Ionome and elemental transport kinetics shaped by parallel evolution in threespine stickleback

The eco-evolutionary dynamics of stoichiometric homeostasis

Stoichiometric homeostasis is the ability of life to maintain inner chemical constancy despite changes in the environment and resources. Organisms can be stoichiometrically homeostatic to different degrees. This variation can be substantial even within species, but is ignored in most studies of ecological stoichiometry. Recent studies suggest that resource limitations are an important selective pressure behind homeostasis, but are contradictory in direction, likely owing to differences in nutrient storage strategies. Understanding the selective pressures underlying stoichiometric homeostasis, and its potential for rapid evolution, are key to predicting eco-evolutionary dynamics. This calls for the development of an evolutionary theory of stoichiometric homeostasis that incorporates rapid evolution, as well as for empirical studies to test the underlying mechanisms.

SEED: A framework for integrating ecological stoichiometry and eco-evolutionary dynamics

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.

Recent advances in the application of ionomics in metabolic diseases

Trace elements and minerals play a significant role in human health and diseases. In recent years, ionomics has been rapidly and widely applied to explore the distribution, regulation, and crosstalk of different elements in various physiological and pathological processes. On the basis of multi-elemental analytical techniques and bioinformatics methods, it is possible to elucidate the relationship between the metabolism and homeostasis of diverse elements and common diseases. The current review aims to provide an overview of recent advances in the application of ionomics in metabolic disease research. We mainly focuses on the studies about ionomic or multi-elemental profiling of different biological samples for several major types of metabolic diseases, such as diabetes mellitus, obesity, and metabolic syndrome, which reveal distinct and dynamic patterns of ion contents and their potential benefits in the detection and prognosis of these illnesses. Accumulation of copper, selenium, and environmental toxic metals as well as deficiency of zinc and magnesium appear to be the most significant risk factors for the majority of metabolic diseases, suggesting that imbalance of these elements may be involved in the pathogenesis of these diseases. Moreover, each type of metabolic diseases has shown a relatively unique distribution of ions in biofluids and hair/nails from patients, which might serve as potential indicators for the respective disease. Overall, ionomics not only improves our understanding of the association between elemental dyshomeostasis and the development of metabolic disease but also assists in the identification of new potential diagnostic and prognostic markers in translational medicine.

Impacts of heavy metal pollution on the ionomes and transcriptomes of Western mosquitofish (Gambusia affinis)

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 to test hypotheses about the mechanisms mediating the persistence of mosquitofish in Tar Creek. 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.

Using seasonal genomic changes to understand historical adaptation to new environments: Parallel selection on stickleback in highly-variable estuaries

Parallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time. The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection under natural conditions, we study six populations of threespine stickleback (Gasterosteus aculeatus) inhabiting bar-built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long-term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole-genome sequencing to track seasonal allele frequency changes in six of these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar-built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.

Disease Ionomics: Understanding the Role of Ions in Complex Disease

Ionomics is a novel multidisciplinary field that uses advanced techniques to investigate the composition and distribution of all minerals and trace elements in a living organism and their variations under diverse physiological and pathological conditions. It involves both high-throughput elemental profiling technologies and bioinformatic methods, providing opportunities to study the molecular mechanism underlying the metabolism, homeostasis, and cross-talk of these elements. While much effort has been made in exploring the ionomic traits relating to plant physiology and nutrition, the use of ionomics in the research of serious diseases is still in progress. In recent years, a number of ionomic studies have been carried out for a variety of complex diseases, which offer theoretical and practical insights into the etiology, early diagnosis, prognosis, and therapy of them. This review aims to give an overview of recent applications of ionomics in the study of complex diseases and discuss the latest advances and future trends in this area. Overall, disease ionomics may provide substantial information for systematic understanding of the properties of the elements and the dynamic network of elements involved in the onset and development of diseases.

Phosphorus limitation does not drive loss of bony lateral plates in freshwater stickleback (Gasterosteus aculeatus)

Connecting the selective forces that drive the evolution of phenotypes to their underlying genotypes is key to understanding adaptation, but such connections are rarely tested experimentally. Threespine stickleback (Gasterosteus aculeatus) are a powerful model for such tests because genotypes that underlie putatively adaptive traits have been identified. For example, a regulatory mutation in the Ectodysplasin (Eda) gene causes a reduction in the number of bony armor plates, which occurs rapidly and repeatedly when marine sticklebacks invade freshwater. However, the source of selection on plate loss in freshwater is unknown. Here, we tested whether dietary reduction of phosphorus can account for selection on plate loss due to a growth advantage of low-plated fish in freshwater. We crossed marine fish heterozygous for the 16 kilobase freshwater Eda haplotype and compared the growth of offspring with different genotypes under contrasting levels of dietary phosphorus in both saltwater and freshwater. Eda genotype was not associated with growth differences in any treatment, or with mechanisms that could mitigate the impacts of phosphorus limitation, such as differential phosphorus deposition, phosphorus excretion, or intestine length. This study highlights the importance of experimentally testing the putative selective forces acting on phenotypes and their underlying genotypes in the wild.

Differential responses of macroinvertebrate ionomes across experimental N:P gradients in detritus-based headwater streams

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.

Does differential iron supply to algae affect Daphnia life history? An ionome-wide study

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.