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Human activity can put non-game fishes at higher risk of extinction because of inappropriate management action. Eastern sand darter (Ammocrypta pellucida), a small benthic fish classified as threatened across much of its northern range, inhabits increasingly fragmented sandy habitats and, as a non-game fish, may be easily overlooked in conservation efforts. In this study, the authors use genotype data from nine microsatellite loci and cytochrome oxidase I (COI) sequencing data across its northern native range to re-assess genetic structure and to characterize a newly discovered, geographically disjunct population. Previous microsatellite marker analyses had identified seven distinct population genetic clusters across the region sampled; the analysis of this study showed that the newly discovered population (West Lake, Ontario) exhibits a divergent structure. COI haplotype analysis suggests that a single haplotype recolonized the Great Lakes and surrounding water bodies after the Wisconsinan glacial period, and subsequent fluctuation in water levels and habitat fragmentation resulted in divergence of genetic clusters. Although the novel West Lake population has a common ancestral source with other populations in the broader region, its divergent genetic signature merits its consideration as a separate conservation unit. The analyses of this study highlight the potential conservation implications of the discovery of new populations, particularly those of at-risk species, even within a region that has been genetically well characterized.

Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in and among natural populations. Previous studies have identified differences in methylation among populations of organisms, although most to date have been in plants and model animal species. Here we obtained eyed eggs from eight populations of Chinook salmon (Oncorhynchus tshawytscha) and assayed DNA methylation at 23 genes involved in development, immune function, stress response, and metabolism using a gene‐targeted PCR‐based assay for next‐generation sequencing. Evidence for population differences in methylation was found at eight out of 23 gene loci after controlling for developmental timing in each individual. However, we found no correlation between freshwater environmental parameters and methylation variation among populations at those eight genes. A weak correlation was identified between pairwise DNA methylation dissimilarity among populations and pairwise F ST based on 15 microsatellite loci, indicating weak effects of genetic drift or geographic distance on methylation. The weak correlation was primarily driven by two genes, GTIIBS and Nkef. However, single‐gene Mantel tests comparing methylation and pairwise F ST were not significant after Bonferroni correction. Thus, population differences in DNA methylation are more likely related to unmeasured oceanic environmental conditions, local adaptation, and/or genetic drift. DNA methylation is an additional mechanism that contributes to among population variation, with potential influences on organism phenotype, adaptive potential, and population resilience., DNA methylation presents a novel evolutionary mechanism for differences among populations due to its ability to respond to environmental change and its transmission among generations. We show population‐level differences in Chinook salmon DNA methylation and attempt to relate these differences to freshwater environmental context and genetic drift.

Many coral reef fishes are fished, often resulting in detrimental genetic effects; however, reef fishes often show unpredictable patterns of genetic variation, which potentially mask the effects of fishing. Our goals were to characterize spatial and temporal genetic variation and determine the effects of fishing on an exploited reef fish, Plectropomus leopardus, Lacepède (the common coral trout). To determine population structure, we genotyped 417 Great Barrier Reef coral trout from four populations sampled in 2 years (1996 and 2004) at nine microsatellite loci. To test for exploitation effects, we additionally genotyped 869 individuals from a single cohort (ages 3–5) across eight different reefs, including fished and control populations. Genetic structure differed substantially in the two sampled years, with only 1 year exhibiting isolation by distance. Thus, genetic drift likely plays a role in shaping population genetic structure in this species. Although we found no loss of genetic diversity associated with exploitation, our relatedness patterns show that pulse fishing likely affects population genetics. Additionally, genetic structure in the cohort samples likely reflected spatial variation in recruitment contributing to genetic structure at the population level. Overall, we show that fishing does impact coral reef fishes, highlighting the importance of repeated widespread sampling to accurately characterize the genetic structure of reef fishes, as well as the power of analysing cohorts to avoid the impacts of recruitment‐related genetic swamping. The high temporal and spatial variability in genetic structure, combined with possible selection effects, will make conservation/management of reef fish species complex.

BackgroundWhile many studies have reported that the structure of the gut and skin microbiome is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (BCs) and assess the extent to which host habitat and phylogeny predict BC similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed BC composition using 16S metabarcoding and tested for community variation. ResultsWe found that the water BC was distinct from the fish microbiome BCs, although the skin BC more closely resembled the water BC. We also found that environmental (sample location), habitat, fish diet and host species factors shape and promote divergence or convergence of the fish BCs. Since host species significantly affected both gut and skin BC (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus BC dissimilarity. We found significant phylogenetic effects on BC dissimilarity, consistent with phylosymbiosis for both the fish skin and gut BCs, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes. ConclusionsAnalyzing the gut content and skin mucus BCs across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host.

Among tropical organisms, heightened habitat specialization, limited natal dispersal, and strong philopatry suggest that many species may experience reduced rates of gene flow. Diverse forms of barriers, including geographic, ecological, and behavioral barriers, further promote genetic divergence among tropical bird populations. Here, we extend our comprehension of gene flow in tropical birds by examining population genetic structure in a widespread insectivorous songbird of the Neotropics, the Rufous-and-white Wren (Thryophilus rufalbus). We explore the effects of geographic distance and habitat connectivity on genetic structure using 10 microsatellite loci, and nuclear and mitochondrial sequence data. We report high levels of genetic divergence and population structure with reduced contemporary gene flow between populations over a 500-km transect in Nicaragua and Costa Rica. Mitochondrial DNA and nuclear sequence data indicate that 2 distinct mtDNA genetic groups came into contact in northwestern Costa Rica; molecular dating suggests that the genetic patterns arose as a result of Pleistocene glaciations. Geographic distance and habitat connectivity predicted genetic structure but explained a relatively low proportion of the observed contemporary genetic variation. Patterns were similar for both males and females. Our research demonstrates the deep genetic divergence in tropical birds, and that genetic differentiation can occur over a relatively short distance. For tropical birds, strong limits to gene flow likely arise as a result of limited dispersal from natal populations.

Transcriptomics provides a mechanistic understanding of an organism’s response to environmental challenges such as increasing temperatures, which can provide key insights into the threats posed by thermal challenges associated with urbanization and climate change. Differential gene expression and alternative splicing are two elements of the transcriptomic stress response that may work in tandem, but relatively few studies have investigated these interactions in fishes of conservation concern. We studied the imperilled redside dace (Clinostomus elongatus) as thermal stress is hypothesised to be an important cause of population declines. We tested the hypothesis that gene expression-splicing interactions contribute to the thermal stress response. Wild fish exposed to acute thermal stress were compared with both handling controls and fish sampled directly from a river. Liver tissue was sampled to study the transcriptomic stress response. Thermally stressed fish showed a prominent transcriptional response (estimated with mRNA transcript abundance) related to transcription regulation and responses to unfolded proteins, and prominent alternatively spliced genes related to gene expression regulation and metabolism. One splicing factor, prpf38b, was upregulated in the thermally stressed group compared to the other treatments. This splicing factor may have a role in the Jun/AP-1 cellular stress response, a pathway with wide-ranging and context-dependent effects. Given large gene interaction networks and the context-dependent nature of transcriptional responses, our results highlight the importance of understanding interactions between gene expression and splicing for understanding transcriptomic responses to thermal stress. Our results also reveal transcriptional pathways that can inform conservation breeding, translocation, and reintroduction programs for redside dace and other imperilled species by identifying appropriate source populations.SUMMARY STATEMENTGene expression and alternative splicing interact in response to thermal stress in an imperilled fish, with implications for conservation and mechanisms of thermal tolerance in vertebrate ectotherms.

Although genetic techniques are moving toward collecting massive amounts of genome-wide data through genome-scans, microsatellite markers (µsats) still provide a simple and cost-effective method for key applications such as parentage analyses, pedigree tracking, assessing likelihoods of disease conditions and DNA fingerprinting, among others. Newer laboratory protocols using high throughput sequencing platforms can now generate µsat data more efficiently than ever before. Yet, there is a dearth of easy to use, interactive software reliably converting raw sequencing data into individual-based multi-locus µsat genotypes suitable for typical downstream analyses. We describe the development and application of NGS-µsat, an R-based software workflow capable of converting raw µsat sequence data produced using next-generation sequencing platforms into multi-locus genotypes. Because the algorithm identifies repeat motifs, it does not rely on identifying and removing extraneous sequence fragments from sequenced reads to score loci. Accordingly, the software scores ‘true’ µsat repeats and provides an accurate, and clean picture of locus information without the typical assessment ambiguity based on fragment lengths. In comparative analyses, results show that NGS-µsat leads to cleaner, more reliable genotypes that are more repeatable than those made by scoring the same data using other software based on fragment lengths. This increased reliability/reproducibility of generated data may expand the use of high throughput sequencing-based techniques to routine DNA profiling, DNA fingerprinting and parentage/pedigree analyses and revitalise the application of µsats more broadly.

Alternative reproductive tactics are widespread in fishes. In Pacific salmon, males either become a competitive hooknose, or a sneaker jack, which is undesirable in aquaculture when overabundant. Juveniles often experience accelerated growth prior to becoming jacks, potentially caused by increased competitiveness. We tested the behaviour of hatchery-reared Chinook salmon (Oncorhynchus tshawytscha) in fresh water and after 1 year in salt water. We also tested the effects of freshwater rearing density (100, 50, or 35 fish per 200 L), food ration (high or low), sire (jack or hooknose) for jacks, hooknoses, and females with and without confirmed jack siblings. Sisters of jacks were further identified to test whether females closely related to jacks also showed behavioural differences. Overall, jacks did not behave as predicted; rearing conditions were the strongest determinant of behaviour, and jack sisters behaved differently than jacks and other females. Our study underscores the complexities of jack behaviour, and of females closely related to jacks, at all development stages and supports the use of behavioural screenings to regulate jacking rates in hatcheries by identifying jack sisters.

Adult size, egg size, fecundity, and mass of gonads are affected by trade‐offs between reproductive investment and environmental conditions shaping the evolution of life history traits among populations for widely distributed species. Coho salmon Oncorhynchus kisutch have a large geographic distribution, and different environmental conditions are experienced by populations throughout their range. We examined the effect of environmental variables on female size, egg size, fecundity, and reproductive investment of populations of Coho Salmon from across British Columbia using an information theoretic approach. Female size increased with latitude and decreased with migration distance from the ocean to spawning locations. Egg size was lowest for intermediate intragravel temperature during incubation, decreased with migration distance, but increased in rivers below lakes. Fecundity increased with latitude, warmer temperature during the spawning period, and river size, but decreased in rivers below lakes compared with rivers with tributary sources. Relative gonad size increased with latitude and decreased with migration distance. Latitude of spawning grounds, migratory distance, and temperatures experienced by a population, but also hydrologic features—river size and headwater source—are influential in shaping patterns of reproductive investment, particularly egg size. Although, relative gonad size varied with latitude and migration distance, how gonadal mass was partitioned gives insight into the trade‐off between egg size and fecundity. The lack of an effect of latitude on egg size suggests that local optima for egg size related to intragravel temperature may drive the variation in fecundity observed among years., We examined the effect of environmental variables on female size, egg size, fecundity, and reproductive investment for populations of Coho Salmon from across British Columbia. Our work is novel because we combined location variables (latitude and migration distance) with environmental variables (water temperature, river size, headwater source, and years of hatchery supplementation). We found that latitude of spawning grounds, migratory distance, and temperatures experienced by a population, but also hydrologic features—river size and headwater source—are influential in shaping patterns of reproductive investment, particularly egg size.

Johansson ML, Lavigne SY, Ramcharan CW, Heath DD, MacIsaac HJ. Detecting a spreading non-indigenous species using multiple methodologies. Lake Reserv Manage. XX:XX–XX. Non-indigenous species (NIS) ...

Genetic architecture and phenotypic plasticity are important considerations when studying trait variation within and among populations. Since environmental change can induce shifts in the genetic architecture and plasticity of traits, it is important to consider both genetic and environmental sources of phenotypic variation. While there is overwhelming evidence for environmental effects on phenotype, the underlying mechanisms are less clear. Variation in DNA methylation is a potential mechanism mediating environmental effects on phenotype due to its sensitivity to environmental stimuli, transgenerational inheritance, and influences on transcription. To characterize the effect of environment on methylation, we created two 6 × 6 (North Carolina II) Chinook salmon breeding crosses and reared the offspring in two environments: uniform hatchery tanks and seminatural stream channels. We sampled the fish twice during development, at the alevin (larval) and fry (juvenile) stages. We measured DNA methylation at 13 genes using a PCR-based bisulfite sequencing protocol. The genetic architecture of DNA methylation differed between rearing environments, with greater additive and nonadditive genetic variance in hatchery fish and greater maternal effects in seminatural channel fish, though gene-specific variation was evident. We observed plasticity in methylation across all assayed genes, as well as gene-specific effects at two genes in alevin and six genes in fry, indicating developmental stage-specific effects of rearing environment on methylation. Characterizing genetic and environmental influences on methylation is critical for future studies on DNA methylation as a potential mechanism for acclimation and adaptation.

Background Aquatic invasive species (AIS) threaten ecosystems and native species. Methods To determine spatial distributions of at‐risk native taxa and AIS in two biologically diverse Laurentian Great Lakes tributaries, we extracted environmental DNA (eDNA) from water samples and used a universal PCR primer set targeting the CO1 gene for metabarcoding of selected taxa. We sampled 43 sites for eDNA in each of the Grand and Sydenham rivers in southwestern Ontario. Results We assigned sequences to 49 taxa at the species level and four mollusks to genus level. Detected AIS included two oligochaete worms (Branchiura sowerbyi, Potamothrix moldaviensis), a freshwater jellyfish (Craspedacusta sowerbyi), a calanoid copepod (Skistodiaptomus pallidus), and a bivalve dreissenid mussel (Dreissena rostriformis bugensis). All but D. r. bugensis were previously unreported in these tributaries. Detected native mollusks included one globally endangered species the rayed bean (Villosa fabalis), one provincially listed threatened species the maple leaf mussel (Quadrula quadrula), and several other at‐risk and unique mollusk species of special interest in Ontario, Canada, and the United States (e.g., Sphaerium fabale, Pyganodon grandis). At several sampling sites in each river, AIS eDNA overlapped with or was near to sites with detections of at‐risk native mollusks. Most AIS and some native taxa demonstrated clustered detection patterns within each river. However, in some cases, independent detections of individual species occurred at individual sites within each river that were relatively far apart. Our findings should be interpreted with some caution due to the limitations of the aquatic “universal” primer set and the availability of comprehensive reference sequence databases. Conclusion Results from eDNA metabarcoding in our study helped reveal invertebrate AIS and at‐risk species distributions and will help direct approaches for conserving biodiversity in each of these Great Lakes tributaries.

Analysis of food webs is important for defining functional components of ecosystems, but dietary data are often difficult to obtain and coarsely characterised. We compared three methods of rainbow trout (Oncorhynchus mykiss (Walbaum); Salmoniformes: Salmonidae) and prickly sculpin (Cottus asper Richardson; Scorpaeniformes: Cottidae) gut content analysis: traditional morphological taxonomy of prey items, genetic sequencing of individual prey items, and next-generation sequencing of homogenised gut contents. Prey analysis of invertebrates by morphological identification allowed order-level classifications and produced ecologically important count and mass data. Sequencing individual specimens provided greater taxonomic resolution, while next-generation sequencing of stomach contents revealed more prey diversity in the diets of both fish species as it was possible to detect prey that were degraded beyond visual recognition. Both fish species exhibited generalist feeding characteristics; however, terrestrial Insecta were a large diet component for rainbow trout. This study demonstrates an efficient approach for prey analysis using molecular techniques that complement traditional taxonomy.

Background Growth regulation is a complex process influenced by genetic and environmental factors. We examined differences between growth hormone (GH) transgenic (T) and non-transgenic (NT) coho salmon to elucidate whether the same loci were involved in controlling body size and gene expression phenotypes, and to assess whether physiological transformations occurring from GH transgenesis were under the influence of alternative pathways. The following genomic techniques were used to explore differences between size classes within and between transgenotypes (T vs. NT): RNA-Seq/Differentially Expressed Gene (DEG) analysis, quantitative PCR (qPCR) and OpenArray analysis, Genotyping-by-Sequencing, and Genome-Wide Association Study (GWAS). Results DEGs identified in comparisons between the large and small tails of the size distributions of T and NT salmon (NTLarge, NTSmall, TLarge and TSmall) spanned a broad range of biological processes, indicating wide-spread influence of the transgene on gene expression. Overexpression of growth hormone led to differences in regulatory loci between transgenotypes and size classes. Expression levels were significantly greater in T fish at 16 of 31 loci and in NT fish for 10 loci. Eleven genes exhibited different mRNA levels when the interaction of size and transgenotype was considered (IGF1, IGFBP1, GH, C3–4, FAS, FAD6, GLUT1, G6PASE1, GOGAT, MID1IP1). In the GWAS, 649 unique SNPs were significantly associated with at least one study trait, with most SNPs associated with one of the following traits: C3_4, ELA1, GLK, IGF1, IGFBP1, IGFII, or LEPTIN. Only 1 phenotype-associated SNP was found in common between T and NT fish, and there were no SNPs in common between transgenotypes when size was considered. Conclusions Multiple regulatory loci affecting gene expression were shared between fast-growing and slow-growing fish within T or NT groups, but no such regulatory loci were found to be shared between NT and T groups. These data reveal how GH overexpression affects the regulatory responses of the genome resulting in differences in growth, physiological pathways, and gene expression in T fish compared with the wild type. Understanding the complexity of regulatory gene interactions to generate phenotypes has importance in multiple fields ranging from applications in selective breeding to quantifying influences on evolutionary processes.

Understanding the diversity of bacteria and E.coli levels at beaches is important for managing health risks. This study compared temporal changes of the bacterial communities of Belle Isle Beach (Detroit, MI) and Sand Point Beach (Windsor, ONT), both located near the Lake St. Clair origin of the Detroit River. Water samples collected 4 days/week for 12 weeks in summer, were subjected to 16S rRNA analysis of amplicon sequencing and E. coli enumeration. Bacterial communities changed over time, as determined by cluster dendrogram analysis, exhibiting different communities in July and August than in June and different communities at the two beaches. After June, alpha diversity decreased and relative abundance of Enterobacter (Gammaproteobacteria) increased at Sand Point; whereas, Belle Isle maintained its alpha diversity and dominance by Betaproteobacteria and Actinobacteria. Contamination at both beaches is dominated by birds (23% to 50% of samples), while only ∼10% had evidence of human-associated bacteria. High E. coli at both beaches was often associated with precipitation. Nearshore sampling counts were higher than waist-deep sampling counts. Despite the dynamic changes in bacterial communities between the two beaches, this analysis based on 16S rRNA amplicon sequencing is able to provide information about bacterial types associated with high E. coli levels and to use bacterial sequences to more precisely determine sources and health relevance of contaminants.

A wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week. During this time, there was no detection of SARS-CoV-2 by reverse transcriptase quantitative PCR (RT-qPCR) in the residence hall wastewater stream. Aiming to obtain a sample more representative of the residence hall community, a decision was made to use passive samplers beginning in late March onwards. Adopting a Moore swab approach, SARS-CoV-2 was detected in wastewater samples just 2 days after passive samplers were deployed. These samples also tested positive for the B.1.1.7 (Alpha) variant of concern (VOC) using RT-qPCR. The positive result triggered a public health case-finding response, including a mobile testing unit deployed to the residence hall the following day, with testing of nearly 200 students and staff, which identified two laboratory-confirmed cases of Alpha variant COVID-19. These individuals were relocated to a separate quarantine facility, averting an outbreak on campus. Aggregating wastewater and clinical data, the campus wastewater surveillance program has yielded the first estimates of fecal shedding rates of the Alpha VOC of SARS-CoV-2 in individuals from a nonclinical setting. IMPORTANCE Among early adopters of wastewater monitoring for SARS-CoV-2 have been colleges and universities throughout North America, many of whom are using this approach to monitor congregate living facilities for early evidence of COVID-19 infection as an integral component of campus screening programs. Yet, while there have been numerous examples where wastewater monitoring on a university campus has detected evidence for infection among community members, there are few examples where this monitoring triggered a public health response that may have averted an actual outbreak. This report details a wastewater-testing program targeting a residence hall on a university campus during spring 2021, when there was mounting concern globally over the emergence of SARS-CoV-2 variants of concern, reported to be more transmissible than the wild-type Wuhan strain. In this communication, we present a clear example of how wastewater monitoring resulted in actionable responses by university administration and public health, which averted an outbreak of COVID-19 on a university campus.

Background Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spatially (6 sampling locations) characterizing BCC variation in lakes Erie and St. Clair; two connected ecosystems in the Laurentian Great Lakes. Results We found a spatial variation of the BCC between the two lakes and among the sampling locations (significant changes in the relative abundance of 16% of the identified OTUs at the sampling location level). We observed five distinct temporal clusters (UPGMA broad-scale temporal variation) corresponding to seasonal variation over the 15 months of sampling. Temporal variation among months was high, with significant variation in the relative abundance of 69% of the OTUs. We identified significant differences in taxonomic composition between summer months of 2016 and 2017, with a corresponding significant reduction in the diversity of BCC in summer 2017. Conclusions As bacteria play a key role in biogeochemical cycling, and hence in healthy ecosystem function our study defines the scope for temporal and spatial variation in large lake ecosystems. Our data also show that freshwater BCC could serve as an effective proxy and monitoring tool to access large lake health.

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.

A wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week. During this time, there was no detection of SARS-CoV-2 by RT-qPCR in the residence hall wastewater stream. Aiming to obtain a sample more representative of the residence hall community, a decision was made to use passive samplers beginning in late March onwards. Adopting a Moore Swab approach, SARS-CoV-2 was detected in wastewater samples on just two days after passive samplers were activated. These samples were also positive for the B.1.1.7 (Alpha) Variant of Concern (VOC) by RT-qPCR. The positive result triggered a public health case finding response including a mobile testing unit deployed to the residence hall the following day with testing of nearly 200 students and staff, which identified two laboratory-confirmed cases of B.1.1.7 variant COVID-19. These individuals were re-located to a separate quarantine facility averting an outbreak on campus. Aggregating wastewater and clinical data, the campus wastewater surveillance program has yielded the first estimates of fecal shedding rates of the B.1.1.7 VOC of SARS-CoV-2 in individuals from a non-clinical setting.

Animal culture changes over time through processes that include drift, immigration, selection, and innovation. Cultural change has been particularly well-studied for animal vocalizations, especially for the vocalizations of male animals in the temperate zone. Here we examine the cultural change in the vocalizations of tropical Rufous-and-white Wrens (Thryophilus rufalbus), quantifying temporal variation in song structure, song type diversity, and population-level distribution of song types in both males and females. We use data from 10 microsatellite loci to quantify patterns of immigration and neutral genetic differentiation over time, to investigate whether cultural diversity changes with rates of immigration. Based on 11 yr of data, we show that the spectro-temporal features of several widely-used persistent song types maintain a relatively high level of consistency for both males and females, whereas the distribution and frequency of particular song types change over time for both sexes. Males and females exhibit comparable levels of cultural diversity (i.e. the diversity of song types across the population), although females exhibit greater rates of cultural change over time. We found that female changes in cultural diversity increased when immigration is high, whereas male cultural diversity did not change with immigration. Our study is the first long-term study to explore cultural evolution for both male and female birds and suggests that cultural patterns exhibit notable differences between the sexes.

Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-throughput sequencing of 16S rRNA gene, we found substantial bi-hourly and day/night variation in the bacterial communities with considerable fluctuation in the relative abundance of Actinobacteria and Proteobacteria phyla. Moreover, relative abundance of Enterobacteriaceae (associated with potential health risk) was significantly high at night in some dial cycles. Diversity was significantly high at night across most of the diel sampling events. qPCR assays showed a substantial bi-hourly variation of Escherichia coli levels with a significant high level of E. coli at night hours in comparison with day hours and the lowest levels at noon and during the afternoon hours. Taken together, these findings highlighted a considerable short-term temporal variation of bacterial communities which helps better understanding of freshwater bacterial dynamics and their ecology. E. coli monitoring showed that multiple samples in different hours will provide more accurate picture of freshwater safety and human health risk. Graphical abstract.

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.