FishResp: R package and GUI application for analysis of aquatic respirometry data.

Intermittent-flow respirometry is widely used to measure oxygen uptake rates and subsequently estimate aerobic metabolic rates of aquatic animals. However, the lack of a standard quality-control software to detect technical problems represents a potential impediment to comparisons across studies in the field of evolutionary and conservation physiology. Here, we introduce 'FishResp', a versatile R package and its graphical implementation for quality-control and filtering of raw respirometry data.

Selection on the morphology-physiology-performance nexus: Lessons from freshwater stickleback morphs.

Conspecifics inhabiting divergent environments frequently differ in morphology, physiology, and performance, but the interrelationships amongst traits and with Darwinian fitness remains poorly understood. We investigated population differentiation in morphology, metabolic rate, and swimming performance in three-spined sticklebacks ( L.), contrasting a marine/ancestral population with two distinct freshwater morphotypes derived from it: the "typical" low-plated morph, and a unique "small-plated" morph.

Challenges and advances for transcriptome assembly in non-model species.

Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence).

Sticklebacks adapted to divergent osmotic environments show differences in plasticity for kidney morphology and candidate gene expression.

Novel physiological challenges in different environments can promote the evolution of divergent phenotypes, either through plastic or genetic changes. Environmental salinity serves as a key barrier to the distribution of nearly all aquatic organisms, and species diversification is likely to be enabled by adaptation to alternative osmotic environments. The threespine stickleback () is a euryhaline species with populations found both in marine and freshwater environments.

Regulatory Architecture of Gene Expression Variation in the Threespine Stickleback Gasterosteus aculeatus.

Much adaptive evolutionary change is underlain by mutational variation in regions of the genome that regulate gene expression rather than in the coding regions of the genes themselves. An understanding of the role of gene expression variation in facilitating local adaptation will be aided by an understanding of underlying regulatory networks. Here, we characterize the genetic architecture of gene expression variation in the threespine stickleback (Gasterosteus aculeatus), an important model in the study of adaptive evolution.

The adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes.

Whilst adaptation and phenotypic plasticity might buffer species against habitat degradation associated with global climate change, few studies making such claims also possess the necessary and sufficient data to support them. Doing so requires demonstration of heritable variation in traits affecting fitness under new environmental conditions. We address this issue using an emerging aquatic system to study adaptation to climate change, the crimson-spotted rainbowfish (Melanotaenia duboulayi), a freshwater species from a region of eastern Australia projected to be affected by marked temperature increases.

Hypoxia and the pharmaceutical diclofenac influence the circadian responses of three-spined stickleback.

Pollution with low concentrations of pharmaceuticals, especially when combined with low-oxygen conditions (hypoxia), is a threat to aquatic ecosystems worldwide. The non-steroidal anti-inflammatory drug diclofenac is commonly detected in wastewater effluents, and has potential to accumulate in the bile of fish. Diclofenac has been shown to activate aryl hydrocarbon receptor (AHR), which induces transcription in the metabolic enzyme cytochrome P450 1a (cyp1a).

The evolution and adaptive potential of transcriptional variation in sticklebacks--signatures of selection and widespread heritability.

Evidence implicating differential gene expression as a significant driver of evolutionary novelty continues to accumulate, but our understanding of the underlying sources of variation in expression, both environmental and genetic, is wanting. Heritability in particular may be underestimated when inferred from genetic mapping studies, the predominant "genetical genomics" approach to the study of expression variation. Such uncertainty represents a fundamental limitation to testing for adaptive evolution at the transcriptomic level.

Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity.

Comparative studies of the divergence of quantitative traits and neutral molecular markers, known as Q(ST)-F(ST) comparisons, provide a means for researchers to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. The use of Q(ST)-F(ST) comparisons has increased rapidly in the last few years, highlighting the utility of this approach for addressing a wide range of questions that are relevant to evolutionary and ecological genetics. These studies have also provided lessons for the design of future Q(ST)-F(ST) comparisons.

Transcription and redox enzyme activities: comparison of equilibrium and disequilibrium levels in the three-spined stickleback.

Evolutionary and acclimatory responses require functional variability, but in contrast with mRNA and protein abundance data, most physiological measurements cannot be obtained in a high-throughput manner. Consequently, one must either rely on high-throughput transcriptomic or proteomic data with only predicted functional information, or accept the limitation that most physiological measurements can give fewer data than those provided by transcriptomics or proteomics. We evaluated how transcriptional and redox enzyme activity data agreed with regard to population differentiation (i.

Multiple evolutionary pathways to decreased lateral plate coverage in freshwater threespine sticklebacks.

Adaptation to novel environments can be based either on standing genetic variation or variation attributable to new mutations. When standing genetic variation for a functional adaptation is lacking, and variation due to new mutations is not yet available, adaptation is possible only through alternative functional solutions. Reduction in the number of bony lateral plates as an adaptation to freshwater colonization by marine threespine sticklebacks (Gasterosteus aculeatus) has occurred in numerous independent cases through allelic substitution in the ectodysplasin-a (Eda) gene.

Plasticity and heritability of morphological variation within and between parapatric stickleback demes.

The threespine stickleback (Gasterosteus aculeatus) has emerged as an important model organism in evolutionary ecology, largely due to the repeated, parallel evolution of divergent morphotypes found in populations having colonized freshwater habitats. However, morphological divergence following colonization is not a universal phenomenon. We explore this in a large-scale estuarine ecosystem inhabited by two parapatric stickleback demes, each physiologically adapted to divergent osmoregulatory environments (fresh vs.

Intraspecific divergence in the lateral line system in the nine-spined stickleback (Pungitius pungitius).

The mechanosensory lateral line system of fishes is an important organ system conveying information crucial to individual fitness. Yet, our knowledge of lateral line diversity is almost exclusively based on interspecific studies, whereas intraspecific variability and possible population divergence have remained largely unexplored. We investigated lateral line system variability in four marine and five pond populations of nine-spined stickleback (Pungitius pungitius).

Adaptive divergence between freshwater and marine sticklebacks: insights into the role of phenotypic plasticity from an integrated analysis of candidate gene expression.

Debate surrounding the integration of phenotypic plasticity within the neo-Darwinian paradigm has recently intensified, but is largely dominated by conceptual abstractions. Advances in our capacities to identify candidate genes, and quantify their levels of expression, now facilitate the study of natural variation in inherently plastic traits, and may lead to a more concrete understanding of plasticity's role in adaptive evolution. We present data from parapatric threespine stickleback (Gasterosteus aculeatus) demes inhabiting geologically recent, freshwater and saltwater zones of a large estuary.

Landscape genetic analyses reveal cryptic population structure and putative selection gradients in a large-scale estuarine environment.

Disentangling the relative contributions of selective and neutral processes underlying phenotypic and genetic variation under natural, environmental conditions remains a central challenge in evolutionary ecology. However, much of the variation that could be informative in this area of research is likely to be cryptic in nature; thus, the identification of wild populations suitable for study may be problematic. We use a landscape genetics approach to identify such populations of three-spined stickleback inhabiting the Saint Lawrence River estuary.

Habitat and home range fidelity in a trophically dimorphic pumpkinseed sunfish (Lepomis gibbosus) population.

We investigated habitat selection in a trophically dimorphic population of pumpkinseed sunfish (Lepomis gibbosus) to determine whether littoral and limnetic ecotypes exhibit habitat or site fidelity. A transplant experiment was conducted, in which 998 pumpkinseeds captured from littoral and limnetic sites were marked and released in either the site of capture, the nearest site of the same habitat type, or the nearest site of the opposite habitat type. Daily recapture attempts over the course of the reproductive and growing season provided a 25% recapture rate, 40% of which were recaptured on multiple occasions at the same site.