It is becoming increasingly clear that local adaptation can occur even in the face of high gene flow and limited overall genomic differentiation among populations (reviewed by Nosil et al. 2009 ). Thus, one important task for molecular ecologists is to sift through genomic data to identify the genes that matter for local adaptation ( Hoffmann & Willi 2008 ; Stapley et al. 2010 ). Recent advances in high‐throughput molecular technologies have facilitated this search, and a variety of approaches can be applied, including those grounded in population genetics [e.g. outlier analysis ( Pavlidis et al. 2008 )], classical and quantitative genetics [e.g. quantitative trait locus analysis ( MacKay et al. 2009 )], and cellular and molecular biology [e.g. transcriptomics ( Larsen et al. 2011 )]. However, applying these approaches in nonmodel organisms that lack extensive genetic and genomic resources has been a formidable challenge. In this issue, Papakostas et al. (2012) . demonstrate how one such approach – high‐throughput label‐free proteomics (reviewed by Gstaiger & Aebersold 2009 ; Domon & Aebersold 2010 ) – can be applied to detect genes that may be involved in local adaptation in a species with limited genomic resources. Using this approach, they identified genes that may be implicated in local adaptation to salinity in European whitefish ( Coregonus lavaretus L. ) and provide insight into the mechanisms by which fish cope with changes in this critically important environmental parameter.
Anthropogenic climate change threatens freshwater biodiversity and poses a challenge for fisheries management, as fish will increasingly be exposed to episodes of high temperature and low oxygen (hypoxia). Here, we examine the extent of variation in tolerance of acute exposure to these stressors within and among five strains of rainbow trout (Oncorhynchus mykiss) currently being used or under consideration for use in stocking programmes in British Columbia, Canada. We used incipient lethal oxygen saturation (ILOS) as an index of acute hypoxia tolerance, critical thermal maximum (CTmax) as an index of acute upper thermal tolerance and mortality following these two acute exposure trials to assess the relative resilience of individuals and strains to climate change-relevant stressors. We measured tolerance across two brood years and two life stages (fry and yearling), using a highly replicated design with hundreds of individuals per strain and life stage. There was substantial within-strain variation in CTmax and ILOS, but differences among strains, although statistically significant, were small. In contrast, there were large differences in post-trial mortality among strains, ranging from less than 2% mortality in the most resilient strain to 55% mortality in the least resilient. There was a statistically significant, but weak, correlation between CTmax and ILOS at both life stages for some strains, with thermally tolerant individuals tending to be hypoxia tolerant. These data indicate that alternative metrics of tolerance may result in different conclusions regarding resilience to climate change stressors, which has important implications for stocking and management decisions for fish conservation in a changing climate.
Anthropogenic climate change threatens freshwater biodiversity and poses a challenge for fisheries management, as fish will increasingly be exposed to episodes of high temperature and low oxygen (hypoxia). Here, we examine the extent of variation in tolerance of acute exposure to these stressors within and among five strains of rainbow trout (Oncorhynchus mykiss) currently being used or under consideration for use in stocking programmes in British Columbia, Canada. We used incipient lethal oxygen saturation (ILOS) as an index of acute hypoxia tolerance, critical thermal maximum (CTmax) as an index of acute upper thermal tolerance and mortality following these two acute exposure trials to assess the relative resilience of individuals and strains to climate change-relevant stressors. We measured tolerance across two brood years and two life stages (fry and yearling), using a highly replicated design with hundreds of individuals per strain and life stage. There was substantial within-strain variation in CTmax and ILOS, but differences among strains, although statistically significant, were small. In contrast, there were large differences in post-trial mortality among strains, ranging from less than 2% mortality in the most resilient strain to 55% mortality in the least resilient. There was a statistically significant, but weak, correlation between CTmax and ILOS at both life stages for some strains, with thermally tolerant individuals tending to be hypoxia tolerant. These data indicate that alternative metrics of tolerance may result in different conclusions regarding resilience to climate change stressors, which has important implications for stocking and management decisions for fish conservation in a changing climate.
Contamination of aquatic systems by metals and polycyclic aromatic hydrocarbons (PAHs) is a prevalent environmental problem. These contaminants are known to impact populations, organismal health, and survival negatively. Most of the organism and ecosystem level changes are a consequence of underlying molecular and subcellular damage. Therefore, molecular bioindicators are likely to be a sensitive tool for environmental assessment. We have demonstrated that both copper and phenanthrenequinone (PHEQ) alter protein expression in Daphnia magna. To investigate altered gene expression in Daphnia magna exposed to copper, PHEQ, and other contaminants, a technique based on the differential display polymerase chain reaction (ddPCR) is being developed for D. magna. This technique promises numerous applications as it permits a survey of the genes being expressed in any given organism. Furthermore, ddPCR allows one to monitor the changes in gene expression that result from any toxicant exposure. This paper reviews the applications of ddPCR and describes our development of ddPCR as a bioindicator of gene expression in D. magna in response to toxicant exposure. This is the first step in the development of a novel gene fingerprinting technique that can be applied to any compound and organism of interest.
Colias eurytheme butterflies display extensive allozyme polymorphism in the enzyme phosphoglucose isomerase (PGI). Earlier studies on biochemical and fitness effects of these genotypes found evidence of strong natural selection maintaining this polymorphism in the wild. Here we analyze the molecular features of this polymorphism by sequencing multiple alleles and modeling their structures. PGI is a dimer with rotational symmetry. Each monomer provides a critical residue to the other monomer's catalytic center. Sequenced alleles differ at multiple amino acid positions, including cryptic charge-neutral variation, but most consistent differences among the electromorph alleles are at the charge-changing amino acid sites. Principal candidate sites of selection, identified by structural and functional analyses and by their variants' population frequencies, occur in interpenetrating loops across the interface between monomers, where they may alter subunit interactions and catalytic center geometry. Comparison to a second (and basal) species, Colias meadii, also polymorphic for PGI under natural selection, reveals one fixed amino acid difference between their PGIs, which is located in the interpenetrating loop and accompanies functional differences among their variants. We also study nucleotide variability among the PGI alleles, comparing these data to similar data from another glycolytic enzyme gene, glyceraldehyde-3-phosphate dehydrogenase. Despite extensive nonsynonymous and synonymous polymorphism at PGI in each species, the only base changes fixed between species are the two causing the amino acid replacement; this absence of synonymous fixation yields a significant McDonald-Kreitman test. Analyses of these data suggest historical population expansion. Positive peaks of Tajima's D statistic, representing regions of neutral "hitchhiking," are found around the principal candidate sites of selection. This study provides novel views of molecular-structural mechanisms, and beginnings of historical evidence, for a long-persistent balanced enzyme polymorphism at PGI in these and perhaps other species.
Summary As part of our efforts to characterize Na,K‐ATPase isoforms in salmonid fish, we investigated the linkage arrangement of genes coding for the α and β ‐subunits of the enzyme complex in the tetraploid‐derived genome of the rainbow trout ( Oncorhynchus mykiss ). Genetic markers were developed from four of five previously characterized α ‐subunit isoforms ( α 1b, α 1c, α 2 and α 3) and four expressed sequence tags derived from yet undescribed β ‐subunit isoforms ( β 1a, β 1b, β 3a and β 3b). Sex‐specific linkage analysis of polymorphic loci in a reference meiotic panel revealed that Na,K‐ATPase genes are generally dispersed throughout the rainbow trout genome. A notable exception was the colocalization of two α ‐subunit genes and one β ‐subunit gene on linkage group RT‐12, which may thus share a conserved orthologous segment with linkage group 1 in zebrafish ( Danio rerio ). Consistent with previously reported homeologous relationships among the chromosomes of the rainbow trout, primers designed from the α 3‐isoform detected a pair of duplicated genes on linkage groups RT‐27 and RT‐31. Similarly, the evolutionary conservation of homeologous regions on linkage groups RT‐12 and RT‐16 was further supported by the map localization of gene duplicates for the β 1b isoform. The detection of homeologs within each gene family also raises the possibility that novel isoforms may be discovered as functional duplicates.
This chapter provides an overview of the various strategies that fishes use to mitigate the effects of temperature change, summarizes how physiologists characterize the thermal niche of fishes and examines the mechanisms fishes use to compensate for the effects of temperature across levels of biological organization. The fundamental thermal niche of a fish species is defined as the range of environmental temperatures over which that species can survive, grow and reproduce. Fishes living in variable environments are typically eurythermal – able to tolerate a wide range of environmental temperatures. The ability of fishes to maintain physiological performance in the face of thermal variation differs among species and is largely reflective of the range of temperatures experienced in their natural environment. For ectothermic fishes, exposure to temperature change causes changes in biochemical processes and metabolism that must be compensated for in order to maintain performance.
