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Animals have an endogenous circadian clock that temporally regulates 24 hour (h) oscillations in behavior and physiology. This highly conserved mechanism consists of two positive regulators, Bmal and Clock, and two negative regulators, Cry and Per, that run with a 24-h cycle that synchronizes itself with environmental changes in light, food, and temperature. We examined the circadian clock in Chinook salmon (Oncorhynchus tshawytscha), a non-model organism in which the function of the clock has not been studied. Recent studies indicate that clock genes in Chinook salmon play a role in its evolution of local adaptation, possibly by influencing migration timing. We designed real-time quantitative PCR (RT-qPCR) assays to quantify the transcription of components of the clock system, and validated these for PCR efficiency and specificity in detecting Chinook target genes. Chinook salmon tissue samples were collected in 3-h intervals, over the course of 24 h, from five different organs. Our data indicate that the circadian clock functions differently in each of these tissues. In the liver, positive and negative regulators exhibit anti-phasic peaking in the evening and morning, respectively. However, in the heart, these same regulators peak and trough with a different timing, indicating that the liver and heart are not synchronous. The digestive tract displays yet another difference: simultaneous phases in the expression of positive and negative clock regulators, and we do not observe significant rhythms in clock gene expression in the retina. Our data show that there is a functional clock in Chinook salmon tissues, but that this clock behaves in a tissue-specific manner, regardless of the whole animal being exposed to the same environmental cues. These results highlight the adaptive role of the clock in Chinook salmon and that it may have different positive and negative effects depending on tissue function.

In British Columbia, Atlantic salmon (Salmo salar) are the top finfish aquaculture export of the province, although native Chinook salmon (Oncorhynchus tshawytscha) are also farmed locally. Few commercial facilities rear Chinook salmon, limiting the availability and development of their broodstocks, potentially reducing the ability to improve product quantity and quality. Due to the potential for inbreeding in these stocks, a need to determine whether product quantity and quality can be improved through outbreeding with wild populations exists. In this study, we examined the effects of outbreeding on farmed salmon by comparing product quantity and quality metrics in six experimental populations of outbred (wild × farmed) Chinook salmon and one farmed (control) population. Specifically, we measured fillet yield, slaughter yield, lipid content and flesh colour score in three-year old market-sized salmon immediately post-slaughter. We found significant differences across populations for slaughter yield, fillet yield and flesh colour score but found no differences across populations in lipid content. For flesh colour score, slaughter and fillet yield, the control farmed population performed similarly to the highest performing outbred populations. These results suggest that outbreeding inbred farmed populations with wild populations can maintain high product quality while adding new genes to a population.

Phenotypic differences among populations within a species have been reported for a variety of traits, ranging from life history to physiology to gene transcription. Population-level phenotypic variation has been attributed to genetic differences resulting from genetic drift and/or local adaptation as well as environmental differences resulting from plasticity. We studied population- and family-level variation in gene transcription for 22 fitness-related genes, comprising immune, growth, metabolic, and stress processes in Chinook salmon (Oncorhynchus tshawytscha). We created hybrid Chinook salmon families from eight populations and treated them with an immune stimulus, a handling stress challenge, and held some as a no-treatment control group. Population effects, sire effects, and narrow-sense heritability (h2 ) were calculated for each candidate gene within each treatment group. We expected population to have a significant effect on gene transcription for many of our genes; however, we found a population effect for transcription at only one immune gene at rest. The limited number of significant population effects on gene transcription, combined with significant additive genetic variance within each population does not support the expectation of past strong selection pressures acting on heritable transcription profiles among populations. Instead, our results indicate that Chinook salmon likely adapt to their local environment through transcriptional plasticity rather than fixed differences. The expectation for fixed population-level differences in gene transcription at fitness-related genes, reflecting accepted models of local adaptation is high; however, comparisons among multiple populations using half-sibling breeding designs are rare. Our work fills an important gap in our growing understanding of the process of among and within-population divergence.

Olfaction mediates behaviors necessary for survival and reproduction in fishes. Anthropogenic inputs of contaminants into aquatic environments, specifically copper, are known to disrupt a broad range of olfactory-mediated behaviors and can cause long-lasting damage even at low concentrations that have profound impacts on the biology of aquatic organisms. The sea lamprey (Petromyzon marinus) is a primitive fish species invasive to the North American Great Lakes that relies on olfaction to navigate during natal homing and in mate choice during reproduction. To investigate effects of copper on sea lamprey olfaction and the potential for maintenance of olfactory function during copper exposure, we exposed juvenile sea lamprey to environmentally ecologically relevant copper concentrations (0, 5, 10 and 30 µg/L) for 24 hr and characterized gene transcription response in olfactory tissue (i.e., peripheral olfactory organ and olfactory bulb) and forebrain using whole transcriptome sequencing. Copper exposure induced a pattern of positive dose-dependent transcriptional response. Expression changes primarily reflected up-regulation of genes involved in apoptosis and wound healing. Unlike higher vertebrates, genes specifically related to the olfactory senses of the sea lamprey, e.g., olfactory receptors, exhibited little transcriptional response to copper exposure, suggesting the mechanism of copper-induced olfactory impairment is through necrosis of the olfactory bulb and not copper-selective inhibition of olfactory receptors. Fully two-thirds of the differentially expressed genes at higher doses of copper have no known function and thus represent important candidates for further study of the responses to copper-induced olfactory injury. Our results shed light on the evolution of vertebrate olfactory repair mechanisms and have important implications for the conservation and management of both invasive and native populations of lamprey.

Despite increased global interest in Chinook salmon aquaculture, little is known of their viral immune defenses. This study describes the establishment and characterization of a continuous cell line derived from Chinook salmon spleen, CHSS, and its use in innate immune studies. Optimal growth was seen at 14–18 °C when grown in Leibovitz's L-15 media with 20% fetal bovine serum. DNA analyses confirmed that CHSS was Chinook salmon and genetically different from the only other available Chinook salmon cell line, CHSE-214. Unlike CHSE-214, CHSS could bind extracellular dsRNA, resulting in the rapid and robust expression of antiviral genes. Receptor/ligand blocking assays confirmed that class A scavenger receptors (SR-A) facilitated dsRNA binding and subsequent gene expression. Although both cell lines expressed three SR-A genes: SCARA3, SCARA4, and SCARA5, only CHSS appeared to have functional cell-surface SR-As for dsRNA. Collectively, CHSS is an excellent cell model to study dsRNA-mediated innate immunity in Chinook salmon.

The genus Beroe Browne, 1756 (Ctenophora, Beroidae) occurs worldwide, with 25 currently-described species. Because the genus is poorly studied, the definitive number of species is uncertain. Recently, a possible new Beroe species was suggested based on internal transcribed spacer 1 (ITS1) sequences from samples collected in Svalbard, Norway. Another species, Beroe ovata, was introduced to Europe from North America, initially in the Black Sea and subsequently (and possibly secondarily) into the Mediterranean and Baltic Seas. In areas where ctenophores have been introduced, they have often had significant detrimental ecological effects. The potential for other cryptic and/or undescribed Beroe species and history of spread of some species in the genus give reason for additional study. When alive, morphological hallmarks may be challenging to spot and photograph owing to the animals' transparency and near-constant motion. We sampled and analyzed 109 putative Beroe specimens from Europe, using morphological and molecular approaches. DNA analyses were conducted using cytochrome oxidase 1 and internal transcribed spacer sequences and, together with published sequences from GenBank, phylogenetic relationships of the genus were explored. Our study suggests the presence of at least 5 genetic lineages of Beroe in Europe, of which 3 could be assigned to known species: Beroe gracilis Künne 1939; Beroe cucumis Fabricius, 1780; and Beroe ovata sensu Mayer, 1912. The other 2 lineages (here provisionally named Beroe "norvegica" and Beroe "anatoliensis") did not clearly coincide with any known species and might therefore reflect new species, but confirmation of this requires further study.

Given the important role that animal vocalizations play in mate attraction and resource defence, acoustic signals are expected to play a significant role in speciation. Most studies, however, have focused on the acoustic traits of male animals living in the temperate zone. In contrast to temperate environments, in the tropics, it is commonplace for both sexes to produce complex acoustic signals. Therefore, tropical birds offer the opportunity to compare the sexes and provide a more comprehensive understanding of the evolution of animal signals. In this study, we quantified patterns of acoustic variation in Rufous-and-white Wrens (Thryophilus rufalbus) from five populations in Central America. We quantified similarities and differences between male and female songs by comparing the role that acoustic adaptation, cultural isolation and neutral genetic divergence have played in shaping acoustic divergence. We found that males and females showed considerable acoustic variation across populations, although females exhibited greater population divergence than males. Redundancy analysis and partial-redundancy analysis revealed significant relationships between acoustic variation and ecological variables, genetic distance, and geographic distance. Both ambient background noise and geographic distance explained a high proportion of variance for both males and females, suggesting that both acoustic adaptation and cultural isolation influence song. Overall, our results indicate that parallel evolutionary forces act on male and female acoustic signals and highlight the important role that cultural drift and selection play in the evolution of both male and female songs.

A fundamental hypothesis about vocal learning is that young animals learn vocalizations in their natal areas and, following postnatal dispersal, they may introduce new types of vocalizations into their breeding areas. We tested this hypothesis in a tropical bird, the Rufous-and-white Wren (Thryophilus rufalbus), a species in which both sexes produce learned songs. We collected blood samples and acoustic recordings from 146 adult wrens from 3 populations in northwestern Costa Rica. We genotyped individuals at 10 polymorphic microsatellite loci and identified first-generation migrants using partial Bayesian genotype assignment. We quantified acoustic variation by comparing fine-scale acoustic structure, song sharing, and repertoire novelty between residents and first-generation migrants. We found significant population-level differences in acoustic structure of songs among the 3 populations. Of the 146 individuals genotyped, 9 individuals were identified as first-generation migrants. In contrast to our predictions, however, we found that these first-generation migrants did not exhibit differences in the acoustic structure of their songs from resident individuals in their breeding population, either for males or females. We conclude that song learning in first-generation migrants must be behaviorally influenced by birds in their breeding populations, following postnatal dispersal. We observed population-level acoustic differences among the 3 study sites, which implies sustained divergent selection pressures at each site, possibly reflecting acoustic adaptation to different environments or social pressure to sing local songs. Understanding and quantifying patterns of cultural evolution at multiple scales provides insight into how behavioral barriers, such as acoustic signals, contribute to population differentiation and even speciation.

Non‐native species may be introduced either intentionally or unintentionally, and their impact can range from benign to highly disruptive. Non‐native salmonids were introduced into Lake Ontario, Canada, to provide recreational fishing opportunities; however, the establishment of those species has been proposed as a significant barrier to the reintroduction of native Atlantic salmon (Salmo salar) due to intense interspecific competition. In this study, we compared population differences of Atlantic salmon in transcriptome response to interspecific competition. We reared Atlantic salmon from two populations (LaHave River and Sebago Lake) with fish of each of three non‐native salmonids (Chinook salmon Oncorhynchus tshawytscha, rainbow trout O. mykiss, and brown trout S. trutta) in artificial streams. We used RNA‐seq to assess transcriptome differences between the Atlantic salmon populations and the responses of these populations to the interspecific competition treatments after 10 months of competition in the stream tanks. We found that population differences in gene expression were generally greater than the effects of interspecific competition. Interestingly, we found that the two Atlantic salmon populations exhibited similar responses to interspecific competition based on functional gene ontologies, but the specific genes within those ontologies were different. Our transcriptome analyses suggest that the most stressful competitor (as measured by the highest number of differentially expressed genes) differs between the two study populations. Our transcriptome characterization highlights the importance of source population selection for conservation applications, as organisms with different evolutionary histories can possess different transcriptional responses to the same biotic stressors. The results also indicate that generalized predictions of the response of native species to interactions with introduced species may not be appropriate without incorporating potential population‐specific response to introduced species.

The extraction and characterization of DNA from aquatic environmental samples offers an alternative, non-invasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next-generation sequencing (“metabarcoding”), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom designed group-specific primer set and next-generation sequencing for the detection of three species at risk; (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada; the Grand River and the Sydenham River. Out of 82 fish species detected in both rivers using capture-based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co-occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture-based methods, for improved mapping of species distribution patterns. This article is protected by copyright. All rights reserved.

Variation in gene transcription is widely believed to be the mechanistic basis of phenotypically plastic traits; however, comparatively little is known about the inheritance patterns of transcriptional variation that would allow us to predict its response to selection. In addition, acclimation to different environmental conditions influences acute transcriptional responses to stress and it is unclear if these effects are heritable. To address these gaps in knowledge, we assayed levels of messenger RNA for 14 candidate genes at rest and in response to a 24-h confinement stress for 72 half-sib families of Chinook salmon reared in two different environments (hatchery and semi-natural stream channel). We observed extensive plasticity for mRNA levels of metabolic and stress response genes and demonstrated that mRNA level plasticity due to rearing environment affects mRNA level plasticity in response to stress. These effects have important implications for natural populations experiencing multiple stressors. We identified genotype-by-environment interactions for mRNA levels that were dominated by maternal effects; however, mRNA level response to challenge also exhibited a non-additive genetic basis. Our results indicate that while plasticity for mRNA levels can evolve, predicting the outcome of selection will be difficult. The inconsistency in genetic architecture among treatment groups suggests there is considerable cryptic genetic variation for gene expression.

The view of maternal effects (nongenetic maternal environmental influence on offspring phenotype) has changed from one of distracting complications in evolutionary genetics to an important evolutionary mechanism for improving offspring fitness. Recent studies have shown that maternal effects act as an adaptive mechanism to prepare offspring for stressful environments. Although research into the magnitude of maternal effects is abundant, the molecular mechanisms of maternal influences on offspring phenotypic variation are not fully understood. Despite recent work identifying DNA methylation as a potential mechanism of nongenetic inheritance, currently proposed links between DNA methylation and parental effects are indirect and primarily involve genomic imprinting. We combined a factorial breeding design and gene-targeted sequencing methods to assess inheritance of methylation during early life stages at 14 genes involved in growth, development, metabolism, stress response, and immune function of Chinook salmon (Oncorhynchus tshawytscha). We found little evidence for additive or nonadditive genetic effects acting on methylation levels during early development; however, we detected significant maternal effects. Consistent with conventional maternal effect data, maternal effects on methylation declined through development and were replaced with nonadditive effects when offspring began exogenous feeding. We mapped methylation at individual CpG sites across the selected candidate genes to test for variation in site-specific methylation profiles and found significant maternal effects at selected CpG sites that also declined with development stage. While intergenerational inheritance of methylated DNA is controversial, we show that CpG-specific methylation may function as an underlying molecular mechanism for maternal effects, with important implications for offspring fitness.

Several studies have demonstrated that environmental DNA (eDNA) can be used to detect the presence of aquatic species, days to weeks after the target species has been removed. However, most studies used eDNA analysis in lentic systems (ponds or lakes), or in controlled laboratory experiments. While eDNA degrades rapidly in all aquatic systems, it also undergoes dilution effects and physical destruction in flowing systems, complicating detection in rivers. However, some eDNA (i.e. residual eDNA) can be retained in aquatic systems, even those subject to high flow regimes. Our goal was to determine residual eDNA detection sensitivity using quantitative real-time polymerase chain reaction (qRT-PCR), in a flowing, uncontrolled river after the eDNA source was removed from the system; we repeated the experiment over 2 years. Residual eDNA had the strongest signal strength at the original source site and was detectable there up to 11.5 h after eDNA source removal. Residual eDNA signal strength decreased as sampling distance downstream from the eDNA source site increased, and was no longer detectable at the source site 48 h after the eDNA source water was exhausted in both experiments. This experiment shows that residual eDNA sampled in surface water can be mapped quantitatively using qRT-PCR, which allows a more accurate spatial identification of the target species location in lotic systems, and relative residual eDNA signal strength may allow the determination of the timing of the presence of target species.

Byproducts from a photocatalytic pretreated model lignin chemical, sodium LS (lignosulfonate), was used to produce electricity in SCMFCs (single chamber microbial fuel cells). Pretreating LS was performed using TiO 2 -UV photocatalysis. Optimization and modeling of the photocatalytic degradation process was performed using the Box-Behnken design method to achieve a maximum BOD 5 to COD ratio. LC-MS (Liquid chromatography–mass spectrometry) analysis was conducted to identify compounds produced from the photocatalysis of LS. The biofilm microbial diversity and performance of SCMFCs fed PrLS (pretreated LS) was compared to SCMFCs fed glucose at the same COD loadings and operating conditions. The PrLS fed SCMFCs, operated at 37 ± 1 °C, generated maximum current and power densities of 6556 ± 360 mA m −3 and 1881 ± 103 mW m −3 , respectively. The corresponding maximum current and power densities normalized to the cathode area were 868 ± 48 mA m −2 and 248 ± 14 mW m −2 , respectively. The SCMFCs removed 77.6 ± 2.3% of the COD of the PrLS and achieved a coulombic efficiency of 17.7 ± 1.2%. This study demonstrated the effectiveness of photocatalysis coupled with a bioelectrochemical system in treating lignin compounds and simultaneously generate electricity.

Inbreeding depression is the loss of fitness resulting from the mating of genetically related individuals. Traditionally, the study of inbreeding depression focused on genetic effects, although recent research has identified DNA methylation as also having a role in inbreeding effects. Since inbreeding depression and DNA methylation change with age and environmental stress, DNA methylation is a likely candidate for the regulation of genes associated with inbreeding depression. Here, we use a targeted, multigene approach to assess methylation at 22 growth-, metabolic-, immune- and stress-related genes. We developed PCR-based DNA methylation assays to test the effects of intense inbreeding on intragenic gene-specific methylation in inbred and outbred Chinook salmon. Inbred fish had altered methylation at three genes, CK-1, GTIIBS and hsp70, suggesting that methylation changes associated with inbreeding depression are targeted to specific genes and are not whole-genome effects. While we did not find a significant inbreeding by age interaction, we found that DNA methylation generally increases with age, although methylation decreased with age in five genes, CK-1, IFN-ɣ, HNRNPL, hsc71 and FSHb, potentially due to environmental context and sexual maturation. As expected, we found methylation patterns differed among tissue types, highlighting the need for careful selection of target tissue for methylation studies. This study provides insight into the role of epigenetic effects on ageing, environmental response and tissue function in Chinook salmon and shows that methylation is a targeted and regulated cellular process. We provide the first evidence of epigenetically based inbreeding depression in vertebrates.

Ability to quantify connectivity among spawning subpopulations and their relative contribution of recruits to the broader population is a critical fisheries management need. By combining microsatellite and age information from larval yellow perch (Perca flavescens) collected in the Lake St. Clair – Detroit River system (SC-DRS) and western Lake Erie with a hydrodynamic backtracking approach, we quantified subpopulation structure, connectivity, and contributions of recruits to the juvenile stage in western Lake Erie during 2006–2007. After finding weak (yet stable) genetic structure between the SC-DRS and two western Lake Erie subpopulations, microsatellites also revealed measurable recruitment of SC-DRS larvae to the juvenile stage in western Lake Erie (17%–21% during 2006–2007). Consideration of precollection larval dispersal trajectories, using hydrodynamic backtracking, increased estimated contributions to 65% in 2006 and 57% in 2007. Our findings highlight the value of complementing subpopulation discrimination methods with hydrodynamic predictions of larval dispersal by revealing the SC-DRS as a source of recruits to western Lake Erie and also showing that connectivity through larval dispersal can affect the structure and dynamics of large lake fish populations.

Aquaculture practices continuously seek to improve efficiency to produce larger fish at lower cost. Selective breeding within brood stocks can result in undesirable effects, promoting hatcheries to use outbreeding to increase or maintain genetic diversity. This practice however, could result in the introduction of wild behavioural phenotypes unable to adapt to captive-living conditions. Using four hatchery first-generation hybrid crosses and two fully domesticated stocks of Chinook salmon (Oncorhynchus tshawytscha) in British Columbia, we examined behavioural responses to common aquaculture practices such as abrupt environmental change and novel feed types in juvenile fish. Controlling for mass, we found crosses varied in their behaviours to a novel setting and preferences for natural versus commercial diets. These differences were furthermore associated with rearing environment and stock-level growth rate and body size. Our results suggest selecting for phenotypes that behaviourally exhibit better coping mechanisms and greater flexibility in response to change is possible, and when in combination with growth metrics, should be an integral part of producing the desired farmed fish. Behaviours that allow commercial anadromous fish to easily transition to captive environmental conditions can benefit production and also animal welfare.

While outbreeding is a common method used to introduce variation to a broodstock in aquaculture to maintain healthy genetic stocks, little consideration is given to identifying stocks that can experience easy acclimation to captivity. Because the ability of individuals to behaviourally adjust to novel captive conditions influences who will reach broodstock age, behaviours can be used to screen for potential source stocks for outbreeding. To determine the effects outbreeding has on the variation of behavioural phenotypes produced, and whether these phenotypes can be predictive of growth and survival to captive conditions, an experimental design was created consisting of seven wild-domestic hybrid stocks of Chinook salmon (Oncorhynchus tshawytscha) and domesticated control stock. Behavioural assays were conducted on the same captive individuals as juveniles in fresh water and sub-adults in salt water to test for the occurrence of acclimation / growth-maximizing behavioural phenotypes such as flexibility: exploration, neophilia, and predator responsiveness; and growth-promotion: sociality, activity, and food-motivation. These behaviours were then contrasted against performance (growth and survival) within and across life-history stages. We found inter-population variation in four distinct behavioural types at each life-history stage. Still, we found individuals that were less shy (LMM: β = -0.14, P < 0.001), or inactive (β = -0.32, P=0.004), or more social (β=0.018, P=0.01) as juveniles; or were risk-averse (β=0.022, P=0.056) as sub-adults experienced greater short and/or long-term performance. While not one behavioural type emerged in predictive power of performance, better performing stocks possessed more of these desired behavioural traits. By identifying which behavioural attributes contribute most to first-generation acclimation, screening tools can be developed to recommend natural populations for outcrossing, balancing both production and animal welfare.

Acid mine drainage (AMD) remediation commonly produces byproducts which must be stored or utilized to reduce the risk of further contamination. A mussel shell bioreactor has been implemented at a coal mine in New Zealand, which is an effective remediation option, although an accumulated sludge layer decreased efficiency which was then removed and requires storage. To understand associated risks related to storage or use of the AMD sludge material, a laboratory mesocosm study investigated the physio-chemical and biological influence in two conditions: anoxic storage (burial deep within a waste rock dump) or exposure to oxic environments (use of sludge on the surface of the mine). Solid phase characterization by Scanning Electron Microscopy (SEM) and selective extraction was completed to compare two environmental conditions (oxic and anoxic) under biologically active and abiotic systems (achieved by gamma irradiation). Changes in microbial community structure were monitored using 16s rDNA amplification and next-generation sequencing. The results indicate that microbes in an oxic environment increase the formation of oxyhydroxides and acidic conditions increase metal mobility. In an oxic and circumneutral environment, the AMD sludge may be repurposed to act as an oxygen barrier for mine tailings or soil amendment. Anoxic conditions would likely promote the biomineralization of sulfide minerals in the AMD sludge by sulfate reducing bacteria (SRB), which were abundant in the system. The anoxic conditions reduced the risk of trace metals (Zn) associated with oxides, but increased Fe associated with organic material. In summary, fewer risks are associated with anoxic burial but repurposing in an oxic condition may be appropriate under favorable conditions.

In oviparous species, maternal carotenoid provisioning can deliver diverse fitness benefits to offspring via increased survival, growth and immune function. Despite demonstrated advantages of carotenoids, large intra- and interspecific variation in carotenoid utilization exists, suggesting trade-offs associated with carotenoids. In Chinook salmon (Oncorhynchus tshawytscha), extreme variation in carotenoid utilization delineates two colour morphs (red and white) that differ genetically in their ability to deposit carotenoids into tissues. Here, we take advantage of this natural variation to examine how large differences in maternal carotenoid provisioning influence offspring fitness. Using a full factorial breeding design crossing morphs and common-garden rearing, we measured differences in a suite of fitness-related traits, including survival, growth, viral susceptibility and host response, in offspring of red (carotenoid-rich eggs) and white (carotenoid-poor eggs) females. Eggs of red females had significantly higher carotenoid content than those of white females (6× more); however, this did not translate into measurable differences in offspring fitness. Given that white Chinook salmon may have evolved to counteract their maternal carotenoid deficiency, we also examined the relationship between egg carotenoid content and offspring fitness within each morph separately. Egg carotenoids only had a positive effect within the red morph on survival to eyed-egg (earliest measured trait), but not within the white morph. Although previous work shows that white females benefit from reduced egg predation, our study also supports a hypothesis that white Chinook salmon have evolved additional mechanisms to improve egg survival despite low carotenoids, providing novel insight into evolutionary mechanisms that maintain this stable polymorphism.

To determine whether early rearing environment and parental breeding strategy affect the social behaviour and the endocrine response to stressors in juvenile Chinook salmon (Oncorhynchus tshawytscha), offspring (1–2 g) from traditional hatchery breeding or parental mate choice breeding were reared in a hatchery setting or in seminatural channels. Once ∼30 g, 9-month-old hatchery and mate choice fish from both rearing environments were exposed to one of four treatments: (i) sampled, (ii) air-exposed (AE) for 60 s and sampled 1 h later, (iii) sampled after 5 days of continuous dyadic social interaction (SI), or (iv) AE and allowed to interact for 5 days (AE/SI). In the hatchery environment, while hatchery fish were dominant in 70% and 80% of the dyadic trials in the SI and AE/SI treatments, respectively, plasma cortisol, growth hormone, and insulin-like growth factor I levels did not differ between hatchery and mate choice fish. In contrast, when reared in a seminatural environment, mate choice fish were dominant in 70% of the dyadic trials in the SI and AE/SI treatments, and clear differences in plasma hormone levels emerged between hatchery and mate choice fish. Therefore, while we found no evidence that breeding strategy affects social status, familiarity with the early rearing environment (i.e., from emergence until 1–2 g) enhanced the competitive ability of juvenile Chinook salmon during dyadic interactions. Early rearing environment also affected the endocrine responses to stressors, and freshwater seminatural channel environments were associated with elevated hormonal responsiveness.

Understanding the spatial context of genetic variation for species at risk is important for effective management and long-term survival of the species. We use multilocus microsatellite data to investigate the population genetic structure of the spotted gar (Lepisosteus oculatus) across its northern range edge in Canada. We then compare these northern individuals with samples taken from the southern core of the species range. For the northern samples, significant genetic differentiation among groups of individuals forming two major genetically distinct populations, and as many as 7-9 smaller subpopulations, was recovered using hierarchical Bayesian assignment methods and non-equilibrial discriminant function analyses. Spatial genetic variation is present, particularly at higher hierarchical groupings; however, some population admixture at sites is evident and is indicative of dispersal and gene flow among some locations or shared ancestry. Gene flow estimates among populations and subpopulations is very low, ranging from essentially complete isolation to as high as 5 %-suggesting that mechanisms in addition to geographic isolation are operating to create genetic structure. In Lake Erie, the physical isolation of Point Pelee appears to confer distinct genetic differentiation for those populations and provide a source of genetic variation for Lake Erie proper when breaches to the barrier beach occur. Results indicate that the northern edge populations are distinct from southern populations and should be conserved to maintain the overall genetic diversity of this species. Additionally, the asymmetrical genetic connectivity among the Point Pelee and Rondeau Bay sites highlights the sensitivity of Point Pelee to environmental perturbation and habitat degradation.

The gut microbial community in vertebrates plays a role in nutrient digestion and absorption, development of intestine and immune systems, resistance to infection, regulation of bone mass and even host behavior and can thus impact host fitness. Atlantic salmon (Salmo salar) reintroduction efforts into Lake Ontario, Canada, have been unsuccessful, likely due to competition with non-native salmonids. In this study, we explored interspecific competition effects on the gut microbiota of two Atlantic salmon populations (LaHave and Sebago) resulting from four non-native salmonids. After 10 months of rearing in semi-natural stream tanks under six interspecific competition treatments, we characterized the gut microbiota of 178 Atlantic salmon by parallel sequencing the 16S rRNA gene. We found 3978 bacterial OTUs across all samples. Microbiota alpha diversity and abundance of 27 OTUs significantly differed between the two populations. Interspecific competition reduced relative abundance of potential beneficial bacteria (six genera of lactic acid bacteria) as well as 13 OTUs, but only in the LaHave population, indicating population-specific competition effects. The pattern of gut microbiota response to interspecific competition may reflect local adaptation of the host-microbiota interactions and can be used to select candidate populations for improved species reintroduction success.

© 2017, Springer International Publishing AG Switzerland. Despite a well-developed theoretical basis for the role of genetic diversity in the colonization process, contemporary investigations of genetic diversity in biological invasions have downplayed its importance. Observed reductions in genetic diversity have been argued to have a limited effect on the success of establishment and impact based on empirical studies; however, those studies rarely include assessment of failed or comparatively less-successful biological invasions. We address this gap by comparing genetic diversity at microsatellite loci for taxonomically and geographically paired aquatic invasive species. Our four species pairs contain one highly successful and one less-successful invasive species (Gobies: Neogobius melanostomus, Proterorhinus semilunaris; waterfleas: Bythotrephes longimanus, Cercopagis pengoi; oysters: Crassostrea gigas, Crassostrea virginica; tunicates: Bortylloides violaceous, Botryllus schlosseri). We genotyped 2717 individuals across all species from multiple locations in multiple years and explicitly test whether genetic diversity is lower for less-successful biological invaders within each species pair. We demonstrate that, for gobies and tunicates, reduced allelic diversity is associated with lower success of invasion. We also found that less-successful invasive species tend to have greater divergence among populations. This suggests that intraspecific hybridization may be acting to convert among-population variation to within-population variation for highly successful invasive species and buffering any loss of diversity. While our findings highlight the species-specific nature of the effects of genetic diversity on invasion success, they do support the use of genetic diversity information in the management of current species invasions and in the risk assessment of potential future invaders.

Hydrogen (H-2) production using mixed anaerobic cultures often suffers severe yield reduction due to the syntrophic association between H-2 consumers (methanogens and homoacetogens) and H-2 producers (acidogens). The objective of this study was to uncouple the syntrophic association between H-2 producers and consumers by optimizing conditions for minimum H-2 consumption using a Box-Behnken design approach. The factors investigated in this study include temperature, pH and linoleic acid (LA) concentration. A quadratic response surface model was developed to predict the H-2 consumed by mixed anaerobic cultures and the optimum conditions for minimum H-2 consumption were 38 degrees C, pH 5.5 and 2 g L-1 LA. Methanogenesis was inhibited in cultures fed 2 g L-1 LA and maintained at pH 6.0 and 53 degrees C. In comparison, both methanogenesis and homoacetogenesis were inhibited in cultures fed 1-2 g L-1 LA and maintained at a pH of 4.5 (Fig. 2B and 2E and Table 2 Expt. # 1, 2 and 11). Microbial diversity analysis revealed that LA fed cultures was dominated by spore forming Clostridium sp. in addition to Syntrophus aciditrophus. In comparison, control cultures were dominated by Eubacterium sp., Methanocalculus halotolerans and Methanococcoides alaskense. This study described an approach for regulating H-2 consumption in mixed cultures by optimizing process and environmental factors. Understanding the effects of these individual factors and their interaction is important in the full-scale operation of H-2 production facilities. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

In this study, hydrogen (H 2 ) production from the fermentation of steam exploded corn stalk (CS) liquor was statistically optimized using a fractional factorial design approach. The factors under consideration included temperature, pH and hydraulic retention time (HRT). Under optimal conditions at 53 °C, a pH at 4.5 and a 9.5 h HRT, the observed maximum H 2 yield of 98 ± 2 mL g −1 TVS together with negligible CH 4 were similar to the model predicted responses. A flux analysis revealed negligible homoacetogenic activity in cultures at 53 °C and low pH (≤5.5). Both homoacetogenic (R17) and methanogenic (R28 and R29) fluxes accounted for more than 68–90% of H 2 consumption in cultures at low temperatures. The low H 2 yields observed in cultures maintained at 21 °C and 37 °C was associated with high lactate and solvent levels. High H 2 yields in cultures at 53 °C were associated with a higher abundance of Clostrdium sp. and CH 4 production at low temperatures was due to the presence of hydrogenotrophic methanogens ( Methanothermobacter marburgensis and Methanobrevibacter ruminatum ) and aceticlastic methanogens ( Methanosaeta sp. and Methanosarcina sp.). The results obtained from this study (within the factor ranges investigated) indicated that steam exploded CS liquor could be a potential substrate for H 2 production using mixed microbial cultures.

Salmon farming is one of Canada's fastest growing industries and contributes to Canada's economy as well as creating jobs in rural areas; however, the industry is challenged by the need to balance production economics against environmental impacts. While Atlantic salmon ( Salmo salar ) are the most commonly farmed species on the west coast of Canada, Chinook salmon ( Oncorhynchus tshawytscha ) are a valuable alternative, as they fill a niche market and generate reduced environmental concerns because they are a native species. However, Chinook salmon have not been systematically domesticated, and their performance remains highly variable. Here we report on the results of a research program designed to develop a performance-enhanced hybrid Chinook salmon stock. Growth and survival were estimated for seven domestic-wild hybrid Chinook salmon crosses at various freshwater stages and during 15 months of saltwater rearing at a British Columbia Chinook salmon farm and compared with domestic-domestic crosses (control). The project included 8640 individually (PIT) tagged offspring from the domestic stock and seven domestic-wild hybrid stocks originating from the Lower Fraser Valley, Lower Mainland Vancouver, and Vancouver Island, British Columbia, Canada. Within each stock, milt from 10 sires was used to fertilize eggs pooled from 15 highly inbred domestic females to produce 80 half-sib families. Our breeding design allows the partitioning of stock and sire effects, and minimises maternal genetic and maternal environment effects. Replicates of all families were reared under common environmental conditions in both fresh- and salt water and monitored for body size and survival. There was significant variation in survival, body size, and saltwater biomass among the Chinook salmon hybrid stocks. The performance of some of the hybrid crosses exceeded that of the fully domesticated stock, although the pattern of performance varied with rearing stage. Overall, two hybrid stocks consistently outperformed the domestic stock in terms of survival, growth, and biomass estimates. We systematically assess production performance across a wide range of wild-domestic hybrid crosses in a Pacific salmon species, and our results highlight opportunities to improve the production performance of Chinook salmon culture.

The impact of different chemical microbial stressors (2-bromoethanesulfonate (BES), furfural, fish oil, lauric acid (LUA) and linoleic acid (LA)) on the inhibition of mesophilic hydrogen (H-2) consumption was examined in this study. Hydrogen consumption half-life values were used to compare the extent of inhibition by the different microbial stressing agents. A statistical analysis of the percent H-2 consumed using Tukey's analysis revealed the following trend: Control > fish oil = linoleic acid (LA (C18:2)) = furfural > BES > lauric acid (LUA (C12:0). The terminal restriction fragment length polymorphism (T-RLFP) results indicated that aceticlastic methanogens (Methanosaeta sp., Methanosarcina sp.) and hydrogenotrophic methanogens (Methanococcus sp.) were inhibited by the different chemical stressing agents. Cultures fed LUA and LA had a high abundance of Clostridium sp., Clostridium propionicum and Propionibacterium acnes. In comparison, BES and furfural fed cultures contained large fractions of Clostridium sp., Eubacteria sp. and Bacteroides sp. while in the fish oil fed cultures, the dominant organism detected was Eubacteria sp. This study indicated that H-2 consumption was affected by the chemical stressing agent concentration. Copyright (C) 2013, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

In this study, controlling an anaerobic microbial community to increase the hydrogen (H-2) yield during the degradation of lignocelluosic sugars was accomplished by adding linoleic acid (LA) at low pH and reducing the hydraulic retention time (HRT) of an anaerobic sequencing batch reactor (ASBR). At pH 5.5 and a 1.7 d HRT, the maximum H2 yield for LA treated cultures fed glucose or xylose reached 2.89 +/- 0.18 mol mol(-1) and 1.94 +/- 0.17 mol mol(-1), respectively. The major soluble metabolites at pH 5.5 with a 1.7 day HRT differed between the control and LA treated cultures. A metabolic shift toward H-2 production resulted in increased hydrogenase activity in both the xylose (13%) and glucose (34%) fed LA treated cultures relative to the controls. In addition, the Clostridia population and the H-2 yield were elevated in cultures treated with LA. A flux balance analysis for the LA treated cultures showed a reduction in homoacetogenic activity which was associated with reducing the Bacteriodes levels from 12% to 5% in the glucose fed cultures and 16% to 10% in the xylose fed cultures. Strategies for controlling the homoacetogens and optimal hydrogen production from glucose and xylose are proposed. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Post-copulatory processes, including sperm competition and cryptic female choice (CFC), can play important roles in the maintenance of polymorphisms. In Chinook salmon (Oncorhynchus tshawytscha), color morphs (red and white) exist due to genetic polymorphisms affecting carotenoid deposition in flesh, skin, and gametes. We investigated the role of post-spawning sexual selection in maintaining the polymorphism in a mixed population. First, we compared sperm velocity differences in water between morphs. Next, we measured color-based CFC via 2 methods: 1) sperm velocity in ovarian fluid and 2) in vitro competitive fertilization using paired red and white males. We found that red males had marginally faster sperm relative to white males in water, suggesting that carotenoid storage may affect sperm performance. However, ovarian fluid of red and white females influenced sperm velocity of red and white males differently, indicative of color-based CFC on sperm velocity. Furthermore, we found evidence of color-based CFC on paternity success during in vitro competitive fertilizations; however, sperm velocity in ovarian fluid did not predict results found under in vitro fertilization. Instead, in our study, sperm velocity in water was a significant predictor of fertilization success. When we accounted for this difference in sperm velocity (in water) between paired males, we partitioned the amount of variation in fertilization success that was attributed to individual level CFC (male pair × female) and male competitiveness (male pair) as 43% and 16%, respectively. In conclusion, post-spawning sexual selection processes represent important mechanisms contributing to the maintenance of the color polymorphism in nature.

Acid mine drainage (AMD) impacted waters are a worldwide concern for the mining industry and countries dealing with this issue; both active and passive technologies are employed for the treatment of such waters. Mussel shell bioreactors (MSB) represent a passive technology that utilizes waste from the shellfish industry as a novel substrate. The aim of this study is to provide insight into the biogeochemical dynamics of a novel full scale MSB for AMD treatment. A combination of water quality data, targeted geochemical extractions, and metagenomic analyses were used to evaluate MSB performance. The MSB raised the effluent pH from 3.4 to 8.3 while removing up to ∼99% of the dissolved Al, and Fe and >90% Ni, Tl, and Zn. A geochemical gradient was observed progressing from oxidized to reduced conditions with depth. The redox conditions helped define the microbial consortium that consists of a specialized niche of organisms that influence elemental cycling (i.e. complex Fe and S cycling). MSB technology represents an economic and effective means of full scale, passive AMD treatment that is an attractive alternative for developing economies due to its low cost and ease of implementation.

The effects of lauric (LUA), myristic (MA), palmitic (PA), and a mixture of myristic:palmitic (MA:PA) acids on hydrogen (H-2) production from glucose degradation using anaerobic mixed cultures were assessed at 37 degrees C with an initial pH set at 5.0 and 7.131 mM of each acid. The maximum H-2 yield (2.53 +/- 0.18 mol mol(-1) glucose) was observed in cultures treated with PA. A principal component analysis (PCA) of the by-products and the microbial population data sets detected similarities between the controls and PA treated cultures; however, differences were observed between the controls and PA treated cultures in comparison to the MA and LUA treated cultures. The flux balance analysis (FBA) showed that PA decreased the quantity of H-2 consumed via homoacetogenesis compared to the other LCFAs. The control culture was dominated by Thermoanaerovibrio acidaminovorans (60%), Geobacillus sp. and Eubacterium sp. (28%), while Clostridium sp. was less than 1%. Treatment with PA, MA, MA:PA, or LUA increased the H-2 producers (Clostridium sp. and Bacillus sp.) population by approximately 48, 67, 86, and 86%, respectively. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Understanding pre- and postcopulatory mechanisms of sexual selection (male-male competition and female choice) can provide insight into the evolution of male ornamentation. In this study, we use an integrative approach to study sexual selection by incorporating measures of both mechanisms using the redside dace, Clinostomus elongatus, a freshwater, externally fertilizing fish found in streams of eastern North America. We measured the success of individual male redside dace in both pre- and postspawning sexual selection and related the success of males to a range of traits, including spectral properties and the size of their red spawning coloration, body size metrics and sperm quality. We found significant sexual dimorphism in the relative amount and spectral properties (saturation and brightness) of the red spawning coloration, with males being more ornamented than females. Using dichotomous mate choice trials, we found that females did not favour males with relatively larger red spawning coloration area and more saturated or brighter red spawning coloration. Males with relatively more red spawning area would be favoured in male-male postspawning sperm competition because they possess sperm with higher velocity, and sperm velocity was determined to be the key predictor of sperm competition success as assessed by paternity analyses related to in vitro sperm competition trials. These results suggest that prespawning selection via female choice is not driving the evolution of red spawning coloration and that postspawning selection via male-male competition is primarily determined by sperm velocity, which was correlated with the relative amount of red spawning coloration. (C) 2012 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

A knowledge of fine-scale population genetic structure and patterns of dispersal is an essential component of any action to conserve genetic diversity and maintain population viability. We genotyped 417 juvenile steelhead Oncorhynchus mykiss from the main stem and tributaries of the Bulkley-Morice River, British Columbia, at 10 microsatellite loci to assess fine-scale population structure and the patterns and magnitude of juvenile dispersal and mixing. We detected significant genetic structuring among juvenile steelhead from seven tributaries of the Bulkley-Morice River (pairwise F-ST: 0.008-0.156) and found significant isolation by distance among the tributary populations (R-2 = 0.198, P = 0.038). These results reflect the homing behavior of spawning adults as well as the temporal stability of those populations. Genotype assignment of tributary-caught juveniles showed that rates of juvenile dispersal varied among tributaries. The assignment of juveniles sampled from the main stem of the river to source tributary populations suggested that long-distance movement in juvenile steelhead is common and that juveniles are well mixed in the main stem. Dispersal and fine-scale genetic structure in pristine steelhead populations are more complex than previously thought. Therefore, actions to conserve Bulkley-Morice River steelhead must strive to maintain the genetic diversity of tributary populations.

One adaptive mechanism aquatic populations use to facilitate tolerance to environmental contaminants is acclimation. Polychlorinated biphenyls (PCBs) are a globally ubiquitous class of persistent organic contaminants that have been linked to reproductive impairments in fish. The authors used female brown bullhead (Ameiurus nebulosus) to test whether acclimation of reproductive life-history traits occurs in response to changes in sum PCB exposure. They compared egg diameter, gonadosomatic index (GSI), and fecundity of fish directly caught from wild populations exposed to a range of contaminant concentrations (acute), to those collected from the same populations a year before, which were placed in a clean environment to clear their contaminants throughout that year (cleared). Sum PCB concentrations were also determined for each individual. Brown bullhead from acute treatments had significantly greater sum PCB concentrations compared with cleared treatments. Egg diameter and GSI metrics were greater in cleared treatments compared with acute treatments (by 6 and 14%, respectively). Treatment effect (i.e., acute or cleared), as opposed to where the fish were collected from, accounts for 72 to 89% of the variation in the reproductive life-history trait variables. No difference in fecundity was found between acute and cleared treatments. The authors found support that acclimation of reproductive life-history traits occurs tochanges in sum PCB concentration. To their knowledge, the present study is thefirst experimental test of acclimation responses of female life-history traits to contaminants in wild populations. Environ. Toxicol. Chem. 2012;31:863-869. # 2012 SETAC Keywords—Acclimation Life-history traits Polychlorinated biphenyls Wild population Adaptation

The persistence and resilience of marine populations in the face of disturbances is directly affected by connectivity among populations. Thus, understanding the magnitude and pattern of connections among populations and the temporal variation in these patterns is critical for the effective management and conservation of marine species. Despite recent advances in our understanding of marine connectivity, few empirical studies have directly measured the magnitude or pattern of connections among populations of marine fishes, and none have explicitly investigated temporal variation in demographic connectivity. We use genetic assignment tests to track the dispersal of 456 individual larval fishes to quantify the extent of connectivity, dispersal, self-recruitment and local retention within and among seven populations of a coral reef fish (Stegastes partitus) over a three-year period. We found that some larvae do disperse long distances (similar to 200 km); however, self-recruitment was a regular phenomenon. Importantly, we found that dispersal distances, self-recruitment, local retention and the pattern of connectivity varied significantly among years. Our data highlight the unpredictable nature of connectivity, and underscore the need for more, temporally replicated, empirical measures of connectivity to inform management decisions.

Spatially restricted endemic species are of special conservation concern as their narrow distributions render them particularly vulnerable to extinction through habitat loss. However, estimates of connectivity among populations can provide a basis for targeted conservation action. Here we quantify population genetic structure and connectivity for two endemic Sailfin silverside species within and among two lakes from the Malili Lakes, Indonesia. For both species, a greater proportion of genetic variance was found among sites within a lake than between lakes, indicative of riverine gene flow and cryptic genetic structure within the lakes. Bayesian genotype clustering revealed substantial population genetic structure within and among lakes, but also showed evidence of dispersal between lakes. These results are timely given the growing anthropogenic stressors in the Malili Lakes watershed, including mining and forestry operations.

Populations experiencing sudden environmental change must be capable of rapidly evolving to survive. Here we explore changes in gene transcription as a mechanism for rapid adaptation at four osmoregulatory genes (CFTR I, NaK ATPase1 alpha a, NaK ATPase1 alpha b and GHRII) in anadromous steelhead trout versus a derived land-locked population after 14 generations. Transcription was measured before and after a 24-h saltwater challenge in pure and reciprocal hybrid offspring of fish from both populations reared in a common environment for two generations. Significant differences between the landlocked and migratory populations were observed, particularly in fresh water at the NaK ATPase1 alpha a and GHRII genes, indicating rapid evolutionary change, possibly associated with reduced energy expenditure in the landlocked lake system. Phenotypic divergence analysis (Q (ST)) shows that the observed transcriptional differences deviate from neutral expectations. Some reciprocal crosses exhibited anomalous transcription consistent with sex-linked epistatic or genetic imprinting effects. Our results highlight unpredictable phenotypic outcomes of hybridization among locally adapted populations and the need to exercise caution when interbreeding populations for conservation purposes.

While predation is widely accepted as a major cause of mortality for fish larvae, its extent is largely unknown because few studies have been able to identify larvae in the stomach contents of predatory fish. Rapid digestion rates probably explain why fish larvae are rarely found in stomach contents, yet quantification of digestion rates of fish larvae is generally lacking, especially in freshwater systems. Using a series of laboratory experiments, we quantified the effects of temperature and larval fish (prey) size on digestion rate. We also evaluated whether species type (both predator and prey) influences digestion rate and described the morphological breakdown of fish larvae during digestion. Bluegills Lepomis macrochirus and yellow perch Perca flavescens were force-fed the larvae of guppies Poecilia spp., rainbow trout Oncorhynchus mykiss, and yellow perch at a range of temperatures (7-22 degrees C), and digestion rates were measured using prey mass before and after digestion (i.e., proportional loss of prey mass after ingestion). As expected, digestion rates increased with water temperature and decreased with prey body mass but were unaffected by species of predator. A confounding effect of prey type (fresh versus frozen) prevented a thorough evaluation of prey species, although yellow perch and rainbow trout (both previously flash-frozen) were digested at similar rates. The complete breakdown of larvae in predator stomachs and the loss of morphological characters needed to identify larvae occurred rapidly, confirming the challenges of evaluating predation mortality based on stomach contents of field-collected predators. Ultimately, our findings can be used to help researchers quantify the likelihood of detecting larval fish in the stomachs of field-caught predators when using conventional stomach content analyses.

Understanding the genetic architecture of phenotypic plasticity is required to assess how populations might respond to heterogeneous or changing environments. Although several studies have examined population-level patterns in environmental heterogeneity and plasticity, few studies have examined individual-level variation in plasticity. Here, we use the North Carolina II breeding design and translocation experiments between two populations of Chinook salmon to detail the genetic architecture and plasticity of offspring survival and growth. We followed the survival of 50,800 offspring through the larval stage and used parentage analysis to examine survival and growth through freshwater rearing. In one population, we found that additive genetic, nonadditive genetic and maternal effects explained 25%, 34% and 55% of the variance in larvae survival, respectively. In the second population, these effects explained 0%, 24% and 61% of the variance in larvae survival. In contrast, fry survival was regulated primarily by additive genetic effects, which indicates a shift from maternal to genetic effects as development proceeds. Fry growth also showed strong additive genetic effects. Translocations between populations revealed that offspring survival and growth varied between environments, the degree of which differed among families. These results indicate genetic differences among individuals in their degree of plasticity and consequently their ability to respond to environmental variation.

Coupled bio-physical models of larval dispersal predict that the Costa Rica–Panama (CR–PAN) reefs should constitute a demographically isolated region in the western Caribbean. We tested the hypothesis that CR–PAN coral reef fish populations would be isolated from Mesoamerican Barrier Reef System (MBRS) populations. To test that, we assessed population genetic structure in bicolor damselfish (Stegastes partitus) from both regions. Adult fish were genotyped from five reefs in CR–PAN and from four reefs along the MBRS at 12 microsatellite loci. Between-region F ST (F ST = 0.0030, P

The major histocompatibility complex (MHC) is thought to be under strong selection pressure because of its integral role in pathogen recognition. Consequently, patterns of MHC genetic variation should reflect selection pressures across the landscape. We examined genetic variation and population genetic structure at the MHC class I-A1 and class II-B1 exons in five Chinook salmon (Oncorhynchus tshawytscha) populations from two geographic regions in British Columbia, Canada. We then compared estimates of population structure at the MHC genes with neutral estimates based on microsatellites to examine the potential for local adaptation at the MHC. Chinook salmon are in decline throughout much of their native range and understanding the degree of local adaptation exhibited by the MHC may be important in conservation planning. Comparisons among populations yielded higher G(ST)' estimates for the MHC class I than expected under neutrality based on the microsatellites. In contrast, the MHC class II tended to exhibit lower G(ST)' values than did the microsatellites. These results suggest that across populations unique selection pressures are driving allele frequency differences at the MHC class I but that the MHC class II may be the subject of homogenizing selection. Rates of nonsynonymous versus synonymous substitutions found in codons associated within the MHC class I and II peptide-binding regions provided strong evidence of positive selection. Together, these results support the hypothesis that selection is influencing genetic variation at the MHC, but suggest that selection pressures may vary at the two classes of loci both at the sequence and population levels. Heredity (2010) 104, 449-459; doi:10.1038/hdy.2009.121; published online 23 September 2009

Understanding how organisms function at the level of gene expression is becoming increasingly important for both ecological and evolutionary studies. It is evident that the diversity and complexity of organisms are not dependent solely on their number of genes, but also the variability in gene expression and gene interactions. Furthermore, slight differences in transcription control can fundamentally affect the fitness of the organism in a variable environment or during development. In this study, triploid and diploid Chinook salmon (Oncorhynchus tshawytscha) were used to examine the effects of polyploidy on specific and genome-wide gene expression response using quantitative real-time PCR (qRT-PCR) and microarray technology after an immune challenge with the pathogen Vibrio anguillarum. Although triploid and diploid fish had significant differences in mortality, qRT-PCR revealed no differences in cytokine gene expression response (interleukin-8, interleukin-1, interleukin-8 receptor and tumor necrosis factor), whereas differences were observed in constitutively expressed genes, (immunoglobulin (Ig) M, major histocompatibility complex (MHC) -II and beta-actin) upon live Vibrio anguillarum exposure. Genome-wide microarray analysis revealed that, overall, triploid gene expression is similar to diploids, consistent with their similar phenotypes. This pattern, however, can subtly be altered under stress (for example, handling, V. anguillarum challenge) as we have observed at some housekeeping genes. Our results are the first report of dosage effect on gene transcription in a vertebrate, and they support the observation that diploid and triploid salmon are generally phenotypically indistinguishable, except under stress, when triploids show reduced performance.

Temporal instability in population genetic structure has significant implications for management and conservation decisions. Here, we evaluate temporal stability in five populations of Chinook salmon ( Oncorhynchus tshawytscha ) from the Upper Fraser River, British Columbia, Canada, based on estimates of temporal allelic variance and effective population size (Ne) at 11 microsatellite loci. Significant temporal variation in allele frequencies was found within individual populations sampled at 5- to 12-year intervals. Removal of migrant fish or correcting for migrants resulted in higher allelic variance or reduced Ne. Populations with higher levels of temporally consistent gene flow show reduced temporal allelic variance (i.e., reduced genetic drift) and higher Ne. This study is an important empirical example of the effect of gene flow on genetic stability and Ne. In salmonids, low straying levels may have evolved to favor local adaptation; however, we show that even such low levels of gene flow can elevate effective population sizes and preserve genetic variability. This study highlights the importance of considering gene flow acting to temporally stabilize populations, particularly small ones, and should migration be interrupted, Nelevels may decline with no obvious change in census population sizes.

The genetic structure of a stream-dwelling fish, the Greenside Darter, Etheostoma blennioides, is described from variation at nine microsatellite loci in 26 populations in the northern-most portions of the species’ range in southern Ontario, Canada in two sampling years. We found relatively high levels of genetic structure at the among- and within-watershed scales, with some watersheds and populations exhibiting very high divergence. The Ausable River populations were especially isolated, containing distinct populations of potential conservation concern. Temporal replicates at selected localities showed evidence of substantial temporal variation in genetic structure, perhaps resulting from movement among sites. We found strong evidence for an effect of river barriers (dams and weirs) on dispersal measured by genotype assignment techniques. However, we found no bias in upstream vs downstream dispersal. Significant isolation-by-distance relationships in both sample years indicate that river distance is an important factor regulating gene flow in these watersheds. The Canadian Greenside Darter populations are expanding their range into more northerly watersheds, but also show substantial within-watershed genetic structure despite substantial dispersal.

The Mytilus species complex consists of three closely related mussel species: Mytilus trossulus, Mytilus edulis, and Mytilus galloprovincialis, which are found globally in temperate intertidal waters. Introduction of one or more of these species have occurred world-wide via shipping and aquaculture. Stable hybrid zones have developed in areas where these species have come into contact, making the invasion process complex. On the east coast of Vancouver Island (VI), British Columbia (BC), Canada, the native (M. trossulus) and introduced species (M. edulis and M. galloprovincialis), as well as their hybrid offspring, occur sympatrically. This study used a common environment experiment to quantify growth and survival differences among native, introduced, and introgressed mussels on VI. Mussels were collected from an area of known hybridization and reared in cages from May to August 2006. The cages were deployed at a local site as well as a remote site (approximately 150 km apart), and the mussels were genotyped at two species-specific loci. Growth and survival, as fitness measures, were monitored: native, introduced, and introgressed individuals were compared between and within sites to determine whether growth and survival were independent of site and genotype. Overall, mussels reared at Quadra Island performed better than locally-reared mussels at Ladysmith. Specifically, introgressed mussels reared at Quadra Island performed better than all genotypes reared at Ladysmith, as well as better than native mussels reared at Quadra Island. Differences in survival and growth among the native, introduced and introgressed mussels may serve to explain the complex hybridization patterns and dynamics characteristic of the VI introgression zone.

In this study, the long term effect of different microbial stressing agents on hydrogen (H-2) production was examined using repeated batch cultivations. When compared to thermophilic cultures, higher H-2 yields were observed in mesophilic cultures receiving repeated glucose addition. Methane production was only observed in control mesophilic cultures receiving repeated 5 glucose additions. Lower hydrogenase evolution specific activity was observed in thermophilic cultures (except alkali-treated cultures) compared to mesophilic cultures. For both mesophilic and thermophilic cultures, the hydrogenase uptake specific activity of the untreated control cultures exhibited higher levels of activity than the pre-treated cultures. A flux balance analysis (FBA) showed negligible homoacetogenic flux in mesophilic cultures pretreated with linoleic acid (IA) and loading shock (LS) after successive batch cultivations. The homoacetogenic flux accounted for approximately 98% loss in the H-2 yield in untreated mesophilic control cultures. Both homoacetogens (Eubacterium sp.) and aceticlastic methanogens (Methanosaeta sp. and Methanosarcina sp.) were abundant in the control cultures. In comparison, Clostridium sp. were dominant in mesophilic stress treated cultures whereas under thermophilic conditions, the dominant microorganisms were Flavobacterium sp., Bacillus sp., Thermoanaerobacter sp., Bacteroides sp., Lactobacillus sp. and Thioalkalivibrio sp. (C) 2015 Elsevier Ltd. All rights reserved.

The multiple discrete hybrid zones that characterize Mytilus blue mussels allow a novel, non-manipulative, examination of the selective pressures that create and maintain species. If endogenous genetic incompatibility is solely responsible for post-zygotic isolation, then individuals of a specified hybrid genotype are expected to show similar average fitness across environments. However, if hybrid fitness differs across environments, then exogenous selection is implicated, either via ecological selection or environment-specific expression of intrinsic genetic incompatibilities. Correspondence between developmental instability of hybrids and heterozygote deficiency, estimated in two M. trossulus×M. galloprovincialis hybrid zones on the coast of North America, indicates that environment-dependent selection against hybrids may contribute to reproductive isolation among Pacific Mytilus species.

© 2015, Springer International Publishing Switzerland. The geographic range of an invasive species is a key determinant of relative impact in the invaded region. Comparison of invasive species that are widespread or rare in invaded ranges can highlight mechanistic traits that determine the risk of impact from invasion. Round Goby (Neogobius melanostomus) is more geographically widespread and abundant than Tubenose Goby (Proterorhinus semilunaris) across invaded ranges of the Laurentian Great Lakes. We used stable isotopes of carbon (δ13C) and nitrogen (δ15N) in liver and muscle to contrast the isotopic niche breadth and niche plasticity of Round Goby and Tubenose Goby near the inflow and outflow of Lake St. Clair and in western Lake Superior. At all sites, Round Goby and Tubenose Goby that matched in size (21–53 mm standard length) had distinct isotopic niches with no overlap, driven by higher δ15N in Round Goby. The variation in isotopic niche, and the mean difference in δ13C and δ15N between muscle and liver, was greater for Round Goby, suggesting both greater seasonal shifts in diet and niche plasticity in this more widely established invader. Round Goby that were significantly larger than Tubenose Goby had broader isotopic niches and greater niche plasticity in the majority of cases and this was associated with isotopic niche overlap with smaller Round Goby and Tubenose Goby. Our findings suggest that a broad and plastic isotopic niche provides scope for wider establishment range in invasive fish species.

The objective of this study was to establish the impact of different steam exploded organic fractions in municipal solid waste (MSW) on electricity production using microbial fuel cells (MFCs). In particular, the influence of individual steam exploded liquefied waste components (food waste (FW), paper-cardboard waste (PCW) and garden waste (GW)) and their blends on chemical oxygen demand (COD) removal, columbic efficiency (CE) and microbial diversity was examined using a mixture design. Maximum power densities from 0.56 to 0.83 W m(-2) were observed for MFCs fed with different feedstocks. The maximum COD removed and minimum CE were observed for a GW feed. However, a reverse trend (minimum COD removed and maximum CE) was observed for the FW feed. A maximum COD removal (78%) accompanied with a maximum CE (24%) was observed for a combined feed of FW, PCW plus GW in a 1:1:1 ratio. Lactate, the major byproduct detected, was unutilized by the anodic biofilm community. The organic fraction of municipal solid waste (OFMSW) could serve as a potential feedstock for electricity generation in MFCs; however, elevated protein levels will lead to reduced COD removal. The microbial communities in cultures fed FW and PCW was highly diversified; however, the communities in cultures fed FW or a feed mixture containing high FW levels were similar and dominated by Bacteroidetes and β-proteobacteria.