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Growth is a function of the net accrual of resources by an organism. Energy and elemental contents of organisms are dynamically linked through their uptake and allocation to biomass production, yet we lack a full understanding of how these dynamics regulate growth rate. Here, we develop a multivariate imbalance framework, the growth efficiency hypothesis, linking organismal resource contents to growth and metabolic use efficiencies, and demonstrate its effectiveness in predicting consumer growth rates under elemental and food quantity limitation. The relative proportions of carbon (%C), nitrogen (%N), phosphorus (%P), and adenosine triphosphate (%ATP) in consumers differed markedly across resource limitation treatments. Differences in their resource composition were linked to systematic changes in stoichiometric use efficiencies, which served to maintain relatively consistent relationships between elemental and ATP content in consumer tissues and optimize biomass production. Overall, these adjustments were quantitatively linked to growth, enabling highly accurate predictions of consumer growth rates., Competing Interests: Competing interests statement:The authors declare no competing interest.

Characterising the extent and sources of intraspecific variation and their ecological consequences is a central challenge in the study of eco-evolutionary dynamics. Ecological stoichiometry, which uses elemental variation of organisms and their environment to understand ecosystem patterns and processes, can be a powerful framework for characterising eco-evolutionary dynamics. However, the current emphasis on the relative content of elements in the body (i.e. organismal stoichiometry) has constrained its application. Intraspecific variation in the rates at which elements are acquired, assimilated, allocated or lost is often greater than the variation in organismal stoichiometry. There is much to gain from studying these traits together as components of an 'elemental phenotype'. Furthermore, each of these traits can have distinct ecological effects that are underappreciated in the current literature. We propose a conceptual framework that explores how microevolutionary change in the elemental phenotype occurs, how its components interact with each other and with other traits, and how its changes can affect a wide range of ecological processes. We demonstrate how the framework can be used to generate novel hypotheses and outline pathways for future research that enhance our ability to explain, analyse and predict eco-evolutionary dynamics., (© 2023 The Authors. Ecology Letters published by John Wiley & Sons Ltd.)

Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister-taxa, Daphnia pulicaria and Daphnia pulex. First, we assembled a phased chromosome-scale genome assembly using trio-binning for D. pulicaria and constructed a genetic map using an F2-intercross panel to understand sex-specific recombination rate heterogeneity. Finally, we used a ddRADseq data set with broad geographic sampling of D. pulicaria, D. pulex, and their hybrids to understand the patterns of genome-scale divergence and demographic parameters. Our study provides the first sex-specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male-biased heterochiasmy in D. pulicaria, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are probably driven by selection on D. pulicaria, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome-wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty., (© 2022 John Wiley & Sons Ltd.)

About 20 elements underlie biology and thus constrain biomass production. Recent systems-level observations indicate that altered supply of one element impacts the processing of most elements encompassing an organism (i.e. ionome). Little is known about the evolutionary tendencies of ionomes as populations adapt to distinct biogeochemical environments. We evolved the bacterium Serratia marcescens under five conditions (i.e. low carbon, nitrogen, phosphorus, iron or manganese) that limited the yield of the ancestor compared with replete medium, and measured the concentrations and use efficiency of these five, and five other elements. Both physiological responses of the ancestor, as well as evolutionary responses of descendants to experimental environments involved changes in the content and use efficiencies of the limiting element, and several others. Differences in coefficients of variation in elemental contents based on biological functions were evident, with those involved in biochemical building (C, N, P, S) varying least, followed by biochemical balance (Ca, K, Mg, Na), and biochemical catalysis (Fe, Mn). Finally, descendants evolved to mitigate elemental imbalances evident in the ancestor in response to limiting conditions. Understanding the tendencies of such ionomic responses will be useful to better forecast biological responses to geochemical changes.

The growth rate hypothesis (GRH) posits that variation in organismal stoichiometry (C:P and N:P ratios) is driven by growth-dependent allocation of P to ribosomal RNA. The GRH has found broad but not uniform support in studies across diverse biota and habitats. We synthesise information on how and why the tripartite growth-RNA-P relationship predicted by the GRH may be uncoupled and outline paths for both theoretical and empirical work needed to broaden the working domain of the GRH. We found strong support for growth to RNA (r 2  = 0.59) and RNA-P to P (r 2  = 0.63) relationships across taxa, but growth to P relationships were relatively weaker (r 2  = 0.09). Together, the GRH was supported in ~50% of studies. Mechanisms behind GRH uncoupling were diverse but could generally be attributed to physiological (P accumulation in non-RNA pools, inactive ribosomes, translation elongation rates and protein turnover rates), ecological (limitation by resources other than P), and evolutionary (adaptation to different nutrient supply regimes) causes. These factors should be accounted for in empirical tests of the GRH and formalised mathematically to facilitate a predictive understanding of growth., (© 2022 The Authors. Ecology Letters published by John Wiley & Sons Ltd.)

Our understanding of the mechanisms mediating the resilience of organisms to environmental change remains lacking. Heavy metals negatively affect processes at all biological scales, yet organisms inhabiting contaminated environments must maintain homeostasis to survive. Tar Creek in Oklahoma, USA, contains high concentrations of heavy metals and an abundance of Western mosquitofish (Gambusia affinis), though several fish species persist at lower frequency. To test hypotheses about the mechanisms mediating the persistence and abundance of mosquitofish in Tar Creek, we integrated ionomic data from seven resident fish species and transcriptomic data from mosquitofish. We predicted that mosquitofish minimize uptake of heavy metals more than other Tar Creek fish inhabitants and induce transcriptional responses to detoxify metals that enter the body, allowing them to persist in Tar Creek at higher density than species that may lack these responses. Tar Creek populations of all seven fish species accumulated heavy metals, suggesting mosquitofish cannot block uptake more efficiently than other species. We found population-level gene expression changes between mosquitofish in Tar Creek and nearby unpolluted sites. Gene expression differences primarily occurred in the gill, where we found upregulation of genes involved with lowering transfer of metal ions from the blood into cells and mitigating free radicals. However, many differentially expressed genes were not in known metal response pathways, suggesting multifarious selective regimes and/or previously undocumented pathways could impact tolerance in mosquitofish. Our systems-level study identified well characterized and putatively new mechanisms that enable mosquitofish to inhabit heavy metal-contaminated environments., (© 2022 John Wiley & Sons Ltd.)

Cyanobacterial harmful algal blooms (HABs) are increasing in frequency and magnitude worldwide. A number of parameters are thought to underlie HABs, including the ratio at which two key elements, nitrogen (N) and phosphorus (P) are supplied, although a predictive understanding eludes us. While the physiological importance of iron (Fe) in electron transport and N-fixation is well known, relatively little is known about its impacts on the growth of freshwater cyanobacteria. Moreover, there is growing appreciation for correlated changes in the quotas of multiple elements encompassing an organism (i.e. the ionome) when the supply of one element changes, indicating that growth differences arise from complex biochemical adjustments rather than limitation of a key anabolic process by a single element. In this study, the effects of supply N:P and Fe on the growth and ionome of Dolichospermum, a nitrogen-fixing cyanobacterium found in freshwater ecosystems, were examined. Changes in both supply N:P and Fe had significant effects on yield. Consistent with prior observations, cyanobacterial growth was higher at N:P = 20, compared to N:P = 5, and quotas of all elements decreased with growth. Yield was negatively related with the degree of imbalance between dissolved supply and intracellular concentrations of not only N and Fe, but also multiple other elements. Changes in Fe supply had a significant effect on yield in N-limited conditions (N:P = 5). Again, ionome-wide imbalances decreased yield. Together, these results indicate that attention to multiple elements encompassing the ionome of a HAB-forming taxon, and the supplies of such elements may help improve the ability to forecast blooms. Such elemental interactions may be critical as limnologists begin to appreciate the staggering variation in the supplies of such elements among lakes, and anthropogenic activities continue to alter global biogeochemical cycles., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Phosphorus (P) is essential for growth of all organisms, and P content is correlated with growth in most taxa. Although P content was initially considered to be a trait fixed at the species level, there is growing evidence for considerable intraspecific variation. Selection on such variation can thus alter the rates at which P fluxes through food webs. Nevertheless, prior work describing the sources and extent of intraspecific variation in P content were not genetically explicit, confounded by unknown genetic background and evolutionary history. We constructed an F2 recombinant population of the dominant freshwater grazer, Daphnia pulicaria to mitigate such issues. F2 recombinants exhibited considerable variation in growth rate, P content (0.49%-1.97%), P use efficiency (PUE; 51-208 mg biomass/mg P), and correlated traits such as hatching time of resting eggs, in common garden conditions. These results clearly demonstrate the scope of genetic recombination in generating variation in ecologically relevant traits. The absence of environmental selection is a likely component driving such variation not observed in natural settings. Although phosphoglucose isomerase (PGI) genotype was significantly associated with variation in hatching time of resting eggs, contrary to prior work with less rigorous designs, and allelic variation at the PGI locus did not explain variation in P content and PUE of Daphnia, indicating that such quantitative traits are under polygenic control. Together, these results suggest that although there is considerable genetic scope for variation in key ecologically relevant traits, such as P content and efficiency of P use, these traits are likely under strong stabilizing selection, most likely due to selection on growth rate and size. Importantly, our observations suggest that anthropogenic alterations to P supply due to eutrophication could alter selection on these traits, thereby rapidly altering the role Daphnia plays in the P cycle of lakes., (© 2020 British Ecological Society.)

Diverse global change processes are reshaping the biogeochemistry of stream ecosystems. Nutrient enrichment is a common stressor that can modify flows of biologically important elements such as carbon (C), nitrogen (N), and phosphorus (P) through stream foodwebs by altering the stoichiometric composition of stream organisms. However, enrichment effects on concentrations of other important essential and trace elements in stream taxa are less understood. We investigated shifts in macroinvertebrate ionomes in response to changes in coarse benthic organic matter (CBOM) stoichiometry following N and P enrichment of five detritus-based headwater streams. Concentrations of most elements (17/19) differed among three insect genera (Maccaffertium sp., Pycnopsyche spp., and Tallaperla spp.) prior to enrichment. Genus-specific changes in the body content of: P, magnesium, and sodium (Na) in Tallaperla; P, Na, and cadmium in Pycnopsyche; and P in Maccaffertium were also found across CBOM N:P gradients. These elements increased in Tallaperla but decreased in the other two taxa due to growth dilution at larger body sizes. Multivariate elemental differences were found across all taxa, and ionome-wide shifts with dietary N and P enrichment were also observed in Tallaperla and Pycnopsyche. Our results show that macroinvertebrates exhibit distinct differences in elemental composition beyond C, N, and P and that the ionomic composition of common stream taxa can vary with body size and N and P enrichment. Thus, bottom-up changes in N and P supplies could potentially influence the cycling of lesser studied biologically essential elements in aquatic environments by altering their relative proportions in animal tissues.

The availability of iron (Fe) varies considerably among diet items, as well as ecosystems. Availability of Fe has also changed due to anthropogenic environmental changes in oceanic as well as inland ecosystems. We know little about its role in the nutrition of ecologically important consumers, particularly in inland ecosystems. Physiological studies in several taxa indicate marked effects of dietary Fe on oogenesis. We predicted that differential Fe supply to algae will impact algal Fe concentration with consequences on the life history of the freshwater grazer, Daphnia magna. We found that algal Fe concentration increased with Fe supply, but did not affect algal growth, indicating that the majority of experimental Fe additions were likely adsorbed to, or stored in algal cells. Regardless, data indicate that algal Fe impacted the reproductive traits (age and size at maturity) but not juvenile growth rate of Daphnia. A subsequent experiment revealed that Fe concentration in eggs was significantly higher than the rest of Daphnia. These results indicate that the concentration of Fe in or on algal cells may vary considerably among ecosystems overlying distinct geological formations differing in Fe, possibly with important implications for zooplankton life histories. Understanding the mechanisms underlying this response is unlikely to be accomplished by a strict focus on Fe because we found correlated shifts in the algal ionome, with concomitant ionome-wide adjustments in Daphnia. Information on ionome-wide responses may be useful in better understanding the responses of biota to changes in the supply of any one element.

Understanding how populations adapt to rising temperatures has been a challenge in ecology. Research often evaluates multiple populations to test whether local adaptation to temperature regimes is occurring. Space-for-time substitutions are common, as temporal constraints limit our ability to observe evolutionary responses. We employed a resurrection ecology approach to understand how thermal tolerance has changed in a Daphnia pulicaria population over time. Temperatures experienced by the oldest genotypes were considerably lower than the youngest. We hypothesized clones were adapted to the thermal regimes of their respective time periods. We performed two thermal shock experiments that varied in length of heat exposure. Overall trends revealed that younger genotypes exhibited higher thermal tolerance than older genotypes; heat shock protein (hsp70) expression increased with temperature and varied among genotypes, but not across time periods. Our results indicate temperature may have been a selective factor on this population, although the observed responses may be a function of multifarious selection. Prior work found striking changes in population genetic structure, and in other traits that were strongly correlated with anthropogenic changes. Resurrection ecology approaches should help our understanding of interactive effects of anthropogenic alterations to temperature and other stressors on the evolutionary fate of natural populations., Competing Interests: We declare we have no competing interests.

Resting eggs banks are unique windows that allow us to directly observe shifts in population genetics, and phenotypes over time as natural populations evolve. Though a variety of planktonic organisms also produce resting stages, the keystone freshwater consumer, Daphnia, is a well-known model for paleogenetics and resurrection ecology. Nevertheless, paleogenomic investigations are limited largely because resting eggs do not contain enough DNA for genomic sequencing. In fact, genomic studies even on extant populations include a laborious preparatory phase of batch culturing dozens of individuals to generate sufficient genomic DNA. Here, we furnish a protocol to generate whole genomes of single ephippial (resting) eggs and single daphniids. Whole genomes of single ephippial eggs and single adults were amplified using Qiagen REPLI-g Single Cell kit reaction, followed by NEBNext Ultra DNA Library Prep Kit for library construction and Illumina sequencing. We compared the quality of the single-egg and single-individual amplified genomes to the standard batch genomic DNA extraction in the absence of genome amplification. At mean 20× depth, coverage was essentially identical for the amplified single individual relative to the unamplified batch extracted genome (>90% of the genome was covered and callable). Finally, while amplification resulted in the slight loss of heterozygosity for the amplified genomes, estimates were largely comparable and illustrate the utility and limitations of this approach in estimating population genetic parameters over long periods of time in natural populations of Daphnia and also other small species known to produce resting stages., (© 2017 John Wiley & Sons Ltd.)

The framework ecological stoichiometry uses elemental composition of species to make predictions about growth and competitive ability in defined elemental supply conditions. Although intraspecific differences in stoichiometry have been observed, we have yet to understand the mechanisms generating and maintaining such variation. We used variation in phosphorus (P) content within a Daphnia species to test the extent to which %P can explain variation in growth and competition. Further, we measured 33 P kinetics (acquisition, assimilation, incorporation and retention) to understand the extent to which such variables improved predictions. Genotypes showed significant variation in P content, 33 P kinetics and growth rate. P content alone was a poor predictor of growth rate and competitive ability. While most genotypes exhibited the typical growth penalty under P limitation, a few varied little in growth between P diets. These observations indicate that some genotypes can maintain growth under P-limited conditions by altering P use, suggesting that decomposing P content of an individual into physiological components of P kinetics will improve stoichiometric models. More generally, attention to the interplay between nutrient content and nutrient-use is required to make inferences regarding the success of genotypes in defined conditions of nutrient supply., Competing Interests: We declare we have no competing interests.

The evolution of tolerance to environmental contaminants in non-target taxa has been largely studied by comparing extant populations experiencing contrasting exposure. Previous research has demonstrated that "resurrected" genotypes from a population of Daphnia pulicaria express temporal variation in sensitivity to the insecticide chlorpyrifos. Ancient genotypes (1301-1646AD.) were on average more sensitive to this chemical compared to the contemporary genotypes (1967-1977AD.). To determine the physiological mechanisms of tolerance, a series of biochemical assays was performed on three ancient and three contemporary genotypes; these six genotypes exhibited the most sensitive and most tolerant phenotypes within the population, respectively. Metabolic tolerance mechanisms were evaluated using acute toxicity testing, while target-site tolerance was assessed via in vitro acetylcholinesterase (AChE) assays. Acute toxicity tests were conducted using i) the toxic metabolite chlorpyrifos-oxon (CPF-oxon) and ii) CPF-oxon co-applied with piperonyl butoxide (PBO), a known Phase-I metabolic inhibitor. Both series of toxicity tests reduced the mean variation in sensitivity between tolerant and sensitive genotypes. Exposure to CPF-O reduced the disparity from a 4.7-fold to 1.6-fold difference in sensitivity. The addition of PBO further reduced the variation to a 1.2-fold difference in sensitivity. In vitro acetylcholinesterase assays yielded no significant differences in constitutive activity or target-site sensitivity. These findings suggest that pathways involving Phase-I detoxification and/or bioactivation of chlorpyrifos play a significant role in dictating the microevolutionary trajectories of tolerance in this population., (Copyright © 2017 Elsevier B.V. All rights reserved.)

This perspective provides an overview to the Special Issue on Resurrection Ecology (RE). It summarizes the contributions to this Special Issue, and provides background information and future prospects for the use of RE in both basic and applied evolutionary studies.

Elemental homeostasis has been largely characterized using three important elements that were part of the Redfield ratio (i.e., carbon: nitrogen: phosphorus). These efforts have revealed substantial diversity in homeostasis among taxonomic groups and even within populations. Understanding the evolutionary basis, and ecological consequences of such diversity is a central challenge. Here, we propose that a more complete understanding of homeostasis necessitates the consideration of other elements beyond C, N, and P. Specifically, we posit that physiological complexity underlying maintenance of elemental homeostasis along a single elemental axis impacts processing of other elements, thus altering elemental homeostasis along other axes. Indeed, transcriptomic studies in a wide variety of organisms have found that individuals differentially express significant proportions of the genome in response to variability in supply stoichiometry in order to maintain varying levels of homeostasis. We review the literature from the emergent field of ionomics that has established the consequences of such physiological trade-offs on the content of the entire suite of elements in an individual. Further, we present experimental data on bacteria exhibiting divergent phosphorus homeostasis phenotypes demonstrating the fundamental interconnectedness among elemental quotas. These observations suggest that physiological adjustments can lead to unexpected patterns in biomass stoichiometry, such as correlated changes among suites of non-limiting microelements in response to limitation by macroelements. Including the entire suite of elements that comprise biomass will foster improved quantitative understanding of the links between chemical cycles and the physiology of organisms.

Endopolyploidy - the existence of higher-ploidy cells within organisms that are otherwise of a lower ploidy level (generally diploid) - was discovered decades ago, but remains poorly studied relative to other genomic phenomena, especially in animals. Our synthetic review suggests that endopolyploidy is more common in animals than often recognized and probably influences a number of fitness-related and ecologically important traits. In particular, we argue that endopolyploidy is likely to play a central role in key traits such as gene expression, body and cell size, and growth rate, and in a variety of cell types, including those responsible for tissue regeneration, nutrient storage, and inducible anti-predator defences. We also summarize evidence for intraspecific genetic variation in endopolyploid levels and make the case that the existence of this variation suggests that endopolyploid levels are likely to be heritable and thus a potential target for natural selection. We then discuss why, in light of evident benefits of endopolyploidy, animals remain primarily diploid. We conclude by highlighting key areas for future research such as comprehensive evaluation of the heritability of endopolyploidy and the adaptive scope of endopolyploid-related traits, the extent to which endopolyploid induction incurs costs, and characterization of the relationships between environmental variability and endopolyploid levels., (© 2015 Cambridge Philosophical Society.)

Understanding the evolutionary consequences of the green revolution, particularly in wild populations, is an important frontier in contemporary biology. Because human impacts have occurred at varying magnitudes or time periods depending on the study ecosystem, evolutionary histories may vary considerably among populations. Paleogenetics in conjunction with paleolimnology enable us to associate microevolutionary dynamics with detailed information on environmental change. We used this approach to reconstruct changes in the temporal population genetic structure of the keystone zooplankton grazer, Daphnia pulicaria, using dormant eggs extracted from sediments in two Minnesota lakes (South Center, Hill). The extent of agriculture and human population density in the catchment of these lakes has differed markedly since European settlement in the late 19th century and is reflected in their environmental histories reconstructed here. The reconstructed environments of these two lakes differed strongly in terms of environmental stability and their associated patterns of Daphnia population structure. We detected long periods of stability in population structure and environmental conditions in South Center Lake that were followed by a dramatic temporal shift in population genetic structure after the onset of European settlement and industrialized agriculture in its watershed. In particular, we noted a 24.3-fold increase in phosphorus (P) flux between pre-European and modern sediment P accumulation rates (AR) in this lake. In contrast, no such shifts were detected in Hill Lake, where the watershed was not as impacted by European settlement and rates of change were less directional with a much smaller increase in sediment P AR (2.3-fold). We identify direct and indirect effects of eutrophication proxies on genetic structure in these lake populations and demonstrate the power of using this approach in understanding the consequences of anthropogenic environmental change on natural populations throughout historic time periods., (© 2016 John Wiley & Sons Ltd.)

Global warming and predation risk can have important impacts on animal physiology and life histories that can have consequences for ecosystem function. Zhang et al. () recently tested the separate and interactive effects of warming and predation risk on the body composition of Daphnia magna. By measuring both the elemental and biochemical composition of individuals, they showed that D. magna body elemental composition responded opposite to theoretical predictions and previous studies but that these changes were explained by adaptive life-history shifts in allocation to protein in eggs versus body lipid reserves. Photograph by Joachim Mergeay. Zhang, C., Jansen, M., De Meester, L. & Stoks, R. (2016) Energy storage and fecundity explain deviations from ecological stoichiometry predictions under global warming and size-selective predation. Journal of Animal Ecology 85, 1431-1441. Understanding the mechanisms through which energy and nutrients flow through ecosystems is critical to predicting and mitigating the consequences of climate change and other ecological disturbances. Ecological stoichiometry and nutritional geometry, using data on elements and macromolecules, respectively, have independently made major contributions towards this goal. Zhang et al. () provide data demonstrating that these two major frameworks can provide complementary insight into the consequences of global warming and predation risk for the physiology and life-history traits of a key aquatic herbivore, Daphnia magna. This study should catalyse further work to unite these two parallel and complementary frameworks., (© 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.)

Although sexually dimorphic traits are often well studied, we know little about sex-specific resource use strategies that should underlie such dimorphism. We measured sex-specific responses in acquisition and assimilation of two fundamental resources, carbon (C) and phosphorus (P) in juvenile and mature Hyalella amphipods given low and high supplies of inorganic phosphate, analogous to oligotrophic and eutrophic conditions, respectively. Additionally, we quantified allocation of resources to sexual traits in males. Dual radiotracer ((14)C and (33)P) assays revealed substantial age- and sex-specific differences in acquisition and assimilation. Furthermore, a phenotypic manipulation experiment revealed that amphipods fed low-P food allocated more C to all traits than those fed high-P food. Importantly, we found that amphipods preferentially allocated more C to the development of a sexually selected trait (the posterior gnathopod), compared with a serially homologous trait (the fifth pereopod) not under sexual selection. Substantial differences in how the sexes use fundamental resources, and the impact of altered nutrient supply on such differences, illuminate sexual dimorphism at the lowest level of biological organization. Such information will be important in understanding how sex- and age-specific life history demands influence nutrient processing in a biosphere characterized by rapidly changing alterations to biogeochemical cycles., (© 2016. Published by The Company of Biologists Ltd.)

Variation in energy availability or maintenance costs in extreme environments can exert selection for efficient energy use, and reductions in organismal energy demand can be achieved in two ways: reducing body mass or metabolic suppression. Whether long-term exposure to extreme environmental conditions drives adaptive shifts in body mass or metabolic rates remains an open question. We studied body size variation and variation in routine metabolic rates in locally adapted populations of extremophile fish (Poecilia mexicana) living in toxic, hydrogen sulfide-rich springs and caves. We quantified size distributions and routine metabolic rates in wild-caught individuals from four habitat types. Compared with ancestral populations in nonsulfidic surface habitats, extremophile populations were characterized by significant reductions in body size. Despite elevated metabolic rates in cave fish, the body size reduction precipitated in significantly reduced energy demands in all extremophile populations. Laboratory experiments on common garden-raised fish indicated that elevated routine metabolic rates in cave fish likely have a genetic basis. The results of this study indicate that adaptation to extreme environments directly impacts energy metabolism, with fish living in cave and sulfide spring environments expending less energy overall during routine metabolism.

This study examined how genotypes of Daphnia pulicaria from a single population, separated by thousands of generations of evolution in the wild, differ in their sensitivity to a novel anthropogenic stressor. These genotypes were resurrected from preserved resting eggs isolated from sediments belonging to three time periods: 2002-2008, 1967-1977, and 1301-1646 A.D. Toxicity of the organophosphate insecticide chlorpyrifos was determined through a series of acute toxicity tests. There was a significant dose-response effect in all genotypes studied. Moreover, significant variation in toxicity among genotypes within each time period was detected. Importantly, a significant effect of time period on sensitivity to chlorpyrifos was found. Analysis of the median effect concentrations (EC50s) for genotypes within each time period indicated that the 1301-1646 genotypes were 2.7 times more sensitive than the 1967-1977 genotypes. This trend may be partially explained by microevolutionary shifts in response to cultural eutrophication.

Little is known about the role of transcriptomic changes in driving phenotypic evolution in natural populations, particularly in response to anthropogenic environmental change. Previous analyses of Daphnia genotypes separated by centuries of evolution in a lake using methods in resurrection ecology revealed striking genetic and phenotypic shifts that were highly correlated with anthropogenic environmental change, specifically phosphorus (P)-driven nutrient enrichment (i.e. eutrophication). Here, we compared the transcriptomes of two ancient (~700-year-old) and two modern (~10-year-old) genotypes in historic (low P) and contemporary (high P) environmental conditions using microarrays. We found considerable transcriptomic variation between 'ancient' and 'modern' genotypes in both treatments, with stressful (low P) conditions eliciting differential expression (DE) of a larger number of genes. Further, more genes were DE between 'ancient' and 'modern' genotypes than within these groups. Expression patterns of individual genes differed greatly among genotypes, suggesting that different transcriptomic responses can result in similar phenotypes. While this confounded patterns between 'ancient' and 'modern' genotypes at the gene level, patterns were discernible at the functional level: annotation of DE genes revealed particular enrichment of genes involved in metabolic pathways in response to P-treatments. Analyses of gene families suggested significant DE in pathways already known to be important in dealing with P-limitation in Daphnia as well as in other organisms. Such observations on genotypes of a single natural population, separated by hundreds of years of evolution in contrasting environmental conditions before and during anthropogenic environmental changes, highlight the important role of transcriptional mechanisms in the evolutionary responses of populations., (© 2014 John Wiley & Sons Ltd.)

Understanding how the genome interacts with the environment to produce a diversity of phenotypes is a central challenge in biology. However, we know little about how traits involved in nutrient processing interact with key ecological parameters, such as the supply of mineral nutrients, particularly in animals. The framework of ecological stoichiometry uses information on the content of key elements such as carbon (C) and phosphorus (P) in individuals to predict the success of species. Nevertheless, intraspecific variation in content and the underlying mechanisms that generate such variation has been poorly explored. We studied two genotypes (G1 and G2) of Daphnia pulex that exhibit striking genotype × environment (G × E) interaction in response to shifts in dietary stoichiometry (C:P). G1 had higher fitness under C:P ∼ 100 diet, while G2 performed better in C:P ∼ 800. Dual (14) C/(33) P radiotracer assays show that G1 was more efficient in C processing, while G2 was more efficient in P use. Microarrays revealed that after 3 days of incubation, the genotypes differentially expressed ∼ 25% (7,224) of the total genes on the array under C:P ∼ 100 diet, and ∼ 30% (8,880) of genes under C:P ∼ 800. These results indicate large differences in C and P use between two coexisting genotypes. Importantly, such physiological differences can arise via differential expression of the genome due to alterations in dietary stoichiometry. Basic frameworks such as ecological stoichiometry enable integration of physiological and transcriptomic data, and represent initial steps toward understanding the interplay between fundamental ecological parameters such as nutrient supply and important evolutionary processes such as G × E interactions., (© 2014 Wiley Periodicals, Inc.)

Understanding the ecological consequences of evolutionary change is a central challenge in contemporary biology. We propose a framework based on the ˜25 elements represented in biology, which can serve as a conduit for a general exploration of poorly understood evolution-to-ecology links. In this framework, known as ecological stoichiometry, the quantity of elements in the inorganic realm is a fundamental environment, while the flow of elements from the abiotic to the biotic realm is due to the action of genomes, with the unused elements excreted back into the inorganic realm affecting ecological processes at higher levels of organization. Ecological stoichiometry purposefully assumes distinct elemental composition of species, enabling powerful predictions about the ecological functions of species. However, this assumption results in a simplified view of the evolutionary mechanisms underlying diversification in the elemental composition of species. Recent research indicates substantial intraspecific variation in elemental composition and associated ecological functions such as nutrient excretion. We posit that attention to intraspecific variation in elemental composition will facilitate a synthesis of stoichiometric information in light of population genetics theory for a rigorous exploration of the ecological consequences of evolutionary change.

Sexual traits are especially sensitive to low food resources. Other environmental parameters (e.g., predation) should also affect sexual trait expression by favoring investment in viability traits rather than sexual traits. We know surprisingly little about how predators alter investment in sexual traits, or how predator and resource environments interact to affect sexual trait investment. We explored how increasing phosphorous (P) availability, at a level mimicking cultural eutrophication, affects the development of sexual, nonsexual, and viability traits of amphipods in the presence and absence of predators. Sexual traits and growth were hypersensitive to low P compared to nonsexual traits. However, a key sexual trait responded to low P only when predator cues were absent. Furthermore, investment trade-offs between sexual traits and growth only occurred when P was low. The phenotypic changes caused by predator cues and increased P availability resulted in higher male mating success. Thus, eutrophication not only affects sexual trait expression but also masks the trade-off between traits with similar P demand. Sensitivity of sexually selected traits to changes in P, combined with the important roles these traits play in determining fitness and driving speciation, suggests that human-induced environmental change can greatly alter the evolutionary trajectories of populations., (© 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.)

Disaccord between the supply and demand of energy (carbon, C) and certain material elements (e.g. phosphorus, P) across trophic levels is common in most ecosystems and impacts the strength of trophic interactions and ecosystem functions such as productivity and nutrient recycling. Yet, we know little about mechanisms operating at the lower levels of biological organization that drive such higher-level ecological processes. Such information should help refine theories integrating biological processes at multiple levels of organization. Understanding the expression and functions of genes that underlie (to a large degree) physiological adjustments made by organisms to stoichiometric imbalances at trophic interfaces is a first step in this enterprise. Here, we investigate adjustments in gene expression to varying supply and demand of phosphorus relative to other dietary components in the keystone limnetic herbivore, Daphnia pulex. Daphniids were fed an algal diet of either LoC-HiP (molar C:P ∼100) or HiC-LoP (molar C:P ∼900) for 5 days, resulting in significant growth reductions under HiC-LoP conditions. Microarrays measured the transcriptional regulation of 8217 annotated protein-coding genes under contrasting dietary conditions and revealed 1818 differentially expressed (DE) genes; 19% are genes unique to the Daphnia lineage. We mapped DE genes onto a global chart of metabolic pathways to obtain a systems-level perspective on the responses to stoichiometric imbalances. Daphnia differentially regulated pathways were involved in sequestering limiting elements, and in dealing with the products of metabolic adjustments that may be triggered by nutrient stress in primary producers. Functional genomics at trophic interfaces illuminate the complexity of processes underlying stoichiometric constraints on energy and nutrient fluxes in ecosystems., (© 2011 Blackwell Publishing Ltd.)

The genic capture model offers a promising solution to the lek paradox. Heightened condition dependency of sexually selected traits is a prerequisite of this model. Condition dependency is empirically inferred by the sensitivity of traits to stressors. The magnitude of ecological stress (e.g., competition and predation) experienced by populations varies considerably. Thus, condition dependence should manifest more in populations experiencing higher levels of stress. We experimentally assessed the sensitivity of a sexually selected trait (posterior gnathopod) to food resource stress in an amphipod species. We found that gnathopod size variation was 59% higher under food stress, with no corresponding effect on nonsexually selected traits. In addition, we assessed levels of gnathopod variation and the allometry of gnathopods for males sampled from natural populations for two amphipod species that experience different levels of stress (driven by contrasting size-selective predation and associated life-history trade-offs). Populations that experience higher resource stress had both steeper allometries and greater gnathopod size variation. These results suggest that the magnitude of ecological stress experienced by natural populations strongly impacts condition dependency of sexually selected traits, and could play an important role in shaping trait variation and thus the opportunity for sexual selection., (© 2010 The Author(s). Journal compilation © 2010 The Society for the Study of Evolution.)

Pervasive relationships between growth rate, genome size and RNA content exist. One interesting potential consequence of these interrelationships is that selection for high growth rate should be associated with small genomes and high RNA content. Here, we use phosphorus (P) and nitrogen (N) demands of growth along with nucleic acid production as the currency to explore the interrelationships between growth rate and genome size in eukaryotes. We argue that reallocation of P (and eventually N) from DNA to RNA under sustained selection for rapid growth in nutritionally limited environments can lead to genome streamlining in eukaryotes, and that this mechanism might contribute to the evolution of reduced genome size., (Copyright 2009 Elsevier Ltd. All rights reserved.)

The genetic basis of organism response to stoichiometric mismatches between environmental availability and somatic demand is still poorly understood. This study reports a consistent genotype x environment interaction related to phosphorus : carbon availability to Daphnia. In multiple pairs of Daphnia pulicaria clones, genetic variation at the phosphoglucose isomerase (Pgi) locus indicated that Pgi-heterozygotes out competed Pgi-homozygotes under high P : C conditions, whereas the opposite outcome was observed under low P : C conditions. Estimates of phosphorus use efficiency indicated that homozygotes were significantly more efficient. However, homozygotes were comparatively less homeostatic. We hypothesize that lower specific activity of Pgi from homozygotes, which results in lowered energetic efficiency during the second glycolytic step, may underlie the competitive advantage enjoyed by homozygotes under low P : C (i.e. excess C) conditions. Our results show that analysing stoichiometric mismatches between diet and consumer should advance our quest for a fundamental understanding of the mechanisms driving genotype-environment interactions.

The maintenance of genetic and species diversity in an assemblage of genotypes (clones) in the Daphnia pulex species complex (Cladocera: Anomopoda) in response to variation in the carbon:phosphorus ratio (quantity and quality) of the green alga, Scenedesmus acutus, was examined in a 90-day microcosm competition experiment. Results indicated that mixed assemblages of seven distinct genotypes (representing clonal lineages of D. pulex, D. pulicaria and interspecific hybrids) showed rapid loss of genetic diversity in all treatments (2 x 2 factorial design, high vs. low quantity, and high vs. low quality). However, the erosion of diversity (measured as the effective number of clones) was slowest under the poorest food conditions (i.e., low quantity, low quality) and by the conclusion of the experiment (90 days) had resulted in the (low, low) treatment having significantly greater genetic diversity than the other three treatments. In addition, significant genotype (clone) x (food) environment interactions were observed, with a different predominant species/clone found under low food quality versus high food quality (no significant differences were detected for the two food quantities). A clone of D. pulex displaced the other clones under low food quality conditions, while a clone of D. pulicaria displaced the other clones in the high food quality treatments. Subsequent life-history experiments were not sufficient to predict the outcome of competitive interactions among members of this clonal assemblage. Our results suggest that genetic diversity among herbivore species such as Daphnia may be impacted not only by differences in food quantity but also by those in food quality and could be important in the overall maintenance of genetic diversity in natural populations.

Organisms require elements to live and reproduce. We already know that availability of certain elements [e.g. phosphorus (P)] is highly variable spatiotemporally. In addition, there is variability in demand for various elements ontogenetically, as well as phylogenetically. Nonetheless, we know little about the underlying causes for such variation. In this study, we surveyed the literature to identify genes involved in the homeostasis of one biogenic element, P. Evidence from the literature suggests that variation in the environmental supply of P affects expression of highly conserved genes (e.g. the phosphate transporter system). In addition, we found evidence for genetic variation in the acquisition, assimilation, and allocation of P. Such effects of P supply should impinge on fitness, and drive evolutionary change. Further understanding of the inter- and intraspecific fitness consequences to imbalances in the availability of P in relation to other biogenic elements may be useful to disentangle primary mechanisms driving diversifications. We argue that studying the interactions between stoichiometric constraints and underlying genes is relevant to the majority of organisms, and conclude by furnishing information on designing and interpreting experiments using this approach.

Metabolism involves multiple elements. While we know much about the allometry in metabolic response of organisms to energy (carbon, C) availability, little is known about how different-sized organisms respond to the relative availability of elements. I experimentally manipulated availability of phosphorus (P) relative to C, to test whether dietary C : P affects metabolism in four species of Daphnia, spanning an order of magnitude in body mass. Results indicated that the slope of the relationship between individual respiration and body mass was M(0.83) under a balanced diet (C : P c. 150), and M(0.67) under an imbalanced diet (C : P c. 800). Increased respiration under dietary imbalance was not due to increased ingestion. The change in the scaling exponent was due to the greater respiratory response of smaller species to altered diets. Diet-induced metabolic plasticity contributes to variation in metabolic allometry, at least at such small scales of body size.