Phenotypic stability in scalar calcium of freshwater fish across a wide range of aqueous calcium availability in nature

Spatial environmental gradients can promote adaptive differences among conspecific populations as a result of local adaptation or phenotypic plasticity. Such divergence can be opposed by various constraints, including gene flow, limited genetic variation, temporal fluctuations, or developmental constraints. We focus on the constraint that can be imposed when some populations are found in locations characterized by low levels of an essential nutrient. We use scales of wild fish to investigate phenotypic effects of spatial variation in a potentially limiting nutrient—calcium. If scale calcium (we use “scalar” calcium for consistency with the physiology literature) simply reflects environmental calcium availability, we expect higher levels of scalar calcium in fish from calcium‐rich water, compared to fish from calcium‐poor water. To consider this “passive response” scenario, we analyzed scalar calcium concentrations from three native fish species (Lepomis gibbosus, Percina caprodes, and Perca flavescens) collected at multiple sites across a dissolved calcium gradient in the Upper St. Lawrence River. Contradicting the “passive response" scenario, we did not detect strong or consistent relationships between scalar calcium and water calcium. Instead, for a given proportional increase in water calcium across the wide environmental gradient, the corresponding proportional change in scalar calcium was much smaller. We thus favor the alternative “active homeostasis” scenario, wherein fish from calcium‐poor water are better able to uptake, mobilize, and deposit calcium than are fish from calcium‐rich water. We further highlight the importance of studying functional traits, such as scales, in their natural setting as opposed to only laboratory studies.     

Drosophila Sirtuin 6 mediates developmental diet‐dependent programming of adult physiology and survival

Organisms in the wild experience unpredictable and diverse food availability throughout their lifespan. Over‐/under‐nutrition during development and in adulthood is known to dictate organismal survival and fitness. Studies using model systems have also established long‐term effects of developmental dietary alterations on life‐history traits. However, the underlining genetic/molecular factors, which differentially couple nutrient inputs during development with fitness later in life are far less understood. Using Drosophila and loss/gain of function perturbations, our serendipitous findings demonstrate an essential role of Sirtuin 6 in regulating larval developmental kinetics, in a nutrient‐dependent manner. The absence of Sirt6 affected ecdysone and insulin signalling and led to accelerated larval development. Moreover, varying dietary glucose and yeast during larval stages resulted in enhanced susceptibility to metabolic and oxidative stress in adults. We also demonstrate an evolutionarily conserved role for Sirt6 in regulating physiological homeostasis, physical activity and organismal lifespan, known only in mammals until now. Our results highlight gene‐diet interactions that dictate thresholding of nutrient inputs and physiological plasticity, operative across development and adulthood. In summary, besides showing its role in invertebrate ageing, our study also identifies Sirt6 as a key factor that programs macronutrient‐dependent life‐history traits.     

Competition dynamics in long‐term propagations of Schizosaccharomyces pombe strain communities

Experimental evolution studies with microorganisms such as bacteria and yeast have been an increasingly important and powerful tool to draw long‐term inferences of how microbes interact. However, while several strains of the same species often exist in natural environments, many ecology and evolution studies in microbes are typically performed with isogenic populations of bacteria or yeast. In the present study, we firstly perform a genotypic and phenotypic characterization of two laboratory and eight natural strains of the yeast Schizosaccharomyces pombe. We then propagated, in a rich resource environment, yeast communities of 2, 3, 4, and 5 strains for hundreds of generations and asked which fitness‐related phenotypes—maximum growth rate or relative competitive fitness—would better predict the outcome of a focal strain during the propagations. While the strain''s growth rates would wrongly predict long‐term coexistence, pairwise competitive fitness with a focal strain qualitatively predicted the success or extinction of the focal strain by a simple multigenotype population genetics model, given the initial community composition. Interestingly, we have also measured the competitive fitness of the ancestral and evolved communities by the end of the experiment (≈370 generations) and observed frequent maladaptation to the abiotic environment in communities with more than three members. Overall, our results aid establishing pairwise competitive fitness as good qualitative measurement of long‐term community composition but also reveal a complex adaptive scenario when trying to predict the evolutionary outcome of those communities.     

Individual heterogeneity in fitness in a long‐lived herbivore

Heterogeneity in the intrinsic quality and nutritional condition of individuals affects reproductive success and consequently fitness. Black brant (Branta bernicla nigricans) are long‐lived, migratory, specialist herbivores. Long migratory pathways and short summer breeding seasons constrain the time and energy available for reproduction, thus magnifying life‐history trade‐offs. These constraints, combined with long lifespans and trade‐offs between current and future reproductive value, provide a model system to examine the role of individual heterogeneity in driving life‐history strategies and individual heterogeneity in fitness. We used hierarchical Bayesian models to examine reproductive trade‐offs, modeling the relationships between within‐year measures of reproductive energy allocation and among‐year demographic rates of individual females breeding on the Yukon‐Kuskokwim Delta, Alaska, using capture–recapture and reproductive data from 1988 to 2014. We generally found that annual survival tended to be buffered against variation in reproductive investment, while breeding probability varied considerably over the range of clutch size‐laying date combinations. We provide evidence for relationships between breeding probability and clutch size, breeding probability and nest initiation date, and an interaction between clutch size and initiation date. Average lifetime clutch size also had a weak positive relationship with apparent survival probability. Our results support the use of demographic buffering strategies for black brant. These results also indirectly suggest associations among environmental conditions during growth, fitness, and energy allocation, highlighting the effects of early growth conditions on individual heterogeneity, and subsequently, lifetime reproductive investment.     

Long non‐coding RNA TINCR suppresses metastatic melanoma dissemination by preventing ATF4 translation

Transition from proliferative‐to‐invasive phenotypes promotes metastasis and therapy resistance in melanoma. Reversion of the invasive phenotype, however, is challenged by the poor understanding of mechanisms underlying its maintenance. Here, we report that the lncRNA TINCR is down‐regulated in metastatic melanoma and its silencing increases the expression levels of invasive markers, in vitro migration, in vivo tumor growth, and resistance to BRAF and MEK inhibitors. The critical mediator is ATF4, a central player of the integrated stress response (ISR), which is activated in TINCR‐depleted cells in the absence of starvation and eIF2α phosphorylation. TINCR depletion increases global protein synthesis and induces translational reprogramming, leading to increased translation of mRNAs encoding ATF4 and other ISR proteins. Strikingly, re‐expression of TINCR in metastatic melanoma suppresses the invasive phenotype, reduces numbers of tumor‐initiating cells and metastasis formation, and increases drug sensitivity. Mechanistically, TINCR interacts with mRNAs associated with the invasive phenotype, including ATF4, preventing their binding to ribosomes. Thus, TINCR is a suppressor of the melanoma invasive phenotype, which functions in nutrient‐rich conditions by repressing translation of selected ISR RNAs.     

Growth,body condition and contest performance after early‐life food restriction in a long‐lived tropical fish

Adverse conditions during early life can cause lasting body size deficits with effects on social and sexual competition, while an accelerated growth response can allow animals to catch up in body size but can be physiologically costly as well. How animals balance growth deficits and growth compensation is predicted to depend on the effects of each on lifetime fitness. We investigated the effects of experimental early‐life food restriction on growth, body condition, and adult contest competition in a cichlid fish (Tropheus sp.). Their longevity and aseasonal breeding suggest that, with view on lifetime reproductive success, temporarily growth‐restricted Tropheus should rather invest extra time in reaching competitive body size than risk the potential costs of accelerated growth. However, size‐selective predation pressure by gape size‐limited piscivores may have favored the evolution of an accelerated growth response to early‐life delays. Experimentally food‐restricted fish temporarily reduced their growth rate compared to a control group, but maintained their body condition factor at the control level throughout the 80‐week study period. There was no evidence for an accelerated growth response following the treatment, as the food‐restricted fish never exceeded the size‐specific growth rates that were measured in the control group. Food‐restricted fish caught up with the body size of the control group several months after the end of the treatment period and were as likely as control fish to win size‐matched contests over territories. Regardless of feeding regime, there were sex‐specific differences in growth rates and in the trajectories of condition factors over time. Females grew more slowly than males but maintained their condition factors at a high level throughout the study period, whereas the males'' condition factors declined over time. These differences may reflect sex‐specific contributions of condition and body size to adult fitness that are associated with female mouthbrooding and male competition for breeding territories.     

Modeling the effects of grassland management intensity on biodiversity

A growing food demand and advanced agricultural techniques increasingly affect farmland ecosystems, threatening invertebrate populations with cascading effects along the food chain upon insectivorous vertebrates. Supporting farmland biodiversity thus optimally requires the delineation of species hotspots at multiple trophic levels to prioritize conservation management. The goal of this study was to investigate the links between grassland management intensity and orthopteran density at the field scale and to upscale this information to the landscape in order to guide management action at landscape scale. More specifically, we investigated the relationships between grassland management intensity, floral indicator species, and orthopteran abundance in grasslands with different land use in the SW Swiss Alps. Field vegetation surveys of indicator plant species were used to generate a management intensity proxy, to which field assessments of orthopterans were related. Orthopteran abundance showed a hump‐shaped response to management intensity, with low values in intensified, nutrient‐rich grasslands and in nutrient‐poor, xeric grasslands, while it peaked in middle‐intensity grasslands. Combined with remote‐sensed data about grassland gross primary productivity, the above proxy was used to build landscape‐wide, spatially explicit projections of the potential distribution of orthopteran‐rich grasslands as possible foraging grounds for insectivorous vertebrates. This spatially explicit multitrophic approach enables the delineation of focal farmland areas in order to prioritize conservation action.     

Early‐life conditions impact juvenile telomere length,but do not predict later life‐history strategies or fitness in a wild vertebrate

Environmental conditions experienced during early life may have long‐lasting effects on later‐life phenotypes and fitness. Individuals experiencing poor early‐life conditions may suffer subsequent fitness constraints. Alternatively, individuals may use a strategic “Predictive Adaptive Response” (PAR), whereby they respond—in terms of physiology or life‐history strategy—to the conditions experienced in early life to maximize later‐life fitness. Particularly, the Future Lifespan Expectation (FLE) PAR hypothesis predicts that when poor early‐life conditions negatively impact an individual''s physiological state, it will accelerate its reproductive schedule to maximize fitness during its shorter predicted life span. We aimed to measure the impact of early‐life conditions and resulting fitness across individual lifetimes to test predictions of the FLE hypothesis in a wild, long‐lived model species. Using a long‐term individual‐based dataset, we investigated how early‐life conditions are linked with subsequent fitness in an isolated population of the Seychelles warbler Acrocephalus sechellensis. How individuals experience early‐life environmental conditions may vary greatly, so we also tested whether telomere length—shorter telomers are a biomarker of an individual''s exposure to stress—can provide an effective measure of the individual‐specific impact of early‐life conditions. Specifically, under the FLE hypothesis, we would expect shorter telomeres to be associated with accelerated reproduction. Contrary to expectations, shorter juvenile telomere length was not associated with poor early‐life conditions, but instead with better conditions, probably as a result of faster juvenile growth. Furthermore, neither juvenile telomere length, nor other measures of early‐life conditions, were associated with age of first reproduction or the number of offspring produced during early life in either sex. We found no support for the FLE hypothesis. However, for males, poor early‐life body condition was associated with lower first‐year survival and reduced longevity, indicating that poor early‐life conditions pose subsequent fitness constraints. Our results also showed that using juvenile telomere length as a measure of early‐life conditions requires caution, as it is likely to not only reflect environmental stress but also other processes such as growth.     

Enhancing protein perdeuteration by experimental evolution of Escherichia coli K‐12 for rapid growth in deuterium‐based media

Deuterium is a natural low abundance stable hydrogen isotope that in high concentrations negatively affects growth of cells. Here, we have studied growth of Escherichia coli MG1655, a wild‐type laboratory strain of E. coli K‐12, in deuterated glycerol minimal medium. The growth rate and final biomass in deuterated medium is substantially reduced compared to cells grown in ordinary medium. By using a multi‐generation adaptive laboratory evolution‐based approach, we have isolated strains that show increased fitness in deuterium‐based growth media. Whole‐genome sequencing identified the genomic changes in the obtained strains and show that there are multiple routes to genetic adaptation to growth in deuterium‐based media. By screening a collection of single‐gene knockouts of nonessential genes, no specific gene was found to be essential for growth in deuterated minimal medium. Deuteration of proteins is of importance for NMR spectroscopy, neutron protein crystallography, neutron reflectometry, and small angle neutron scattering. The laboratory evolved strains, with substantially improved growth rate, were adapted for recombinant protein production by T7 RNA polymerase overexpression systems and shown to be suitable for efficient production of perdeuterated soluble and membrane proteins for structural biology applications.     

Calcicole–calcifuge plant strategies limit restoration potential in a regional semi‐arid flora

AimTo examine calcicole and calcifuge plant strategies, as well as nutrient‐acquisition strategies, as drivers of the distribution of species in response to edaphic factors, and the degree to which these strategies may act as filters to species establishment in ecological restoration on heavily altered or reconstructed substrates.LocationAn 82,000‐ha area within a major mining province in the Mid‐West region of Western Australia, harboring vegetation communities ranging from species‐poor halophytic scrub on saline flats to dense biodiverse shrubland on the skeletal soils of ancient Banded Ironstone Formations (BIF).MethodsUnivariate and multivariate analyses were employed to examine how variation in soil chemistry and landscape position (undulating plains, slopes, and BIF crests and ridges) influenced patterns of floristic diversity, calcifuge plant strategies, and nutrient‐acquisition strategies in 538 plant species from 830 relevés.ResultsLandscape position was the strongest driver of species richness and vegetation functional composition. Soils became increasingly acidic and P‐impoverished along an increasing elevational gradient. Vegetation from different landscape positions was not compositionally dissimilar, but vegetation of BIF crests and ridges was up to twice as biodiverse as vegetation from adjacent lower‐relief areas and harbored higher proportions of calcifuge species and species with mycorrhizal associations.Main conclusionsTopographic and edaphic complexity of BIF landforms in an otherwise relatively homogenous landscape has likely facilitated species accumulation over long time periods. They represent musea of regional floristic biodiversity, excluding only species that cannot establish or are inferior competitors in heavily weathered, acidic, skeletal, and nutrient‐impoverished soils. Plant strategies likely represent a major filter in establishing biodiverse, representative vegetation on postmining landforms in geologically ancient regions.     

Multistability maintains redox homeostasis in human cells

Cells metabolize nutrients through a complex metabolic and signaling network that governs redox homeostasis. At the core of this, redox regulatory network is a mutually inhibitory relationship between reduced glutathione and reactive oxygen species (ROS)—two opposing metabolites that are linked to upstream nutrient metabolic pathways (glucose, cysteine, and glutamine) and downstream feedback loops of signaling pathways (calcium and NADPH oxidase). We developed a nutrient‐redox model of human cells to understand system‐level properties of this network. Combining in silico modeling and ROS measurements in individual cells, we show that ROS dynamics follow a switch‐like, all‐or‐none response upon glucose deprivation at a threshold that is approximately two orders of magnitude lower than its physiological concentration. We also confirm that this ROS switch can be irreversible and exhibits hysteresis, a hallmark of bistability. Our findings evidence that bistability modulates redox homeostasis in human cells and provide a general framework for quantitative investigations of redox regulation in humans.     

Physiological Role of β-Phosphoglucomutase in Lactococcus lactis

A β-phosphoglucomutase (β-PGM) mutant of Lactococcus lactis subsp. lactis ATCC 19435 was constructed using a minimal integration vector and double-crossover recombination. The mutant and the wild-type strain were grown under controlled conditions with different sugars to elucidate the role of β-PGM in carbohydrate catabolism and anabolism. The mutation did not significantly affect growth, product formation, or cell composition when glucose or lactose was used as the carbon source. With maltose or trehalose as the carbon source the wild-type strain had a maximum specific growth rate of 0.5 h⁻¹, while the deletion of β-PGM resulted in a maximum specific growth rate of 0.05 h⁻¹ on maltose and no growth at all on trehalose. Growth of the mutant strain on maltose resulted in smaller amounts of lactate but more formate, acetate, and ethanol, and approximately 1/10 of the maltose was found as β-glucose 1-phosphate in the medium. Furthermore, the β-PGM mutant cells grown on maltose were considerably larger and accumulated polysaccharides which consisted of α-1,4-bound glucose units. When the cells were grown at a low dilution rate in a glucose and maltose mixture, the wild-type strain exhibited a higher carbohydrate content than when grown at higher growth rates, but still this content was lower than that in the β-PGM mutant. In addition, significant differences in the initial metabolism of maltose and trehalose were found, and cell extracts did not digest free trehalose but only trehalose 6-phosphate, which yielded β-glucose 1-phosphate and glucose 6-phosphate. This demonstrates the presence of a novel enzymatic pathway for trehalose different from that of maltose metabolism in L. lactis.     

Endosome maturation links PI3Kα signaling to lysosome repopulation during basal autophagy

Autophagy depends on the repopulation of lysosomes to degrade intracellular components and recycle nutrients. How cells co‐ordinate lysosome repopulation during basal autophagy, which occurs constitutively under nutrient‐rich conditions, is unknown. Here, we identify an endosome‐dependent phosphoinositide pathway that links PI3Kα signaling to lysosome repopulation during basal autophagy. We show that PI3Kα‐derived PI(3)P generated by INPP4B on late endosomes was required for basal but not starvation‐induced autophagic degradation. PI(3)P signals were maintained as late endosomes matured into endolysosomes, and served as the substrate for the 5‐kinase, PIKfyve, to generate PI(3,5)P₂. The SNX‐BAR protein, SNX2, was recruited to endolysosomes by PI(3,5)P₂ and promoted lysosome reformation. Inhibition of INPP4B/PIKfyve‐dependent lysosome reformation reduced autophagic clearance of protein aggregates during proteotoxic stress leading to increased cytotoxicity. Therefore under nutrient‐rich conditions, PI3Kα, INPP4B, and PIKfyve sequentially contribute to basal autophagic degradation and protection from proteotoxic stress via PI(3,5)P₂‐dependent lysosome reformation from endolysosomes. These findings reveal that endosome maturation couples PI3Kα signaling to lysosome reformation during basal autophagy.     

S3QELs protect against diet‐induced intestinal barrier dysfunction

The underlying causes of aging remain elusive, but may include decreased intestinal homeostasis followed by disruption of the intestinal barrier, which can be mimicked by nutrient‐rich diets. S3QELs are small‐molecule suppressors of site III_Qo electron leak; they suppress superoxide generation at complex III of the mitochondrial electron transport chain without inhibiting oxidative phosphorylation. Here we show that feeding different S3QELs to Drosophila on a high‐nutrient diet protects against greater intestinal permeability, greater enterocyte apoptotic cell number, and shorter median lifespan. Hif‐1α knockdown in enterocytes also protects, and blunts any further protection by S3QELs. Feeding S3QELs to mice on a high‐fat diet also protects against the diet‐induced increase in intestinal permeability. Our results demonstrate by inference of S3QEL use that superoxide produced by complex III in enterocytes contributes to diet‐induced intestinal barrier disruption in both flies and mice.     

Plasticity is a locally adapted trait with consequences for ecological dynamics in novel environments

Phenotypic plasticity is predicted to evolve in more variable environments, conferring an advantage on individual lifetime fitness. It is less clear what the potential consequences of that plasticity will have on ecological population dynamics. Here, we use an invertebrate model system to examine the effects of environmental variation (resource availability) on the evolution of phenotypic plasticity in two life history traits—age and size at maturation—in long‐running, experimental density‐dependent environments. Specifically, we then explore the feedback from evolution of life history plasticity to subsequent ecological dynamics in novel conditions. Plasticity in both traits initially declined in all microcosm environments, but then evolved increased plasticity for age‐at‐maturation, significantly so in more environmentally variable environments. We also demonstrate how plasticity affects ecological dynamics by creating founder populations of different plastic phenotypes into new microcosms that had either familiar or novel environments. Populations originating from periodically variable environments that had evolved greatest plasticity had lowest variability in population size when introduced to novel environments than those from constant or random environments. This suggests that while plasticity may be costly it can confer benefits by reducing the likelihood that offspring will experience low survival through competitive bottlenecks in variable environments. In this study, we demonstrate how plasticity evolves in response to environmental variation and can alter population dynamics—demonstrating an eco‐evolutionary feedback loop in a complex animal moderated by plasticity in growth.     

Influence of Carbohydrate Starvation and Arginine on Culturability and Amino Acid Utilization of Lactococcus lactis subsp. lactis

Two strains of Lactococcus lactis subsp. lactis were used to determine the influence of lactose and arginine on viability and amino acid use during carbohydrate starvation. Lactose provided energy for logarithmic-phase growth, and amino acids such as arginine provided energy after carbohydrate exhaustion. Survival time, cell numbers, and ATP concentrations increased with the addition of arginine to the basal medium. By the onset of lactose exhaustion, the concentrations of glycine-valine and glutamate had decreased by as much as 67% in L. lactis ML3, whereas the serine concentration increased by 97% during the same period. When no lactose was added, the concentrations of these amino acids remained constant. Similar trends were observed for L. lactis 11454. Without lactose or arginine, L. lactis ML3 was nonculturable on agar but was viable after 2 days, as measured by fluorescent viability stains and intracellular ATP levels. However, L. lactis 11454 without lactose or arginine remained culturable for at least 14 days. These data suggest that lactococci become viable but nonculturable in response to carbohydrate depletion. Additionally, these data indicate that amino acids other than arginine facilitate the survival of L. lactis during carbohydrate starvation.     

Biogeography of curimatid fishes reveals multiple lowland–upland river transitions and differential diversification in the Neotropics (Teleostei,Curimatidae)

The Neotropics harbors a megadiverse ichthyofauna comprising over 6300 species with approximately 80% in just three taxonomic orders within the clade Characiphysi. This highly diverse group has evolved in tropical South America over tens to hundreds of millions of years influenced mostly by re‐arrangements of river drainages in lowland and upland systems. In this study, we investigate patterns of spatial diversification in Neotropical freshwater fishes in the family Curimatidae, a species‐rich clade of the order Characiformes. Specifically, we examined ancestral areas, dispersal events, and shifts in species richness using spatially explicit biogeographic and macroevolutionary models to determine whether lowlands–uplands serve as museums or cradles of diversification for curimatids. We used fossil information to estimate divergence times in BEAST, multiple time‐stratified models of geographic range evolution in BioGeoBEARS, and alternative models of geographic state‐dependent speciation and extinction in GeoHiSSE. Our results suggest that the most recent common ancestor of curimatids originated in the Late Cretaceous likely in lowland paleodrainages of northwestern South America. Dispersals from lowland to upland river basins of the Brazilian and Guiana shields occurred repeatedly across independently evolving lineages in the Cenozoic. Colonization of upland drainages was often coupled with increased rates of net diversification in species‐rich genera such as Cyphocharax and Steindachnerina. Our findings demonstrate that colonization of novel aquatic environments at higher elevations is associated with an increased rate of diversification, although this pattern is clade‐dependent and driven mostly by allopatric speciation. Curimatids reinforce an emerging perspective that Amazonian lowlands act as a museum by accumulating species along time, whereas the transitions to uplands stimulate higher net diversification rates and lineage diversification.