Genomic vulnerability of a freshwater salmonid under climate change.

Understanding the adaptive potential of populations and species is pivotal for minimizing the loss of biodiversity in this era of rapid climate change. Adaptive potential has been estimated in various ways, including based on levels of standing genetic variation, presence of potentially beneficial alleles, and/or the severity of environmental change. Kokanee salmon, the non-migratory ecotype of sockeye salmon (Oncorhynchus nerka), is culturally and economically important and has already been impacted by the effects of climate change. To assess its climate vulnerability moving forward, we integrated analyses of standing genetic variation, genotype-environment associations, and climate modeling based on sequence and structural genomic variation from 224 whole genomes sampled from 22 lakes in British Columbia and Yukon (Canada). We found that variables for extreme temperatures, particularly warmer temperatures, had the most pervasive signature of selection in the genome and were the strongest predictors of levels of standing variation and of putatively adaptive genomic variation, both sequence and structural. Genomic offset estimates, a measure of climate vulnerability, were significantly correlated with higher increases in extreme warm temperatures, further highlighting the risk of summer heat waves that are predicted to increase in frequency in the future. Levels of standing genetic variation, an important metric for population viability and resilience, were not correlated with genomic offset. Nonetheless, our combined approach highlights the importance of integrating different sources of information and genomic data to formulate more comprehensive and accurate predictions on the vulnerability of populations and species to future climate change.

Genotyping-in-Thousands by sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon.

Stocking programs have been widely implemented to re-establish extirpated fish species to their historical ranges; when employed in species with complex life histories, such management activities should include careful consideration of resulting hybridization dynamics with resident stocks and corresponding outcomes on recovery initiatives. Genetic monitoring can be instrumental for quantifying the extent of introgression over time, however conventional markers typically have limited power for the identification of advanced hybrid classes, especially at the intra-specific level. Here, we demonstrate a workflow for developing, evaluating and deploying a Genotyping-in-Thousands by Sequencing (GT-seq) SNP panel with the power to detect advanced hybrid classes to assess the extent and trajectory of intra-specific hybridization, using the sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake, British Columbia as a case study. Previous analyses detected significant levels of hybridization between the anadromous (sockeye) and freshwater resident (kokanee) forms of O. nerka, but were restricted to assigning individuals to pure-stock or "hybrid". Simulation analyses indicated our GT-seq panel had high accuracy, efficiency and power (> 94.5%) of assignment to pure-stock sockeye salmon/kokanee, F1, F2, and B2 backcross-sockeye/kokanee. Re-analysis of 2016/2017 spawners previously analyzed using TaqMan® assays and otolith microchemistry revealed shifts in assignment of some hybrids to adjacent pure-stock or B2 backcross classes, while new assignment of 2019 spawners revealed hybrids comprised 31% of the population, ~ 74% of which were B2 backcross or F2. Overall, the GT-seq panel development workflow presented here could be applied to virtually any system where genetic stock identification and intra-specific hybridization are important management parameters.

Assessing conservation status with extensive but low-resolution data: Application of frequentist and Bayesian models to endangered Athabasca River rainbow trout.

Use of extensive but low-resolution abundance data is common in the assessment of species at-risk status based on quantitative decline criteria under International Union for Conservation of Nature (IUCN) and national endangered species legislation. Such data can be problematic for 3 reasons. First, statistical power to reject the null hypothesis of no change is often low because of small sample size and high sampling uncertainty leading to a high frequency of type II errors. Second, range-wide assessments composed of multiple site-specific observations do not effectively weight site-specific trends into global trends. Third, uncertainty in site-specific temporal trends and relative abundance are not propagated at the appropriate spatial scale. A common result is the propensity to underestimate the magnitude of declines and therefore fail to identify the appropriate at-risk status for a species. We used 3 statistical approaches, from simple to more complex, to estimate temporal decline rates for a designatable unit (DU) of rainbow trout in the Athabasca River watershed in western Canada. This DU is considered a native species for purposes of listing because of its genetic composition characterized as >0.95 indigenous origin in the face of continuing introgressive hybridization with introduced populations in the watershed. Analysis of abundance trends from 57 time series with a fixed-effects model identified 33 sites with negative trends, but only 2 were statistically significant. By contrast, a hierarchical linear mixed model weighted by site-specific abundance provided a DU-wide decline estimate of 16.4% per year and a 3-generation decline of 93.2%. A hierarchical Bayesian mixed model yielded a similar 3-generation decline trend of 91.3% and the posterior distribution showed that the estimate had a >99% probability of exceeding thresholds for an endangered listing. We conclude that the Bayesian approach was the most useful because it provided a probabilistic statement of threshold exceedance in support of an at-risk status recommendation.

El uso de datos extensivos, pero de baja resolución, de la abundancia es una práctica común en la evaluación del estado de riesgo de una especie con base en los criterios cuantitativos de declinación establecidos por la Unión Internacional para la Conservación de la Naturaleza (UICN) y la legislación nacional sobre especies en peligro extinción. Dicha información puede ser problemática por tres razones: primero, el poder estadístico para rechazar la hipótesis nula de ningún cambio es frecuentemente bajo debido a un tamaño pequeño de la muestra y a la elevada incertidumbre del muestreo, lo que resulta en una frecuencia elevada de errores de tipo II; segundo, las evaluaciones de amplia variedad compuestas de varias observaciones específicas de sitio no sopesan efectivamente las tendencias específicas de sitio dentro de las tendencias globales; y tercero, la incertidumbre en las tendencias temporales específicas de sitio y en la abundancia relativa no se propagan a la escala espacial apropiada. Un resultado común del uso de esta información es la propensión a subestimar la magnitud de las declinaciones, y por lo tanto equivocarse en la identificación del estado de riesgo apropiado para la especie. Usamos tres estrategias estadísticas, de simples a más complejas, para estimar las tasas de declinación temporal para una unidad designable (UD) de trucha arcoíris en la cuenca del río Athabasca al oeste de Canadá. Esta UD es considerada una especie nativa por razones de listado debido a su composición genética, caracterizada como >0-95 de origen nativo de frente a la continua hibridación introgresiva con poblaciones introducidas a la cuenca. El análisis de las tendencias de abundancia de 57 series de tiempo con un modelo de efectos fijos identificó 33 sitios con tendencias negativas, pero sólo dos fueron estadísticamente significativas. En contraste, un modelo lineal mixto de jerarquías sopesado por abundancia específica de sitio proporcionó una estimación de declinación en toda la UD de 16.4% año−1 y una declinación a tres generaciones de 93.2%. Un modelo bayesiano de jerarquías produjo una tendencia de declinación a tres generaciones de 91.3% y la distribución posterior mostró que el estimado tuvo una probabilidad >99% de exceder los umbrales para la categorización como especie en peligro. Concluimos que la estrategia bayesiana fue la más útil porque proporcionó una afirmación probabilística de la superación del umbral a favor de una recomendación de categorizar el estado como en riesgo.

Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales.

The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the freshwater resident form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan® SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.

Metabolic acidosis in a lactating woman induced by a deliberate ketogenic diet.

ABSTRACT: This article describes a rare case of lactation ketoacidosis in a patient who started a ketogenic diet while nursing an infant and toddler. The patient presented to the ED with a history of nausea, vomiting, and postural dizziness, and was found to have a significant metabolic acidosis and elevated lipase level. The metabolic changes induced in this patient could occur in anyone with high metabolic demands who also is on a strict ketogenic diet. The case highlights the importance of a dietary history in patients with unexplained metabolic derangements.

Citrobacter koseri meningitis with cerebral edema and pneumocephalus in a neonate.

Sometimes the only indicator of a serious infection in a neonate is a fever. Citrobacter koseri (C. koseri) has been reported to cause neonatal brain abscesses in the setting of meningitis. Although rare, pneumocephalus, secondary to C. koseri, carries a very high mortality. A 17-day-old male presented to the emergency department with a fever, decreased oral intake, and lethargy. The patient developed pneumocephalus and cerebral edema and was diagnosed with C. koseri meningitis, leading to death. This case demonstrates the presentation of C. koseri meningitis with pneumocephalus and cerebral edema in a neonate presenting with fever.

Differentiating salmonid migratory ecotypes through stable isotope analysis of collagen: Archaeological and ecological applications.

The ability to distinguish between different migratory behaviours (e.g., anadromy and potamodromy) in fish can provide important insights into the ecology, evolution, and conservation of many aquatic species. We present a simple stable carbon isotope (δ13C) approach for distinguishing between sockeye (anadromous ocean migrants) and kokanee (potamodromous freshwater residents), two migratory ecotypes of Oncorhynchus nerka (Salmonidae) that is applicable throughout most of their range across coastal regions of the North Pacific Ocean. Analyses of kokanee (n = 239) and sockeye (n = 417) from 87 sites spanning the North Pacific (Russia to California) show that anadromous and potamodromous ecotypes are broadly distinguishable on the basis of the δ13C values of their scale and bone collagen. We present three case studies demonstrating how this approach can address questions in archaeology, archival, and conservation research. Relative to conventional methods for determining migratory status, which typically apply chemical analyses to otoliths or involve genetic analyses of tissues, the δ13C approach outlined here has the benefit of being non-lethal (when applied to scales), cost-effective, widely available commercially, and should be much more broadly accessible for addressing archaeological questions since the recovery of otoliths at archaeological sites is rare.

Clinical and Demographic Parameters of Patients Treated Using a Sepsis Protocol.

PURPOSE: The purpose of this study was to investigate potential differences by sex in the demographic and clinical characteristics of patients treated utilizing a sepsis electronic bundle order set. Risk factors for in-hospital mortality were also assessed. METHODS: Data on patients in whom the sepsis order set was initiated in the emergency department over a 16-month period were entered into the hospital database. Data were analyzed for differences by sex in demographic and clinical factors, treatment modalities, and in-hospital mortality. The Bonferroni correction was applied to account for multiple comparisons; α was set at 0.006 for sex differences. FINDINGS: A total of 2204 patients were included. Male and female cohorts were similar with regard to a variety of demographic and clinical factors, including age, Emergency Severity Index (ESI) levels 1 and 2, time to disposition, appropriateness of antibiotics, and total fluids given by weight. The ESI is an assessment score ranging from 1 to 5 (1 is emergent). There were modest differences in the source of infection (genitourinary was 4% more common in women; P = 0.03) and mode of arrival (men were 4% more likely to arrive by ambulance; P = 0.03). These differences did not achieve our predefined α of 0.006 when the Bonferroni correction was applied. Factors associated with in-hospital mortality were advanced age, arrival by ambulance, and an ESI level of 1 or 2 (all, P < 0.01). IMPLICATIONS: Women were more likely to have a genitourinary cause of sepsis and less likely to arrive by ambulance. Risk factors of in-hospital mortality were older age, arrival by ambulance, and an ESI level of 1 or 2, but not sex.

Interaction of ecological and angler processes: experimental stocking in an open access, spatially structured fishery.

Effective management of socioecological systems requires an understanding of the complex interactions between people and the environment. In recreational fisheries, which are prime examples of socioecological systems, anglers are analogous to mobile predators in natural predator-prey systems, and individual fisheries in lakes across a region are analogous to a spatially structured landscape of prey patches. Hence, effective management of recreational fisheries across large spatial scales requires an understanding of the dynamic interactions among ecological density dependent processes, landscape-level characteristics, and angler behaviors. We focused on the stocked component of the open access rainbow trout (Oncorhynchus mykiss) fishery in British Columbia (BC), and we used an experimental approach wherein we manipulated stocking densities in a subset of 34 lakes in which we monitored angler effort, fish abundance, and fish size for up to seven consecutive years. We used an empirically derived relationship between fish abundance and fish size across rainbow trout populations in BC to provide a measure of catch-based fishing quality that accounts for the size-abundance trade off in this system. We replicated our experimental manipulation in two regions known to have different angler populations and broad-scale access costs. We hypothesized that angler effort would respond to variation in stocking density, resulting in spatial heterogeneity in angler effort but homogeneity in catch-based fishing quality within regions. We found that there is an intermediate stocking density for a given lake or region at which angler effort is maximized (i.e., an optimal stocking density), and that this stocking density depends on latent effort and lake accessibility. Furthermore, we found no clear effect of stocking density on our measure of catch-based fishing quality, suggesting that angler effort homogenizes catch-related attributes leading to an eroded relationship between stocking density and catch-based fishing quality at the timescale of annual surveys. We conclude that declines in fishing quality resulting from understocking (due to declines in catch rate with low fish abundance) and overstocking (due to suppressed growth and limited recruitment at high density) give an optimal stocking rate that depends on accessibility and latent effort.

Supply-demand equilibria and the size-number trade-off in spatially structured recreational fisheries.

Recreational fishing effort varies across complex inland landscapes (e.g., lake-districts) and appears influenced by both angler preferences and qualities of the fishery resource, like fish size and abundance. However, fish size and abundance have an ecological trade-off within a population, thereby structuring equal-quality isopleths expressing this trade-off across the fishing landscape. Since expressed preferences of recreational anglers (i.e., site-selection of high-quality fishing opportunities among many lakes) can be analogous to optimal foraging strategies of natural predators, adopting such concepts can aid in understanding scale-dependence in fish-angler interactions and impacts of fishing across broad landscapes. Here, we assumed a fish supply-angler demand equilibria and adapted a novel bivariate measure of fishing quality based on fish size and catch rates to assess how recreational anglers influence fishing quality among a complex inland landscape. We then applied this metric to evaluate (1) angler preferences for caught and released fish compared to harvested fish, (2) the nonlinear size-numbers trade-off with uncertainty in both traits, and (3) the spatial-scale of the equilibria across 62 lakes and four independent management regions in British Columbia's (BC) rainbow trout Oncorhynchus mykiss fishery. We found anglers had low preference for caught and released fish (~10% of the value compared to harvested fish), which modified anglers' perception of fishing quality. Hence, fishing quality and angler effort was not influenced simply by total fish caught, but largely by harvested fish catch rates. Fishing quality varied from BC's northern regions (larger fish and more abundant) compared to southern regions (smaller fish and less abundant) directly associated with a 2.5 times increase in annual fishing effort in southern regions, suggesting that latent fishing pressure can structure the size-numbers trade-off in rainbow trout populations. The presence of two different equal-quality isopleths suggests at least two effective landscapes support co-occurring ideal free distributions of recreational fishing effort in BC's rainbow fishery. Anglers' expressed preferences among lakes interacted with density dependent growth and survival within lakes to structure a size-numbers trade-off influencing how anglers perceive fishing quality and, ultimately, distribute across complex inland landscapes.