The biological importance of measuring individual variation

Counter-gradient variation in gene expression between fish populations facilitates colonization of low-dissolved oxygen environments

The role of phenotypic plasticity during colonization remains unclear due to the shifting importance of plasticity across timescales. In the early stages of colonization, plasticity can facilitate persistence in a novel environment; but over evolutionary time, processes such as genetic assimilation may reduce variation in plastic traits such that species with a longer evolutionary history in an environment can show lower levels of plasticity than recent invaders. Therefore, comparing species in the early stages of colonization to long-established species provides a powerful approach for uncovering the role of phenotypic plasticity during different stages of colonization. We compared gene expression between low-dissolved oxygen (DO) and high-DO populations of two cyprinid fish: Enteromius apleurogramma, a species that has undergone a recent range expansion, and E. neumayeri, a long-established native species in the same region. We sampled tissue either immediately after capture from the field or after a 2-week acclimation under high-DO conditions, allowing us to test for both evolved and plastic differences in low-DO vs high-DO populations of each species. We found that most genes showing candidate-evolved differences in gene expression did not overlap with those showing plastic differences in gene expression. However, in the genes that did overlap, there was counter-gradient variation such that plastic and evolved gene expression responses were in opposite directions in both species. Additionally, E. apleurogramma had higher levels of plasticity and evolved divergence in gene expression between field populations. We suggest that the higher level of plasticity and counter-gradient variation may have allowed rapid genetic adaptation in E. apleurogramma and facilitated colonization. This study shows how counter-gradient variation may impact the colonization of divergent oxygen environments.

Evaluation of species thermal sensitivity with individual-based physiological performance

Ignoring intraspecific variations can prevent us from accurately assessing species' thermal sensitivity to global warming. Individual-based physiological performance provides a feasible solution to depict species' thermal sensitivity using a bottom-up approach. We measured the cardiac performance of intertidal bivalves (1159 individuals from multiple populations of six bivalves), determined the upper thermal limit of each individual, calculated the proportions of individuals suffering sublethal/lethal heat stress, and mapped sensitive regions to high temperatures. Results showed that high inter-individual variations of physiological performance existed in levels of populations and species, and species' thermal sensitivity was positively related to the intraspecific variations of heat tolerance. This bottom-up approach scaled up from individual, population to species emphasizes the importance of individual-based physiology performance in assessing thermal sensitivity across different hierarchical levels and enables better evaluating and forecasting of species responses to global warming.

The antibacterials ciprofloxacin, trimethoprim and sulfadiazine modulate gene expression, biomarkers and metabolites associated with stress and growth in gilthead sea bream (Sparus aurata)

The high consumption and subsequent input of antibacterial compounds in marine ecosystems has become a worldwide problem. Their continuous presence in these ecosystems allows a direct interaction with aquatic organisms and can cause negative effects over time. The objective of the present study was to evaluate the effects of exposure to three antibacterial compounds of high consumption and presence in marine ecosystems (Ciprofloxacin CIP, Sulfadiazine SULF and Trimethoprim TRIM) on the physiology of the gilthead sea bream, Sparus aurata. Plasma parameters, enzymatic biomarkers of oxidative stress and damage and expression of genes related to stress and growth were assessed in exposed S. aurata specimens. For this purpose, sea bream specimens were exposed to individual compounds at concentrations of 5.2 ± 2.1 μg L^-1 for CIP, 3.8 ± 2.7 μg L^-1 for SULF and 25.7 ± 10.8 μg L^-1 for TRIM during 21 days. Exposure to CIP up-regulated transcription of genes associated with the hypothalamic-pituitary-thyroid (HPT) (thyrotropin-releasing hormone, trh) and hypothalamic-pituitary-interrenal (HPI) axes (corticotropin-releasing hormone-binding protein, crhbp) in the brain, as well as altering several hepatic stress biomarkers (catalase, CAT; glutathione reductase, GR; and lipid peroxidation, LPO). Similar alterations at the hepatic level were observed after exposure to TRIM. Overall, our study indicates that S. aurata is vulnerable to environmentally relevant concentrations of CIP and TRIM and that their exposure could lead to a stress situation, altering the activity of antioxidant defense mechanisms as well as the activity of HPT and HPI axes.

Interindividual variation in maximum aerobic metabolism varies with gill morphology and myocardial bioenergetics

This study asked whether interindividual variation in maximum and standard aerobic metabolic rates of the Gulf killifish, Fundulus grandis, correlate with gill morphology and cardiac mitochondrial bioenergetics, traits reflecting critical steps in the O2 transport cascade from the environment to the tissues. Maximum metabolic rate (MMR) was positively related to body mass, total gill filament length, and myocardial oxygen consumption during maximum oxidative phosphorylation (multiple R2=0.836). Standard metabolic rate (SMR) was positively related to body mass, total gill filament length, and myocardial oxygen consumption during maximum electron transport system activity (multiple R2=0.717). After controlling for body mass, individuals with longer gill filaments, summed over all gill arches, or greater cardiac respiratory capacity had higher whole-animal metabolic rates. The overall model fit and the explanatory power of individual predictor variables were better for MMR than for SMR, suggesting that gill morphology and myocardial bioenergetics are more important in determining active rather than resting metabolism. After accounting for body mass, heart ventricle mass was not related to variation in MMR or SMR, indicating that the quality of the heart (i.e., the capacity for mitochondrial metabolism) was more influential than heart size. Finally, the myocardial oxygen consumption required to offset the dissipation of the transmembrane proton gradient in the absence of ATP synthesis was not correlated with either MMR or SMR. The results support the idea that interindividual variation in aerobic metabolism, particularly maximum metabolic rate, is associated with variation in specific steps in the O2 transport cascade.

Environment-driven shifts in inter-individual variation and phenotypic integration within subnetworks of the mussel transcriptome and proteome

The environment can alter the magnitude of phenotypic variation among individuals, potentially influencing evolutionary trajectories. However, environmental influences on variation are complex and remain understudied. Populations in heterogeneous environments might exhibit more variation, the amount of variation could differ between benign and stressful conditions, and/or variation might manifest in different ways among stages of the gene‐to‐protein expression cascade or among physiological functions. Here, we explore these three issues by quantifying patterns of inter‐individual variation in both transcript and protein expression levels among California mussels, Mytilus californianus Conrad. Mussels were exposed to five ecologically relevant treatments that varied in the mean and interindividual heterogeneity of body temperature. To target a diverse set of physiological functions, we assessed variation within 19 expression subnetworks, including canonical stress‐response pathways and empirically derived coexpression clusters that represent a diffuse set of cellular processes. Variation in expression was particularly pronounced in the treatments with high mean and heterogeneous body temperatures. However, with few exceptions, environment‐dependent shifts of variation in the transcriptome were not reflected in the proteome. A metric of phenotypic integration provided evidence for a greater degree of constraint on relative expression levels (i.e., stronger correlation) within expression subnetworks in benign, homogeneous environments. Our results suggest that environments that are more stressful on average – and which also tend to be more heterogeneous – can relax these expression constraints and reduce phenotypic integration within biochemical subnetworks. Context‐dependent “unmasking” of functional variation may contribute to interindividual differences in physiological phenotype and performance in stressful environments.

Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis

Background and objectives

Peripheral blood mononuclear cells (PBMCs) have shown promise as a tissue sensitive to subtle and possibly systemic transcriptomic changes, and as such may be useful in identifying responses to weight loss interventions. The primary aim was to comprehensively evaluate the transcriptomic changes that may occur during weight loss and to determine if there is a consistent response across intervention types in human populations of all ages.

Methods

Included studies were randomised control trials or cohort studies that administered an intervention primarily designed to decrease weight in any overweight or obese human population. A systematic search of the literature was conducted to obtain studies and gene expression databases were interrogated to locate corresponding transcriptomic datasets. Datasets were normalised using the ArrayAnalysis online tool and differential gene expression was determined using the limma package in R. Over-represented pathways were explored using the PathVisio software. Heatmaps and hierarchical clustering were utilised to visualise gene expression.

Results

Seven papers met the inclusion criteria, five of which had raw gene expression data available. Of these, three could be grouped into high responders (HR, ≥ 5% body weight loss) and low responders (LR). No genes were consistently differentially expressed between high and low responders across studies. Adolescents had the largest transcriptomic response to weight loss followed by adults who underwent bariatric surgery. Seven pathways were altered in two out of four studies following the intervention and the pathway ‘cytoplasmic ribosomal proteins’ (WikiPathways: WP477) was altered between HR and LR at baseline in the two datasets with both groups. Pathways related to ‘toll-like receptor signalling’ were altered in HR response to the weight loss intervention in two out of three datasets.

Conclusions

Transcriptomic changes in PBMCs do occur in response to weight change. Transparent and standardised data reporting is needed to realise the potential of transcriptomics for investigating phenotypic features.

Registration number

PROSPERO: CRD42019106582

Supplementary Information

The online version contains supplementary material available at 10.1186/s12263-021-00692-6.

Interindividual plasticity in metabolic and thermal tolerance traits from populations subjected to recent anthropogenic heating

To better understand temperature's role in the interaction between local evolutionary adaptation and physiological plasticity, we investigated acclimation effects on metabolic performance and thermal tolerance among natural Fundulus heteroclitus (small estuarine fish) populations from different thermal environments. Fundulus heteroclitus populations experience large daily and seasonal temperature variations, as well as local mean temperature differences across their large geographical cline. In this study, we use three populations: one locally heated (32°C) by thermal effluence (TE) from the Oyster Creek Nuclear Generating Station, NJ, and two nearby reference populations that do not experience local heating (28°C). After acclimation to 12 or 28°C, we quantified whole-animal metabolic (WAM) rate, critical thermal maximum (CTmax) and substrate-specific cardiac metabolic rate (CaM, substrates: glucose, fatty acids, lactate plus ketones plus ethanol, and endogenous (i.e. no added substrates)) in approximately 160 individuals from these three populations. Populations showed few significant differences due to large interindividual variation within populations. In general, for WAM and CTmax, the interindividual variation in acclimation response (log2 ratio 28/12°C) was a function of performance at 12°C and order of acclimation (12-28°C versus 28-12°C). CTmax and WAM were greater at 28°C than 12°C, although WAM had a small change (2.32-fold) compared with the expectation for a 16°C increase in temperature (expect 3- to 4.4-fold). By contrast, for CaM, the rates when acclimatized and assayed at 12 or 28°C were nearly identical. The small differences in CaM between 12 and 28°C temperature were partially explained by cardiac remodeling where individuals acclimatized to 12°C had larger hearts than individuals acclimatized to 28°C. Correlation among physiological traits was dependent on acclimation temperature. For example, WAM was negatively correlated with CTmax at 12°C but positively correlated at 28°C. Additionally, glucose substrate supported higher CaM than fatty acid, and fatty acid supported higher CaM than lactate, ketones and alcohol (LKA) or endogenous. However, these responses were highly variable with some individuals using much more FA than glucose. These findings suggest interindividual variation in physiological responses to temperature acclimation and indicate that additional research investigating interindividual may be relevant for global climate change responses in many species.

Nonparallel transcriptional divergence during parallel adaptation

How underlying mechanisms bias evolution toward predictable outcomes remains an area of active debate. In this study, we leveraged phenotypic plasticity and parallel adaptation across independent lineages of Trinidadian guppies (Poecilia reticulata) to assess the predictability of gene expression evolution during parallel adaptation. Trinidadian guppies have repeatedly and independently adapted to high- and low-predation environments in the wild. We combined this natural experiment with a laboratory breeding design to attribute transcriptional variation to the genetic influences of population of origin and developmental plasticity in response to rearing with or without predators. We observed substantial gene expression plasticity, as well as the evolution of expression plasticity itself, across populations. Genes exhibiting expression plasticity within populations were more likely to also differ in expression between populations, with the direction of population differences more likely to be opposite those of plasticity. While we found more overlap than expected by chance in genes differentially expressed between high- and low-predation populations from distinct evolutionary lineages, the majority of differentially expressed genes were not shared between lineages. Our data suggest alternative transcriptional configurations associated with shared phenotypes, highlighting a role for transcriptional flexibility in the parallel phenotypic evolution of a species known for rapid adaptation.

Modeling molecular development of breast cancer in canine mammary tumors

Understanding the changes in diverse molecular pathways underlying the development of breast tumors is critical for improving diagnosis, treatment, and drug development. Here, we used RNA-profiling of canine mammary tumors (CMTs) coupled with a robust analysis framework to model molecular changes in human breast cancer. Our study leveraged a key advantage of the canine model, the frequent presence of multiple naturally occurring tumors at diagnosis, thus providing samples spanning normal tissue and benign and malignant tumors from each patient. We showed human breast cancer signals, at both expression and mutation level, are evident in CMTs. Profiling multiple tumors per patient enabled by the CMT model allowed us to resolve statistically robust transcription patterns and biological pathways specific to malignant tumors versus those arising in benign tumors or shared with normal tissues. We showed that multiple histological samples per patient is necessary to effectively capture these progression-related signatures, and that carcinoma-specific signatures are predictive of survival for human breast cancer patients. To catalyze and support similar analyses and use of the CMT model by other biomedical researchers, we provide FREYA, a robust data processing pipeline and statistical analyses framework.

Natural variation of the cardiac transcriptome in humans

We investigated the gene-expression variation among humans by analysing previously published mRNA-seq and ribosome footprint profiling of heart left-ventricles from healthy donors. We ranked the genes according to their coefficient of variation values and found that the top 5% most variable genes had special features compared to the rest of the genome, such as lower mRNA levels and shorter half-lives coupled to increased translation efficiency. We observed that these genes are mostly involved with immune response and have a pleiotropic effect on disease phenotypes, indicating that asymptomatic conditions contribute to the gene expression diversity of healthy individuals.

An Integrated Biomarker Approach Using Flounder to Improve Chemical Risk Assessments in the Heavily Polluted Seine Estuary

The objective of this study was to develop an integrative approach in ecotoxicology (from biomarkers to population genetics) to assess the ecological status of fish populations. Flounders (Platichthys flesus) collected after the spawning season in the heavily polluted Seine estuary were compared with the moderately polluted Bay of Douarnenez. The muscle energetic reserves were highly depleted in Seine vs. Douarnenez fish. The Seine fish displaying a reduced capacity to manage the oxidative stress and a higher energetic metabolism. An increase in the content of muscle membrane phospholipids (sphingomyelin, phosphatidylserine, free sterols) was detected in the Seine vs. Douarnenez fish. The data integration allowed to hypothesize relationships between membrane phospholipids, xenobiotic metabolism, bioenergetics, and antioxidant defence. The genetic diversity considering neutral markers was maintained in the heavily polluted Seine population compared with the Douarnenez population. Finally, we suggest that the high physiological cost of tolerance to toxicants in the Seine flounder population could compromise its capacity to respond in the future to an additional stressor like warming waters in shallow depth. Thus, this population could be submitted to an ecological risk.

Transcriptome profiling revealed potentially important roles of defensive gene expression in the divergence of insect biotypes: a case study with the cereal aphid Sitobion avenae

Background

Many insects can develop differential biotypes on variable host plants, but the underlying molecular factors and mechanisms are not well understood. To address this issue, transcriptome profiling analyses were conducted for two biotypes of the cereal aphid, Sitobion avenae (Fabricius), on both original and alternative plants.

Results

Comparisons between both biotypes generated 4174 differentially expressed unigenes (DEGs). In their response to host plant shift, 39 DEGs were shared by both biotypes, whereas 126 and 861 DEGs occurred only in biotypes 1 and 3, respectively. MMC (modulated modularity clustering) analyses showed that specific DEGs of biotypes 1 and 3 clustered into five and nine transcriptional modules, respectively. Among these DEGs, defense-related genes underwent intensive expression restructuring in both biotypes. However, biotype 3 was found to have relatively lower gene transcriptional plasticity than biotype 1. Gene enrichment analyses of the abovementioned modules showed functional divergence in defensive DEGs for the two biotypes in response to host transfer. The expression plasticity for some defense related genes was showed to be directly related to fecundity of S. avenae biotypes on both original and alternative plants, suggesting that expression plasticity of key defensive genes could have significant impacts on the adaptive potential and differentiation of S. avenae biotypes on different plants.

Conclusions

The divergence patterns of transcriptional plasticity in defense related genes may play important roles in the phenotypic evolution and differentiation of S. avenae biotypes. Our results can provide insights into the role of gene expression plasticity in the divergence of insect biotypes and adaptive evolution of insect populations.

Distinctive Gene Expression Profiles and Effectors Consistent With Host Specificity in Two Formae Speciales of Marssonina brunnea

The knowledge on the host specificity of a pathogen underlying an interaction is becoming an urgent necessity for global warming. In this study, the gene expression profiles and the roles of effectors in host specificity were integrally characterized with two formae speciales, multigermtubi and monogermtubi, of a hemibiotrophic pathogen Marssonina brunnea when they were infecting respective susceptible poplar hosts. With a functional genome comparison referring to a de novo transcriptome of M. brunnea and Pathogen-Host Interaction database functional annotations, the multigermtubi strain showed abundant and significant differentially expressed unigenes (DEGs) (more than 40%) in colonizing the initial invasion stage and in the necrotrophic stage. The monogermtubi strain induced less than 10% of DEGs in the initial invasion stage but which abruptly increased to more than 80% DEGs in the necrotrophic stage. Both strains induced the least DEGs in the biotrophic stage compared to the initial invasion and necrotrophic stages. The orthologs of the effector genes Ecp6, PemG1, XEG1, ACE1, and Mg3LysM were exclusively induced by one of the two formae speciales depending on the infection stages. Some unigenes homologous to carbohydrate lytic enzyme genes, especially pectate lyases, were notably induced with multigermtubi forma specialis infection but not expressed in the monogermtubi forma specialis at an earlier infection stage. The extraordinary differences in the functional genome level between the two formae speciales of M. brunnea could be fundamental to exploring their host specificity determinant and evolution. This study also firstly provided the fungal transcriptome of the monogermtubi forma specialis for M. brunnea.

Inter-individual physiological variation in responses to environmental variation and environmental change: Integrating across traits and time

Greater understanding of physiological responses to climate change demands deeper comprehension of the causes and consequences of physiological variation. Increasingly, population trait means are being deconstructed into variable signals at the level of individuals. We advocate for greater consideration of such inter-individual physiological variation and how it both depends on and interacts with environmental variability. First, we review several studies on the intertidal mussel Mytilus californianus to illustrate how the magnitude of inter-individual variation may depend on the environmental context analyzed (i.e., is the mean condition benign or stressful?) and/or on the specific physiological metric investigated. Stressful conditions may reveal or mask variation in disparate ways at different levels of analysis (e.g., transcriptome vs. proteome), but we often lack crucial information regarding the relationships among these different physiological metrics and their consequences for fitness. We then reanalyze several published datasets to ask whether individuals employ divergent strategies over time in response to acute heat stress; such time-dependence would further complicate interpretation of physiological variation. However, definitive conclusions are precluded by limited sample sizes and short timescales in extant datasets. A key remaining challenge is to extend these analytical frameworks to longer periods over which individuals in a population experience repeated, but spatially variable, episodic stress events. We conclude that variation at multiple levels of analysis should be investigated over longer periods and, where possible, within individuals (or genotypes) experiencing repeated environmental challenges. Although difficult in practice, such studies will facilitate improved understanding of potential population-level physiological responses to climate change.

Genetic Variation for Ontogenetic Shifts in Metabolism Underlies Physiological Homeostasis in Drosophila

Organismal physiology emerges from metabolic pathways and subcellular structures like the mitochondria that can vary across development and among individuals. Here, we tested whether genetic variation at one level of physiology can be buffered at higher levels of biological organization during development by the inherent capacity for homeostasis in physiological systems. We found that the fundamental scaling relationship between mass and metabolic rate, as well as the oxidative capacity per mitochondria, changed significantly across development in the fruit fly Drosophila However, mitochondrial respiration rate was maintained at similar levels across development. Furthermore, larvae clustered into two types-those that switched to aerobic, mitochondrial ATP production before the second instar, and those that relied on anaerobic, glycolytic production of ATP through the second instar. Despite genetic variation for the timing of this metabolic shift, metabolic rate in second-instar larvae was more robust to genetic variation than was the metabolic rate of other instars. We found that larvae with a mitochondrial-nuclear incompatibility that disrupts mitochondrial function had increased aerobic capacity and relied more on anaerobic ATP production throughout development relative to larvae from wild-type strains. By taking advantage of both ways of making ATP, larvae with this mitochondrial-nuclear incompatibility maintained mitochondrial respiratory capacity, but also had higher levels of whole-body reactive oxygen species and decreased mitochondrial membrane potential, potentially as a physiological defense mechanism. Thus, genetic defects in core physiology can be buffered at the organismal level via physiological plasticity, and natural populations may harbor genetic variation for distinct metabolic strategies in development that generate similar organismal outcomes.

Evolved genetic and phenotypic differences due to mitochondrial-nuclear interactions

The oxidative phosphorylation (OxPhos) pathway is responsible for most aerobic ATP production and is the only pathway with both nuclear and mitochondrial encoded proteins. The importance of the interactions between these two genomes has recently received more attention because of their potential evolutionary effects and how they may affect human health and disease. In many different organisms, healthy nuclear and mitochondrial genome hybrids between species or among distant populations within a species affect fitness and OxPhos functions. However, what is less understood is whether these interactions impact individuals within a single natural population. The significance of this impact depends on the strength of selection for mito-nuclear interactions. We examined whether mito-nuclear interactions alter allele frequencies for ~11,000 nuclear SNPs within a single, natural Fundulus heteroclitus population containing two divergent mitochondrial haplotypes (mt-haplotypes). Between the two mt-haplotypes, there are significant nuclear allele frequency differences for 349 SNPs with a p-value of 1% (236 with 10% FDR). Unlike the rest of the genome, these 349 outlier SNPs form two groups associated with each mt-haplotype, with a minority of individuals having mixed ancestry. We use this mixed ancestry in combination with mt-haplotype as a polygenic factor to explain a significant fraction of the individual OxPhos variation. These data suggest that mito-nuclear interactions affect cardiac OxPhos function. The 349 outlier SNPs occur in genes involved in regulating metabolic processes but are not directly associated with the 79 nuclear OxPhos proteins. Therefore, we postulate that the evolution of mito-nuclear interactions affects OxPhos function by acting upstream of OxPhos.

Demystifying animal 'personality' (or not): why individual variation matters to experimental biologists

Animal 'personality', defined as repeatable inter-individual differences in behaviour, is a concept in biology that faces intense controversy. Critics argue that the field is riddled with terminological and methodological inconsistencies and lacks a sound theoretical framework. Nevertheless, experimental biologists are increasingly studying individual differences in physiology and relating these to differences in behaviour, which can lead to fascinating insights. We encourage this trend, and in this Commentary we highlight some of the benefits of estimating variation in (and covariation among) phenotypic traits at the inter- and intra-individual levels. We focus on behaviour while drawing parallels with physiological and performance-related traits. First, we outline some of the confusion surrounding the terminology used to describe repeatable inter-individual differences in behaviour. Second, we argue that acknowledging individual behavioural differences can help researchers avoid sampling and experimental bias, increase explanatory power and, ultimately, understand how selection acts on physiological traits. Third, we summarize the latest methods to collect, analyse and present data on individual trait variation. We note that, while measuring the repeatability of phenotypic traits is informative in its own right, it is only the first step towards understanding how natural selection and genetic architecture shape intra-specific variation in complex, labile traits. Thus, understanding how and why behavioural traits evolve requires linking repeatable inter-individual behavioural differences with core aspects of physiology (e.g. neurophysiology, endocrinology, energy metabolism) and evolutionary biology (e.g. selection gradients, heritability).

On the Role of Neurogenesis and Neural Plasticity in the Evolution of Animal Personalities and Stress Coping Styles

Individual variation in how animals react to stress and environmental change has become a central topic in a wide range of biological disciplines, from evolutionary ecology to biomedicine. Such variation manifests phenotypically as correlated trait-clusters (referred to as coping styles, behavioral syndromes, shyness-boldness, or personality traits). Thresholds for switching from active coping (fight-flight) to inhibition and passive behavior when exposed to stress depend on experience and genetic factors. Comparative research has revealed a range of neuroendocrine-behavioral associations which are conserved throughout the vertebrate subphylum, including factors affecting perception, learning, and memory of stimuli and events. Here we review conserved aspects of the contribution of neurogenesis and other aspects of neural plasticity to stress coping. In teleost fish, brain cell proliferation and neurogenesis have received recent attention. This work reveals that brain cell proliferation and neurogenesis are associated with heritable variation in stress coping style, and they are also differentially affected by short- and long-term stress in a biphasic manner. Routine-dependent and inflexible behavior in proactive individuals is associated with limited neural plasticity. These evolutionarily conserved relationships hold the potential to illuminate the biological background for stress-related neurobiological disorders.

Differential responses to environmental challenge by common carp Cyprinus carpio highlight the importance of coping style in integrative physiology

Common carp Cyprinus carpio displaying proactive or reactive stress coping styles were acclimated to two environmental regimes (low oxygen and low temperature), and selected groups were tested for response to an inflammatory challenge (Escherichia coli lipopolysaccharide, LPS). Plasma glucose and lactate levels were measured, as were selected C. carpio-specific messenger (m)RNA transcript abundance, including cortisol receptor (CR), enolase (ENO), glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and interleukin-1-beta (IL1β) was measured in individual whole brain samples. Basal levels (in sham injected fish held in normoxic conditions at 25° C) of plasma lactate and glucose differed between coping styles, being significantly lower in proactive individuals. Both variables increased in response to LPS challenge, with the exception of plasma glucose in reactive fish held in hypoxia. Baseline levels of gene expression under control conditions were significantly different for GAPDH between behavioural phenotypes. The responses to experimental challenge were sometimes diametrically opposed between stress-coping styles in a transcript-specific manner. For CR and GAPDH, for example, the response to LPS injection in hypoxia were opposite between proactive and reactive animals. Proactive fish showed decreased CR and increased GAPDH, whereas reactive showed the opposite response. These results further highlight that screening for stress-coping styles prior to experiments in adaptive physiology can significantly affect the interpretation of data obtained. Further, this leads to a more finely tuned analytical output providing an improved understanding of variation in individual responses to both environmental and inflammatory challenge.

Acclimation and acute temperature effects on population differences in oxidative phosphorylation

Temperature changes affect metabolism on acute, acclamatory, and evolutionary time scales. To better understand temperature's affect on metabolism at these different time scales, we quantified cardiac oxidative phosphorylation (OxPhos) in three Fundulus taxa acclimated to 12 and 28°C and measured at three acute temperatures (12, 20, and 28°C). The Fundulus taxa (northern Maine and southern Georgia F. heteroclitus, and a sister taxa, F. grandis) were used to identify evolved changes in OxPhos. Cardiac OxPhos metabolism was quantified by measuring six traits: state 3 (ADP and substrate-dependent mitochondrial respiration); E state (uncoupled mitochondrial activity); complex I, II, and IV activities; and LEAK ratio. Acute temperature affected all OxPhos traits. Acclimation only significantly affected state 3 and LEAK ratio. Populations were significantly different for state 3. In addition to direct effects, there were significant interactions between acclimation and population for complex I and between population and acute temperature for state 3. Further analyses suggest that acclimation alters the acute temperature response for state 3, E state, and complexes I and II: at the low acclimation temperature, the acute response was dampened at low assay temperatures, and at the high acclimation temperature, the acute response was dampened at high assay temperatures. Closer examination of the data also suggests that differences in state 3 respiration and complex I activity between populations were greatest between fish acclimated to low temperatures when assayed at high temperatures, suggesting that differences between the populations become more apparent at the edges of their thermal range.

Thermal variation, thermal extremes and the physiological performance of individuals

In this review we consider how small-scale temporal and spatial variation in body temperature, and biochemical/physiological variation among individuals, affect the prediction of organisms' performance in nature. For ‘normal’ body temperatures – benign temperatures near the species' mean – thermal biology traditionally uses performance curves to describe how physiological capabilities vary with temperature. However, these curves, which are typically measured under static laboratory conditions, can yield incomplete or inaccurate predictions of how organisms respond to natural patterns of temperature variation. For example, scale transition theory predicts that, in a variable environment, peak average performance is lower and occurs at a lower mean temperature than the peak of statically measured performance. We also demonstrate that temporal variation in performance is minimized near this new ‘optimal’ temperature. These factors add complexity to predictions of the consequences of climate change. We then move beyond the performance curve approach to consider the effects of rare, extreme temperatures. A statistical procedure (the environmental bootstrap) allows for long-term simulations that capture the temporal pattern of extremes (a Poisson interval distribution), which is characterized by clusters of events interspersed with long intervals of benign conditions. The bootstrap can be combined with biophysical models to incorporate temporal, spatial and physiological variation into evolutionary models of thermal tolerance. We conclude with several challenges that must be overcome to more fully develop our understanding of thermal performance in the context of a changing climate by explicitly considering different forms of small-scale variation. These challenges highlight the need to empirically and rigorously test existing theories.

Ocean acidification research in the 'post-genomic' era: Roadmaps from the purple sea urchin Strongylocentrotus purpuratus

Advances in nucleic acid sequencing technology are removing obstacles that historically prevented use of genomics within ocean change biology. As one of the first marine calcifiers to have its genome sequenced, purple sea urchins (Strongylocentrotus purpuratus) have been the subject of early research exploring genomic responses to ocean acidification, work that points to future experiments and illustrates the value of expanding genomic resources to other marine organisms in this new 'post-genomic' era. This review presents case studies of S. purpuratus demonstrating the ability of genomic experiments to address major knowledge gaps within ocean acidification. Ocean acidification research has focused largely on species vulnerability, and studies exploring mechanistic bases of tolerance toward low pH seawater are comparatively few. Transcriptomic responses to high pCO₂ seawater in a population of urchins already encountering low pH conditions have cast light on traits required for success in future oceans. Secondly, there is relatively little information on whether marine organisms possess the capacity to adapt to oceans progressively decreasing in pH. Genomics offers powerful methods to investigate evolutionary responses to ocean acidification and recent work in S. purpuratus has identified genes under selection in acidified seawater. Finally, relatively few ocean acidification experiments investigate how shifts in seawater pH combine with other environmental factors to influence organism performance. In S. purpuratus, transcriptomics has provided insight into physiological responses of urchins exposed simultaneously to warmer and more acidic seawater. Collectively, these data support that similar breakthroughs will occur as genomic resources are developed for other marine species.

Statistical analysis of the individual variability of 1D protein profiles as a tool in ecology: an application to parasitoid venom

Understanding the forces that shape eco-evolutionary patterns often requires linking phenotypes to genotypes, allowing characterization of these patterns at the molecular level. DNA-based markers are less informative in this aim compared to markers associated with gene expression and, more specifically, with protein quantities. The characterization of eco-evolutionary patterns also usually requires the analysis of large sample sizes to accurately estimate interindividual variability. However, the methods used to characterize and compare protein samples are generally expensive and time-consuming, which constrains the size of the produced data sets to few individuals. We present here a method that estimates the interindividual variability of protein quantities based on a global, semi-automatic analysis of 1D electrophoretic profiles, opening the way to rapid analysis and comparison of hundreds of individuals. The main original features of the method are the in silico normalization of sample protein quantities using pictures of electrophoresis gels at different staining levels, as well as a new method of analysis of electrophoretic profiles based on a median profile. We demonstrate that this method can accurately discriminate between species and between geographically distant or close populations, based on interindividual variation in venom protein profiles from three endoparasitoid wasps of two different genera (Psyttalia concolor, Psyttalia lounsburyi and Leptopilina boulardi). Finally, we discuss the experimental designs that would benefit from the use of this method.

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole-genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.

The Elizabeth River Story: A Case Study in Evolutionary Toxicology

The Elizabeth River system is an estuary in southeastern Virginia, surrounded by the towns of Chesapeake, Norfolk, Portsmouth, and Virginia Beach. The river has played important roles in U.S. history and has been the location of various military and industrial activities. These activities have been the source of chemical contamination in this aquatic system. Important industries, until the 1990s, included wood treatment plants that used creosote, an oil-derived product that is rich in polycyclic aromatic hydrocarbons (PAH). These plants left a legacy of PAH pollution in the river, and in particular Atlantic Wood Industries is a designated Superfund site now undergoing remediation. Numerous studies examined the distribution of PAH in the river and impacts on resident fauna. This review focuses on how a small estuarine fish with a limited home range, Fundulus heteroclitus (Atlantic killifish or mummichog), has responded to this pollution. While in certain areas of the river this species has clearly been impacted, as evidenced by elevated rates of liver cancer, some subpopulations, notably the one associated with the Atlantic Wood Industries site, displayed a remarkable ability to resist the marked effects PAH have on the embryonic development of fish. This review provides evidence of how pollutants have acted as evolutionary agents, causing changes in ecosystems potentially lasting longer than the pollutants themselves. Mechanisms underlying this evolved resistance, as well as mechanisms underlying the effects of PAH on embryonic development, are also described. The review concludes with a description of ongoing and promising efforts to restore this historic American river.

Effects of seawater acidification on gene expression: resolving broader-scale trends in sea urchins

Sea urchins are ecologically and economically important calcifying organisms threatened by acidification of the global ocean caused by anthropogenic CO2 emissions. Propelled by the sequencing of the purple sea urchin (Strongylocentrotus purpuratus) genome, profiling changes in gene expression during exposure to high pCO2 seawater has emerged as a powerful and increasingly common method to infer the response of urchins to ocean change. However, analyses of gene expression are sensitive to experimental methodology, and comparisons between studies of genes regulated by ocean acidification are most often made in the context of major caveats. Here we perform meta-analyses as a means of minimizing experimental discrepancies and resolving broader-scale trends regarding the effects of ocean acidification on gene expression in urchins. Analyses across eight studies and four urchin species largely support prevailing hypotheses about the impact of ocean acidification on marine calcifiers. The predominant expression pattern involved the down-regulation of genes within energy-producing pathways, a clear indication of metabolic depression. Genes with functions in ion transport were significantly over-represented and are most plausibly contributing to intracellular pH regulation. Expression profiles provided extensive evidence for an impact on biomineralization, epitomized by the down-regulation of seven spicule matrix proteins. In contrast, expression profiles provided limited evidence for CO2-mediated developmental delay or induction of a cellular stress response. Congruence between studies of gene expression and the ocean acidification literature in general validates the accuracy of gene expression in predicting the consequences of ocean change and justifies its continued use in future studies.

The rapid cold hardening response of Drosophila melanogaster: complex regulation across different levels of biological organization

Rapid cold hardening (RCH) is a form of thermal acclimation that allows ectotherms to fine-tune their physiological state to match rapid changes in thermal environment. Despite progress in recent years, there is still a considerable uncertainty regarding the physiological basis of RCH in insects. Here we investigated the physiological response of adult Drosophila melanogaster to a gradual reduction of temperature from 25 to 0°C followed by 1h at 0°C. As expected, this RCH treatment promoted cold tolerance, and so we hypothesized that this change could be detected at the proteomic level. Using 2D-DIGE, we found that only a few proteins significantly changed in abundance, and of these, we identified a set of four proteins of particular interest. These were identified as two different variants of glycogen phosphorylase (GlyP) of which three spots were up-regulated and another was down regulated. In subsequent experiments, we quantified upstream events by measuring the GlyP mRNA amount, but we found no marked effect of RCH. We also examined downstream events by measuring GlyP activity and the level of free sugars. We found no effect of RCH on GlyP activity. On the other hand, screening of whole animal sugar contents revealed a small increase in glucose levels following RCH while trehalose content was unaltered. This study highlights a complex regulation of GlyP in relation to RCH where we found associations between the cold tolerance, the protein abundance and the metabolite concentrations but no changes in mRNA expression and enzyme activity. These data stress the necessity of combining the hypothesis-generating power of an 'Omics' approach with subsequent targeted validations across several levels of the biological organization. We discuss reasons why different biological linked levels do not necessarily change stoichiometrically.

Energy and metabolism

Although firmly grounded in metabolic biochemistry, the study of energy metabolism has gone well beyond this discipline and become integrative and comparative as well as ecological and evolutionary in scope. At the cellular level, ATP is hydrolyzed by energy-expending processes and resynthesized by pathways in bioenergetics. A significant development in the study of bioenergetics is the realization that fluxes through pathways as well as metabolic rates in cells, tissues, organs, and whole organisms are "system properties." Therefore, studies of energy metabolism have become, increasingly, experiments in systems biology. A significant challenge continues to be the integration of phenomena over multiple levels of organization. Body mass and temperature are said to account for most of the variation in metabolic rates found in nature. A mechanistic foundation for the understanding of these patterns is outlined. It is emphasized that evolution, leading to adaptation to diverse lifestyles and environments, has resulted in a tremendous amount of deviation from popularly accepted scaling "rules." This is especially so in the deep sea which constitutes most of the biosphere.

Combining animal personalities with transcriptomics resolves individual variation within a wild-type zebrafish population and identifies underpinning molecular differences in brain function

Resolving phenotype variation within a population in response to environmental perturbation is central to understanding biological adaptation. Relating meaningful adaptive changes at the level of the transcriptome requires the identification of processes that have a functional significance for the individual. This remains a major objective towards understanding the complex interactions between environmental demand and an individual's capacity to respond to such demands. The interpretation of such interactions and the significance of biological variation between individuals from the same or different populations remain a difficult and under-addressed question. Here, we provide evidence that variation in gene expression between individuals in a zebrafish population can be partially resolved by a priori screening for animal personality and accounts for >9% of observed variation in the brain transcriptome. Proactive and reactive individuals within a wild-type population exhibit consistent behavioural responses over time and context that relates to underlying differences in regulated gene networks and predicted protein-protein interactions. These differences can be mapped to distinct regions of the brain and provide a foundation towards understanding the coordination of underpinning adaptive molecular events within populations.

Assessing gene network stability and individual variability in the fathead minnow (Pimephales promelas) transcriptome

Transcriptomics is increasingly used to assess biological responses to environmental stimuli and stressors such as aquatic pollutants. However, fundamental studies characterizing individual variability in mRNA levels are lacking, which currently limits the use of transcriptomics in environmental monitoring assessments. To address individual variability in transcript abundance, we performed a meta-analysis on 231 microarrays that were conducted in the fathead minnow (FHM), a widely used toxicological model. The mean variability for gene probes was ranked from most to least variable based upon the coefficient of variation. Transcripts that were the most variable in individual tissues included NADH dehydrogenase flavoprotein 1, GTPase IMAP family member 7-like and v-set domain-containing T-cell activation inhibitor 1-like while genes encoding ribosomal proteins (rpl24 and rpl36), basic transcription factor 3, and nascent polypeptide-associated complex alpha subunit were the least variable in individuals across a range of microarray experiments. Gene networks that showed high variability (based upon the variation in expression of individual members within the network) included cell proliferation, metabolism (steroid, lipids, and glucose), cell adhesion, vascularization, and regeneration while those that showed low variability (more stability) included mRNA and rRNA processing, regulation of translational fidelity, RNA splicing, and ribosome biogenesis. Real-time PCR was conducted on a subset of genes for comparison of variability collected from the microarrays. There was a significant positive relationship between the two methods when measuring individual variability, suggesting that variability detected in microarray data can be used to guide decisions on sample sizes for measuring transcripts in real-time PCR experiments. A power analysis revealed that measuring estrogen receptor ba (esrba) requires fewer biological replicates than that of estrogen receptor bb (esrbb) in the gonad and samples sizes required to detect a 50% change for reproductive-related transcripts is between 12 and 20. Characterizing individual variability at the molecular level will prove necessary as efforts are made toward integrating molecular tools into environmental risk assessments.

High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

BACKGROUND

Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act.

RESULTS

We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers.

CONCLUSION

Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown.

Interindividual variation in Complex I activity in Fundulus heteroclitus along a steep thermocline

The first enzyme in the oxidative phosphorylation pathway is Complex I (EC 1.6.5.3). Complex I is a large heteromeric enzyme complex with 45 protein subunits that translocates H(+) ions across the mitochondrial inner membrane. Among northern and southern populations of the teleost fish Fundulus heteroclitus, Complex I subunits have fixed amino acid substitutions. Additionally, there are differences in oxidative phosphorylation activity among populations of F. heteroclitus. To investigate whether these differences are related to Complex I, enzyme activity was measured in 121 individuals from five populations of F. heteroclitus and its sister species Fundulus grandis acclimated to a constant 20°C temperature. Within each population, Complex I activity is highly variable among individuals of F. heteroclitus (coefficient of variation percentage among individuals has a mean of 90% in the five F. heteroclitus populations), and the mean Complex I activity among populations is significantly different at the latitudinal extremes of the range. Importantly, Complex I activity is more similar between F. heteroclitus from the southernmost population and its sister species F. grandis than to the northern populations of F. heteroclitus, suggesting important evolutionary differences. Unexpectedly, the activity is nearly fourfold higher in southern populations than northern populations. Mitochondrial density appears to compensate partially for decreased activity in northern individuals; activity per wet weight is only twofold higher in southern populations. We suggest that some of the variation in Complex I activity is genetically based and thus is being influenced by directional selection. However, this conclusion presents a conundrum: there should not be so much variation in Complex I activity within a population if this variation is biologically important.

The relationship between phenotypic and environmental variation: do physiological responses reduce interindividual differences?

What is the effect of a variable environment on phenotypic variation? Does the physiological response to a new environment increase or decrease the differences among individuals? We provide a speculative hypothesis suggesting that the induction of a physiological response to environmental change minimizes phenotypic differences among individuals in outbred genetically variable populations. Although this suggestion runs counter to the general idea that environmental variation induces phenotypic variation, we provide evidence that this is not always the case. One explanation for this counterintuitive hypothesis is that in a variable environment, the physiological mechanism that maintains homeostasis changes the concentrations of active transcription factors (TFs). This change in TFs reduces the effectiveness of nucleotide polymorphisms in TF binding sites and thus reduces the variation among individuals in mRNA expression and in the phenotypes affected by these mRNA transcripts. Thus, there are fewer differences among individuals in a variable environment compared with the variation observed in a constant environment. Our conjecture is that the physiological mechanisms that maintain homeostasis in response to environmental variation canalize phenotypic variation. If our hypothesis is correct, then the physiological canalization of gene expression in a variable environment hides genetic variation and thereby reduces the evolutionary costs of polymorphism. This hypothesis provides a new perspective on the mechanisms by which high levels of genetic variation can persist in real-world populations.

Metabolism in the age of ‘omes’

Much research in comparative physiology is now performed using ‘omics’ tools and many results are interpreted in terms of the effects of changes in gene expression on energy metabolism. However, ‘metabolism’ is a complex phenomenon that spans multiple levels of biological organization. In addition rates and directions of flux change dynamically under various physiological circumstances. Within cells, message level cannot be equated with protein level because multiple mechanisms are at play in the ‘regulatory hierarchy’ from gene to mRNA to enzyme protein. This results in many documented instances wherein change in mRNA levels and change in enzyme levels are unrelated. It is also known from metabolic control analysis that the influence of single steps in pathways on flux is often small. Flux is a system property and its control tends to be distributed among multiple steps. Consequently, change in enzyme levels cannot be equated with change in flux. Approaches developed by Hans Westerhoff and colleagues, called ‘hierarchical regulation analysis’, allow quantitative determination of the extent to which ‘hierarchical regulation’, involving change in enzyme level, and ‘metabolic regulation’, involving the modulation of the activity of preexisting enzyme, regulate flux. We outline these approaches and provide examples to show their applicability to problems of interest to comparative physiologists.

Variation in gene expression along a salinity gradient in wild populations of the euryhaline black-chinned tilapia Sarotherodon melanotheron

This study evaluated variation in expression of 11 genes within and among six wild populations of the black-chinned tilapia Sarotherodon melanotheron distributed along a salinity gradient from 0 to 100. Previous laboratory studies had shown that expression of these genes was sensitive to water salinity; the current study confirmed that a number of them also varied in expression in wild populations along the salinity gradient. Principal component analysis (PCA) first distinguished two, not mutually exclusive, sets of genes: trade-off genes that were highly expressed at one or other extreme of the salinity gradient and stress genes that were up-regulated at the two salinity extremes (i.e. a U-shaped expression pattern). The PCA clearly partitioned the populations into three groups based on their gene expression patterns and their position along the salinity gradient: a freshwater (GL; 0) population, four brackish and seawater (GB, HB, SM, SF; ranging from 20 to 50) populations and a hypersaline (SK, 100) population. Individual variation in gene expression was significantly greater within the populations at the extreme compared to intermediate salinities. These results reveal phenotypically plastic regulation of gene expression in S. melanotheron, and greater osmoregulatory and plasticity costs at extreme salinities, where fitness-related traits are known to be altered.

Comparative genomics in ecological physiology: toward a more nuanced understanding of acclimation and adaptation

Organisms that live in variable environments must adjust their physiology to compensate for environmental change. Modern functional genomics technologies offer global top-down discovery-based tools for identifying and exploring the mechanistic basis by which organisms respond physiologically to a detected change in the environment. Given that populations and species from different niches may exhibit different acclimation abilities, comparative genomic approaches may offer more nuanced understanding of acclimation responses, and provide insight into the mechanistic and genomic basis of variable acclimation. The physiological genomics literature is large and growing, as is the comparative evolutionary genomics literature. Yet, expansion of physiological genomics experiments to exploit taxonomic variation remains relatively undeveloped. Here, recent advances in the emerging field of comparative physiological genomics are considered, including examples of plants, bees and fish, and opportunities for further development are outlined particularly in the context of climate change research. Elements of robust experimental design are discussed with emphasis on the phylogenetic comparative approach. Understanding how acclimation ability is partitioned among populations and species in nature, and knowledge of the relevant genes and mechanisms, will be important for characterizing and predicting the ecological and evolutionary consequences of human-accelerated environmental change.

Proteomics in evolutionary ecology: linking the genotype with the phenotype

The study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein-protein interactions, as well as the combined use of the different -omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.

The effect of short-term hypoxic exposure on metabolic gene expression

The long-term effect of hypoxia is to decrease both the production and use of ATP and thus decrease the reliance on mitochondrial oxidative energy production. Yet, recent studies include more immediate affects of hypoxia on gene expression and these data suggest the maintenance of mitochondrial function. To better understand the short-term physiological response to hypoxia, we quantified metabolic mRNA expression in the heart ventricles and livers of the teleost fish Fundulus grandis exposed to partial oxygen pressure of 2.8 kPa (-13.5% air saturation).Twenty-eight individuals from a single population were exposed to hypoxia for 0, 4, 8, 12, 24, 48, and 96  hr. Liver and cardiac tissues were sampled from the same individuals at 0-48  hr. At 96  hr, only cardiac tissue was assayed. Gene expression was significantly different (ANOVA, P < 0.05) for 17 of 226 metabolic genes (7.5%) in cardiac tissue and for 20 of 256 (7.8%) metabolic genes in hepatic tissue. For the two tissues examined in this study, the maximum response occurred at different times. For cardiac tissue, using Dunnett's post hoc test, most of these significant differences occurred at 96  hr of exposure. For liver, all but one significant difference occurred at 4  hr. Surprisingly, too many (relative to random expectations) of the genes with significant increase in mRNA are involved in the oxidative phosphorylation pathway: 44% of the significant genes at 96  hr in the heart and 33% of the significant genes at 4  hr in the liver are involved in the oxidative phosphorylation pathway. These data indicate that there are tissue-specific differences in the timing of the response to hypoxia, yet both cardiac and hepatic tissues have increases in mRNA that code for enzyme in the oxidative phosphorylation pathway. If these changes in mRNA produce a similar change in protein, then these data suggest that the initial response to hypoxia involves an increase in the oxidative pathway potentially as a mechanism to maintain ATP production.

Life or death? A physiogenomic approach to understand individual variation in responses to hemorrhagic shock

Severe hemorrhage due to trauma is a major cause of death throughout the world. It has often been observed that some victims are able to withstand hemorrhage better than others. For decades investigators have attempted to identify physiological mechanisms that distinguish survivors from nonsurvivors for the purpose of providing more informed therapies. As an alternative approach to address this issue, we have initiated a research program to identify genes and genetic mechanisms that contribute to this phenotype of survival time after controlled hemorrhage. From physiogenomic studies using inbred rat strains, we have demonstrated that this phenotype is a heritable quantitative trait, and is therefore a complex trait regulated by multiple genes. Our work continues to identify quantitative trait loci as well as potential epigenetic mechanisms that might influence survival time after severe hemorrhage. Our ultimate goal is to improve survival to traumatic hemorrhage and attendant shock via regulation of genetic mechanisms and to provide knowledge that will lead to genetically-informed personalized treatments.

Functional genomics of life history variation in a butterfly metapopulation

In fragmented landscapes, small populations frequently go extinct and new ones are established with poorly understood consequences for genetic diversity and evolution of life history traits. Here, we apply functional genomic tools to an ecological model system, the well-studied metapopulation of the Glanville fritillary butterfly. We investigate how dispersal and colonization select upon existing genetic variation affecting life history traits by comparing common-garden reared 2-day adult females from new populations with those from established older populations. New-population females had higher expression of abdomen genes involved in egg provisioning and thorax genes involved in the maintenance of flight muscle proteins. Physiological studies confirmed that new-population butterflies have accelerated egg maturation, apparently regulated by higher juvenile hormone titer and angiotensin converting enzyme mRNA, as well as enhanced flight metabolism. Gene expression varied between allelic forms of two metabolic genes (Pgi and Sdhd), which themselves were associated with differences in flight metabolic rate, population age and population growth rate. These results identify likely molecular mechanisms underpinning life history variation that is maintained by extinction-colonization dynamics in metapopulations.

Developmental and genetic origins of murine long bone length variation

If we wish to understand whether development influences the rate or direction of morphological evolution, we must first understand the developmental bases of morphological variation within species. However, quantitative variation in adult morphology is the product of molecular and cellular processes unfolding from embryonic development through juvenile growth to maturity. The Atchley-Hall model provides a useful framework for dissecting complex morphologies into their component parts as a way of determining which developmental processes contribute to variation in adult form. We have examined differences in postnatal allometry and the patterns of genetic correlation between age-specific traits for ten recombinant inbred strains of mice generated from an intercross of LG/J and SM/J. Long bone length is closely tied to body size, but variation in adult morphology is more closely tied to differences in growth rate between 3 and 5 weeks of age. These analyses show that variation generated during early development is overridden by variation generated later in life. To more precisely determine the cellular processes generating this variation we then examined the cellular dynamics of long bone growth plates at the time of maximum elongation rate differences in the parent strains. Our analyses revealed that variation in long bone length is the result of faster elongation rates of the LG/J stain. The developmental bases for these differences in growth rate involve the rate of cell division and chondrocyte hypertrophy in the growth plate.

Transcriptional plasticity of a soil arthropod across different ecological conditions

Ecological functional genomics, dealing with the responses of organisms to their natural environment is confronted with a complex pattern of variation and a large number of confounding environmental factors. For gene expression studies to provide meaningful information on conditions deviating from normal, a baseline or normal operating range (NOR) response needs to be established which indicates how an organism's transcriptome reacts to naturally varying ecological factors. Here we determine the transcriptional plasticity of a soil arthropod, Folsomia candida, exposed to various natural environments, as part of a first attempt in establishing such a NOR. Animals were exposed to 26 different field soils after which gene expression levels were measured. The main factor found to regulate gene expression was soil-type (sand or clay). Cell homeostasis and DNA replication were affected in collembolans exposed to sandy soil, indicating general stress. Multivariate analysis identified soil fertility as the main factor influencing gene expression. Regarding land-use, only forest soils showed an expression pattern deviating from the others. No significant effect of land-use, agricultural practice or soil type on fitness was observed, but arsenic concentration was negatively correlated with reproductive output. In conclusion, transcriptional responses remained within a limited range across the different land-uses but were significantly affected by soil-type. This may be caused by the contrasting soil physicochemical properties to which F. candida strongly responds. The broad range of conditions over which this soil-living detritivore is able to survive and reproduce, indicates a strategy of high plasticity, which comes with extensive gene expression regulation.

Gene expression analysis for the identification of selection and local adaptation in fishes

In recent years, variation in gene expression has been recognized as an important component of environmental adaptation in multiple model species, including a few fish species. There is, however, still little known about the genetic basis of adaptation in gene expression resulting from variation in the aquatic environment (e.g. temperature, salinity and oxygen) and the physiological effect and costs of such differences in gene expression. This review presents and discusses progress and pitfalls of applying gene expression analyses to fishes and suggests simple frameworks to get started with gene expression analysis. It is emphasized that well-planned gene expression studies can serve as an important tool for the identification of selection in local populations of fishes, even for non-traditional model species where limited genomic information is available. Recent studies focusing on gene expression variation among natural fish populations are reviewed, highlighting the latest applications that combine genetic evidence from neutral markers and gene expression data.