Integrative and genomics approaches to uncover the mechanistic bases of fish behavior and its diversity

An Investigation of Post-radiation Gene Expression Profiles: A System Biology Study

Introduction: Genomics and bioinformatics are useful methods for exploring unclear aspects of radiation effects on biological systems. Many radiation-induced alterations in irradiated samples are post-radiation time-dependent. This study aims to evaluate the post-irradiation effects of the gamma ray on human Jurkat cells. Methods: Gene expression profiles of the samples harvested 6 and 24 hours after radiation to find the critical differential expressed genes and the related pathways. Samples are provided from Gene Expression Omnibus (GEO) and analyzed by ClueGO. Results: Twnety-nine critical genes were determined as the important affected genes and 7 classes of related pathways were introduced. CCNE2, PSMD11, CDC25C, ANAPC1, PLK1, AURKA, and CCNB1 that were associated with more than 6 pathways were related to one of the determined pathway groups. Conclusion: Cell protecting pathways were associated with the genes (HSPA5, HSPA8, HSP90B1, HMMR, CEBPB, RXRA, and PSMD11) which were related to the minimum numbers of pathways. The finding of this study corresponds to repair processes which depend on post-radiation time. It seems these sets of genes are suitable candidates for further investigation.

Genomics: moving behavioural ecology beyond the phenotypic gambit

Researchers studying the adaptive significance of behaviour typically assume that genetic mechanisms will not inhibit evolutionary trajectories, an assumption commonly known as the 'phenotypic gambit'. Although the phenotypic gambit continues to be a useful heuristic for behavioural ecology, here we discuss how genomic methods provide new tools and conceptual approaches that are relevant to behavioural ecology. We first describe how the concept of a genetic toolkit for behaviour can allow behavioural ecologists to synthesize both genomic and ecological information when assessing behavioural adaptation. Then we show how gene expression profiles can be viewed as complex phenotypic measurements, used to (1) predict behaviour, (2) evaluate phenotypic plasticity and (3) devise methods to manipulate behaviour in order to test adaptive hypotheses. We propose that advances in genomics and bioinformatics may allow researchers to overcome some of the logistical obstacles that motivated the inception of the phenotypic gambit. Behavioural ecology and genomics are mutually informative, providing potential synergy that could lead to powerful advances in the field of animal behaviour.

The relationship between DRD4 polymorphisms and phenotypic correlations of behaviors in the collared flycatcher

There is increasing evidence that the genetic architecture of exploration behavior includes the dopamine receptor D4 gene (DRD4). Such a link implies that the within-individual consistency in the same behavior has a genetic basis. Behavioral consistency is also prevalent in the form of between-individual correlation of functionally different behaviors; thus, the relationship between DRD4 polymorphism and exploration may also be manifested for other behaviors. Here, in a Hungarian population of the collared flycatcher, Ficedula albicollis, we investigate how males with distinct DRD4 genotypes differ in the consistent elements of their behavioral displays during the courtship period. In completely natural conditions, we assayed novelty avoidance, aggression and risk-taking, traits that were previously shown repeatable over time and correlate with each other, suggesting that they could have a common mechanistic basis. We identified two single-nucleotide polymorphisms (SNP554 and SNP764) in the exon 3 of the DRD4 gene by sequencing a subsample, then we screened 202 individuals of both sexes for these SNPs. Focusing on the genotypic variation in courting males, we found that “AC” heterozygote individuals at the SNP764 take lower risk than the most common “AA” homozygotes (the “CC” homozygotes were not represented in our subsample of males). We also found a considerable effect size for the relationship between SNP554 polymorphism and novelty avoidance. Therefore, in addition to exploration, DRD4 polymorphisms may also be associated with the regulation of behaviors that may incur fear or stress. Moreover, polymorphisms at the two SNPs were not independent indicating a potential role for genetic constraints or another functional link, which may partially explain behavioral correlations.

Proximate perspectives on the evolution of female aggression: good for the gander, good for the goose?

Female-female aggression often functions in competition over reproductive or social benefits, but the proximate mechanisms of this apparently adaptive behaviour are not well understood. The sex steroid hormone testosterone (T) and its metabolites are well-established mediators of male-male aggression, and several lines of evidence suggest that T-mediated mechanisms may apply to females as well. However, a key question is whether mechanisms of female aggression primarily reflect correlated evolutionary responses to selection acting on males, or whether direct selection acting on females has made modifications to these mechanisms that are adaptive in light of female life history. Here, I examine the degree to which female aggression is mediated at the level of T production, target tissue sensitivity to T, or downstream genomic responses in order to test the hypothesis that selection favours mechanisms that facilitate female aggression while minimizing the costs of systemically elevated T. I draw heavily from avian systems, including the dark-eyed junco (Junco hyemalis), as well as other organisms in which these mechanisms have been well studied from an evolutionary/ecological perspective in both sexes. Findings reveal that the sexes share many behavioural and hormonal mechanisms, though several patterns also suggest sex-specific adaptation. I argue that greater attention to multiple levels of analysis-from hormone to receptor to gene network, including analyses of individual variation that represents the raw material of evolutionary change-will be a fruitful path for understanding mechanisms of behavioural regulation and intersexual coevolution.

Fish welfare and genomics

There is a considerable public and scientific debate concerning welfare of fish in aquaculture. In this review, we will consider fish welfare as an integration of physiological, behavioral, and cognitive/emotional responses, all of which are essentially adaptative responses to stressful situations. An overview of fish welfare in this context suggests that understanding will rely on knowledge of all components of allostatic responses to stress and environmental perturbations. The development of genomic technologies provides new approaches to this task, exemplified by how genome-wide analysis of genetic structures and corresponding expression patterns can lead to the discovery of new aspects of adaptative responses. We will illustrate how the genomic approach may give rise to new biomarkers for fish welfare and also increase our understanding of the interaction between physiological, behavioral, and emotional responses. In a first part, we present data on expression of candidate genes selected a priori. This is a common avenue to develop molecular biomarkers capable of diagnosing a stress condition at its earliest onset, in order to allow quick corrective intervention in an aquaculture setting. However, most of these studies address isolated physiological functions and stress responses that may not be truly indicative of animal welfare, and there is only rudimentary understanding of genes related to possible cognitive and emotional responses in fish. We also present an overview on transcriptomic analysis related to the effect of aquaculture stressors, environmental changes (temperature, salinity, hypoxia), or concerning specific behavioral patterns. These studies illustrate the potential of genomic approaches to characterize the complexity of the molecular mechanisms which underlies not only physiological but also behavioral responses in relation to fish welfare. Thirdly, we address proteomic studies on biological responses to stressors such as salinity change and hypoxia. We will also consider proteomic studies developed in mammals in relation to anxiety and depressive status which may lead to new potential candidates in fish. Finally, in the conclusion, we will suggest new developments to facilitate an integrated view of fish welfare. This includes use of laser microdissection in the transcriptomic/proteomic studies, development of meta-analysis methods for extracting information from genomic data sets, and implementation of technological advances for high-throughput proteomic studies. Development of these new approaches should be as productive for our understanding of the biological processes underlying fish welfare as it has been for the progress of pathophysiological research.

Behavioural syndromes in fishes: a review with implications for ecology and fisheries management

This review examines the contribution of research on fishes to the growing field of behavioural syndromes. Current knowledge of behavioural syndromes in fishes is reviewed with respect to five main axes of animal personality: (1) shyness-boldness, (2) exploration-avoidance, (3) activity, (4) aggressiveness and (5) sociability. Compared with other taxa, research on fishes has played a leading role in describing the shy-bold personality axis and has made innovative contributions to the study of the sociability dimension by incorporating social network theory. Fishes are virtually the only major taxon in which behavioural correlations have been compared between populations. This research has guided the field in examining how variation in selection regime may shape personality. Recent research on fishes has also made important strides in understanding genetic and neuroendocrine bases for behavioural syndromes using approaches involving artificial selection, genetic mapping, candidate gene and functional genomics. This work has illustrated consistent individual variation in highly complex neuroendocrine and gene expression pathways. In contrast, relatively little work on fishes has examined the ontogenetic stability of behavioural syndromes or their fitness consequences. Finally, adopting a behavioural syndrome framework in fisheries management issues including artificial propagation, habitat restoration and invasive species, may promote restoration success. Few studies, however, have examined the ecological relevance of behavioural syndromes in the field. Knowledge of how behavioural syndromes play out in the wild will be crucial to incorporating such a framework into management practices.

Promise and progress in environmental genomics: a status report on the applications of gene expression-based microarray studies in ecologically relevant fish species

The advent of any new technology is typically met with great excitement. So it was a few years ago, when the combination of advances in sequencing technology and the development of microarray technology made measurements of global gene expression in ecologically relevant species possible. Many of the review papers published around that time promised that these new technologies would revolutionize environmental biology as they had revolutionized medicine and related fields. A few years have passed since these technological advancements have been made, and the use of microarray studies in non-model fish species has been adopted in many laboratories internationally. Has the relatively widespread adoption of this technology really revolutionized the fields of environmental biology, including ecotoxicology, aquaculture and ecology, as promised? Or have these studies merely become a novelty and a potential distraction for scientists addressing environmentally relevant questions? In this review, the promises made in early review papers, in particular about the advances that the use of microarrays would enable, are summarized; these claims are compared to the results of recent studies to determine whether the forecasted changes have materialized. Some applications, as discussed in the paper, have been realized and have led to advances in their field, others are still under development.

Neuroendocrinology of sexual plasticity in teleost fishes

The study of sex differences has produced major insights into the organization of animal phenotypes and the regulatory mechanisms generating phenotypic variation from similar genetic templates. Teleost fishes display the greatest diversity of sexual expression among vertebrate animals. This diversity appears to arise from diversity in the timing of sex determination and less functional interdependence among the components of sexuality relative to tetrapod vertebrates. Teleost model systems therefore provide powerful models for understanding gonadal and non-gonadal influences on behavioral and physiological variation. This review addresses socially-controlled sex change and alternate male phenotypes in fishes. These sexual patterns are informative natural experiments that illustrate how variation in conserved neuroendocrine pathways can give rise to a wide range of reproductive adaptations. Key regulatory factors underlying sex change and alternative male phenotypes that have been identified to date include steroid hormones and the neuropeptides GnRH and arginine vasotocin, but genomic approaches are now implicating a diversity of other influences as well.

Gene-expression signatures of Atlantic salmon's plastic life cycle

How genomic expression differs as a function of life history variation is largely unknown. Atlantic salmon exhibits extreme alternative life histories. We defined the gene-expression signatures of wild-caught salmon at two different life stages by comparing the brain expression profiles of mature sneaker males and immature males, and early migrants and late migrants. In addition to life-stage-specific signatures, we discovered a surprisingly large gene set that was differentially regulated-at similar magnitudes, yet in opposite direction-in both life history transitions. We suggest that this co-variation is not a consequence of many independent cellular and molecular switches in the same direction but rather represents the molecular equivalent of a physiological shift orchestrated by one or very few master regulators.