and performed morphological and behavioral analyses to test for prey-specific trait utility. Second, we tested if the traits that explain variation in foraging performance among all individuals could also explain the dietary divergence between the lineages. Overall, we found evidence for the utility of several foraging traits, but these traits did not explain the observed dietary divergence between the lineages in a common garden. This work suggests that evolved dietary divergence results not only from differences in morphology but also from divergence in behaviors that underlie prey capture success in species-rich prey communities. [ABSTRACT FROM AUTHOR]

Analysing and interpreting long-term phytoplankton time series present a number of challenges, arising from potential historical inconsistencies in data collection and taxonomic identification of organisms. In a previous paper, Pomati et al. (2012) found a remarkable increase in phytoplankton diversity that coincided with oligotrophication and warming of Lake Zurich over a 32-year period. These findings were recently challenged on the basis of potential biases in detection limits and taxonomic classification over the time series (Straile, Jochimsen & Kümmerlin, 2013). We agree that being cautious with long-term phytoplankton data series is extremely important, but argue that the increase in richness detected in Lake Zurich cannot be due only to methodological bias., Following additional analysis of the Lake Zurich phytoplankton dataset, we found that the shift in taxon detection limits reported by Straile et al. (2013) is not supported by the data and stems from a rounding error in the calculation of density in the dataset available to those authors. We found a decline in the proportional abundance for common taxa, an increase in the annual prevalence of taxa and reduced community turnover over the time series. Taken together, the data clearly indicate a trend of decreasing dominance, while more taxa coexist simultaneously. We also argue that the taxonomic classification has been robust (at least at the family level) and propose a diagnostic plot that can help detect an unbiased signal of change in plankton richness through time., Straile et al. (2013) observed perfect synchrony in species occurrence between Lake Zurich and nearby Lake Walen. While we agree that such perfect synchrony in community composition can reflect a bias in the database compilation, it can also be an important ecological signal of changes in regional species pools that deserves further analysis., We conclude that the results of Pomati et al. (2012) are robust and not substantially undermined by the criticisms of Straile et al. (2013). More generally, it is indeed possible to extract meaningful signals of biodiversity change from long-term phytoplankton monitoring datasets, provided there is a clear understanding of how the data have been sampled, recorded and analysed over the history of the time series. [ABSTRACT FROM AUTHOR]

Quaternary climate fluctuations can affect speciation in regional biodiversity assembly in two non-mutually exclusive ways: a glacial species pump, where isolation in glacial refugia accelerates allopatric speciation, and adaptive radiation in underused adaptive zones during ice-free periods. We detected biogeographic and genetic signatures associated with both mechanisms in the assembly of the biota of the European Alps. Age distributions of endemic and widespread species within aquatic and terrestrial taxa (amphipods, fishes, amphibians, butterflies and flowering plants) revealed that endemic fish evolved only in lakes, are highly sympatric, and mainly of Holocene age, consistent with adaptive radiation. Endemic amphipods are ancient, suggesting preglacial radiation with limited range expansion and local Pleistocene survival, perhaps facilitated by a groundwater-dwelling lifestyle. Terrestrial endemics are mostly of Pleistocene age and are thus more consistent with the glacial species pump. The lack of evidence for Holocene adaptive radiation in the terrestrial biome is consistent with faster recolonization through range expansion of these taxa after glacial retreats. More stable and less seasonal ecological conditions in lakes during the Holocene may also have contributed to Holocene speciation in lakes. The high proportion of young, endemic species makes the Alpine biota vulnerable to climate change, but the mechanisms and consequences of species loss will likely differ between biomes because of their distinct evolutionary histories. [ABSTRACT FROM AUTHOR]

Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Although this process is a major generator of biodiversity, its genetic basis is still poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces the growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but depend on the ecological context. [ABSTRACT FROM AUTHOR]

Long‐chain polyunsaturated fatty acids are biologically important lipids that are unevenly distributed between and throughout environments. This heterogeneity can affect the evolution of metabolic processes, as populations adapt to the resource landscape that they encounter. Here, we compare fatty acid phenotypes of stickleback over two time scales of evolutionary divergence: between two lineages with different metabolic capacities for fatty acid synthesis (i.e. different copy number of the fatty acid desaturase gene; FADS2) that independently colonized European freshwaters during the Pleistocene and Holocene; and between two ecotypes within each lineage that have diverged more recently (~150 years) in different habitats (i.e. lake and stream). We measured fatty acid profiles of wild‐caught and lab‐reared fish for each lineage and ecotype combination after rearing lab fish on a diet deficient in omega‐3 long‐chain polyunsaturated fatty acids. Since these lineages hybridize in nature, we also measured profiles of lab‐reared hybrids and backcrosses raised on the same deficient diet. Wild fish showed strong compositional differences in fatty acids between habitats, lineages and sexes. Common garden fish had generally lower polyunsaturated fatty acid levels than wild fish, and females had lower omega‐6:omega‐3 than males. Fish from the lineage with fewer FADS2 copies also had lower levels of docosahexaenoic acid. Overall, we document divergence in fatty acid phenotypes between stickleback lineages with different histories of freshwater colonization, and between ecotypes in the early stages of adaptive population divergence. [ABSTRACT FROM AUTHOR]

The field of paleolimnology has made tremendous progress in reconstructing past biotic and abiotic environmental conditions of aquatic ecosystems based on sediment records. This, together with the rapid development of molecular technologies, provides new opportunities for studying evolutionary processes affecting lacustrine communities over multicentennial to millennial timescales. From an evolutionary perspective, such analyses provide important insights into the chronology of past environmental conditions , the dynamics of phenotypic evolution, and species diversification. Here, we review recent advances in paleolimnological, paleogenetic, and molecular approaches and highlight how their integrative use can help us better understand the ecological and evolutionary responses of species and communities to environmental change. Paleolimnological data can help to reconstruct past environmental conditions and their changes over time in aquatic ecosystems, providing important information for inferring past ecological conditions, trends in community assembly through time, and rates and directions of evolution. New approaches to analyzing ancient sedimentary DNA, RNA, or proteins, lipid biomarkers, and stable isotopes can be combined with phenotypic analyses of (sub)fossils to test novel hypotheses about past community assembly, and evolutionary processes such as phenotypic change and adaptation, as well as phenotypic diversification and adaptive radiation. Integration of these new and classical approaches is expanding our ability to understand organism–environment interactions and evolutionary responses to environmental change. [ABSTRACT FROM AUTHOR]

In recent years, there has been a renewed interest in the ecological consequences of individual trait variation within populations. Given that individual variability arises from evolutionary dynamics, to fully understand eco-evolutionary feedback loops, we need to pay special attention to how standing trait variability affects ecological dynamics. There is mounting empirical evidence that intra-specific phenotypic variation can exceed species-level means, but theoretical models of multi-trophic species coexistence typically neglect individual-level trait variability. What is needed are multispecies datasets that are resolved at the individual level that can be used to discriminate among alternative models of resource selection and species coexistence in food webs. Here, using one the largest individual-based datasets of a food web compiled to date, along with an individual trait-based stochastic model that incorporates Approximate Bayesian computation methods, we document intra-population variation in the strength of prey selection by different classes or predator phenotypes which could potentially alter the diversity and coexistence patterns of food webs. In particular, we found that strongly connected individual predators preferentially consumed common prey, whereas weakly connected predators preferentially selected rare prey. Such patterns suggest that food web diversity may be governed by the distribution of predator connectivity and individual trait variation in prey selection. We discuss the consequences of intra-specific variation in prey selection to assess fitness differences among predator classes (or phenotypes) and track longer term food web patterns of coexistence accounting for several phenotypes within each prey and predator species. [ABSTRACT FROM AUTHOR]