Application of machine learning and acoustic predation tags to classify migration fate of Atlantic salmon smolts.

Mortality and predation of tagged fishes present a serious challenge to interpreting results of acoustic telemetry studies. There is a need for standardized methods to identify predated individuals and reduce the impacts of "predation bias" on results and conclusions. Here, we use emerging approaches in machine learning and acoustic tag technology to classify out-migrating Atlantic salmon (Salmo salar) smolts into different fate categories. We compared three methods of fate classification: predation tag pH sensors and detection data, unsupervised k-means clustering, and supervised random forest combined with tag pH sensor data. Random forest models increased predation estimates by 9-32% compared to relying solely on pH sensor data, while clustering reduced estimates by 3.5-30%. The greatest changes in fate class estimates were seen in years with large class imbalance (one or more fate classes underrepresented compared to the others) or low model accuracy. Both supervised and unsupervised approaches were able to classify smolt fate; however, in-sample model accuracy improved when using tag sensor data to train models, emphasizing the value of incorporating such sensors when studying small fish. Sensor data may not be sufficient to identify predation in isolation due to Type I and Type II error in predation sensor triggering. Combining sensor data with machine learning approaches should be standard practice to more accurately classify fate of tagged fish.

Effectiveness of portable HEPA air cleaners on reducing indoor endotoxin, PM10, and coarse particulate matter in an agricultural cohort of children with asthma: A randomized intervention trial.

We conducted a randomized trial of portable HEPA air cleaners in the homes of children age 6-12 years with asthma in the Yakima Valley, Washington. All families received asthma education while intervention families also received two HEPA cleaners (child's bedroom, living room). We collected 14-day integrated samples of endotoxin in settled dust and PM10 and PM10-2.5 in the air of the children's bedrooms at baseline and one-year follow-up, and used linear regression to compare follow-up levels, adjusting for baseline. Seventy-one families (36 HEPA, 35 control) completed the study. Baseline geometric mean (GSD) endotoxin loadings were 1565 (6.3) EU/m2 and 2110 (4.9) EU/m2 , respectively, in HEPA vs. control homes while PM10 and PM10-2.5 were 22.5 (1.9) µg/m3 and 9.5 (2.9) µg/m3 , respectively, in HEPA homes, and 19.8 (1.8) µg/m3 and 7.7 (2.0) µg/m3 , respectively, in control homes. At follow-up, HEPA families had 46% lower (95% CI, 31%-57%) PM10 on average than control families, consistent with prior studies. In the best-fit heterogeneous slopes model, HEPA families had 49% (95% CI, 6%-110%) and 89% lower (95% CI, 28%-177%) PM10-2.5 at follow-up, respectively, at 50th and 75th percentile baseline concentrations. Endotoxin loadings did not differ significantly at follow-up (4% lower, HEPA homes; 95% CI, -87% to 50%).

Effectiveness of portable HEPA air cleaners on reducing indoor PM2.5 and NH3 in an agricultural cohort of children with asthma: A randomized intervention trial.

We conducted a randomized trial of portable HEPA air cleaners with pre-filters designed to also reduce NH3 in non-smoking homes of children age 6-12 with asthma in Yakima Valley (Washington, USA). Participants were recruited through the Yakima Valley Farm Workers Clinic asthma education program. All participants received education on home triggers while intervention families additionally received two HEPA cleaners (child's sleeping area, main living area). Fourteen-day integrated samples of PM2.5 and NH3 were measured at baseline and one-year follow-up. We fit ANCOVA models to compare follow-up concentrations in HEPA vs control homes, adjusting for baseline concentrations. Seventy-one households (36 HEPA, 35 control) completed the study. Most were single-family homes, with electric heat and stove, A/C, dogs/cats, and mean (SD) 5.3 (1.8) occupants. In the sleeping area, baseline geometric mean (GSD) PM2.5 was 10.7 (2.3) µg/m3 (HEPA) vs 11.2 (1.9) µg/m3 (control); in the living area, it was 12.5 (2.3) µg/m3 (HEPA) vs 13.6 (1.9) µg/m3 (control). Baseline sleeping area NH3 was 62.4 (1.6) µg/m3 (HEPA) vs 65.2 (1.8) µg/m3 (control). At follow-up, HEPA families had 60% (95% CI, 41%-72%; p < .0001) and 42% (19%-58%; p = .002) lower sleeping and living area PM2.5 , respectively, consistent with prior studies. NH3 reductions were not observed.

Feasibility of using surgical implantation methods for acoustically tagging alewife (Alosa pseudoharengus) with V5 acoustic transmitters.

Anadromous alewives (Alosa pseudoharengus) are abundant in the Canadian Maritimes, where they support lucrative commercial fisheries. Little is known about their coastal movement, and their potential to interact with anthropogenic structures. Acoustic telemetry can provide detailed information on the spatiotemporal distribution and survival of fishes in coastal areas, using information transmitted from tagged fishes and recorded by moored receivers. However, few acoustic telemetry studies have been performed on clupeids as they are extremely sensitive to handling, and are often compromised by surgical tag implantation. This research assesses the feasibility of a surgical tagging protocol using novel High Residency acoustic tags in alewives, and establishes a baseline of short-term tagging effects. Alewives from the Gaspereau River population were tagged between 2018 (n = 29) and 2019 (n = 96) with non-transmitting models of Vemco/Innovasea V5 HR tags. Tagging effects were evaluated based on recovery rate, reflex impairment, and necropsy-based health assessments. Alewives responded well to tagging, with low mortality (3%) and no observed instances of tag shedding 72 hours post-surgery. The use of sutures to close the incision site had no effect on recovery times. Water temperature and spawning condition had the greatest effect on the behavioural response of fish to tagging. Our findings suggest that, with proper handling and smaller acoustic tags, telemetry studies on alewives are feasible.

Evolutionary and ecological feedbacks of the survival cost of reproduction.

Arguably the most fundamental of trade-offs in life-history evolution is the increase in natural mortality resulting from sexual maturity and reproduction. Despite its central importance, this increase in mortality, a survival cost, garners surprisingly little attention in fish and fisheries modeling studies. We undertook an exploratory analysis to evaluate the consequences of this omission for life-history projections. To this end, we developed a simulation approach that integrates quantitative genetics into the ecological dynamics of a fish population and parameterized the model for Atlantic cod (Gadus morhua, L.). When compared to simulations in which the mortality of immature and mature individuals is equal, the inclusion of a survival cost results in larger asymptotic body size, older age at maturity, and larger size at maturity. We also find that measures of population productivity (spawning stock biomass, recruits-per-spawner) are overestimated if the survival cost is excluded. This sensitivity of key metrics of population growth rate and reproductive capacity to the magnitude of the survival cost of reproduction underscores the need to explicitly account for this trade-off in projections of fish population responses to natural and anthropogenic environmental change, including fisheries.

Evaluating SNP ascertainment bias and its impact on population assignment in Atlantic cod, Gadus morhua.

The increasing use of single nucleotide polymorphisms (SNPs) in studies of nonmodel organisms accentuates the need to evaluate the influence of ascertainment bias on accurate ecological or evolutionary inference. Using a panel of 1641 expressed sequence tag-derived SNPs developed for northwest Atlantic cod (Gadus morhua), we examined the influence of ascertainment bias and its potential impact on assignment of individuals to populations ranging widely in origin. We hypothesized that reductions in assignment success would be associated with lower diversity in geographical regions outside the location of ascertainment. Individuals were genotyped from 13 locations spanning much of the contemporary range of Atlantic cod. Diversity, measured as average sample heterozygosity and number of polymorphic loci, declined (c. 30%) from the western (H(e) = 0.36) to eastern (H(e) = 0.25) Atlantic, consistent with a signal of ascertainment bias. Assignment success was examined separately for pools of loci representing differing degrees of reductions in diversity. SNPs displaying the largest declines in diversity produced the most accurate assignment in the ascertainment region (c. 83%) and the lowest levels of correct assignment outside the ascertainment region (c. 31%). Interestingly, several isolated locations showed no effect of assignment bias and consistently displayed 100% correct assignment. Contrary to expectations, estimates of accurate assignment range-wide using all loci displayed remarkable similarity despite reductions in diversity. Our results support the use of large SNP panels in assignment studies of high geneflow marine species. However, our evidence of significant reductions in assignment success using some pools of loci suggests that ascertainment bias may influence assignment results and should be evaluated in large-scale assignment studies.

Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature.

Despite the enormous economic and ecological importance of marine organisms, the spatial scales of adaptation and biocomplexity remain largely unknown. Yet, the preservation of local stocks that possess adaptive diversity is critical to the long-term maintenance of productive stable fisheries and ecosystems. Here, we document genomic evidence of range-wide adaptive differentiation in a broadcast spawning marine fish, Atlantic cod (Gadus morhua), using a genome survey of single nucleotide polymorphisms. Of 1641 gene-associated polymorphisms examined, 70 (4.2%) tested positive for signatures of selection using a Bayesian approach. We identify a subset of these loci (n=40) for which allele frequencies show parallel temperature-associated clines (p<0.001, r2=0.89) in the eastern and western north Atlantic. Temperature associations were robust to the statistical removal of geographic distance or latitude effects, and contrasted 'neutral' loci, which displayed no temperature association. Allele frequencies at temperature-associated loci were significantly correlated, spanned three linkage groups and several were successfully annotated supporting the involvement of multiple independent genes. Our results are consistent with the evolution and/or selective sweep of multiple genes in response to ocean temperature, and support the possibility of a new conservation paradigm for non-model marine organisms based on genomic approaches to resolving functional and adaptive diversity.

The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes.

Cytological and organismal characteristics associated with cellular DNA content underpin most adaptionist interpretations of genome size variation. Since fishes are the only group of vertebrate for which relationships between genome size and key cellular parameters are uncertain, the cytological correlates of genome size were examined in this group. The cell and nuclear areas of erythrocytes showed a highly significant positive correlation with each other and with genome size across 22 cartilaginous and 201 ray-finned fishes. Regressions remained significant at all taxonomic levels, as well as among different fish lineages. However, the results revealed that cartilaginous fishes possess higher cytogenomic ratios than ray-finned fishes, as do cold-water fishes relative to their warm-water counterparts. Increases in genome size owing to ploidy shifts were found to influence cell and nucleus size in an immediate and causative manner, an effect that persists in ancient polyploid lineages. These correlations with cytological parameters known to have important influences on organismal phenotypes support an adaptive interpretation for genome size variation in fishes.

From pixels to picograms: a beginners' guide to genome quantification by Feulgen image analysis densitometry.

The study of genome size variation is important from a number of practical and theoretical perspectives. For example, the long-standing "C-value enigma" relating to the more than 200,000-fold range in eukaryotic genome sizes is best studied from a broad comparative standpoint. Genome size data are also required in detailed analyses of genome structure and evolution. The choice of future genome sequencing projects will be dependent on knowledge regarding the sizes of genomes to be sequenced, and so on. To date, genome size data have been acquired primarily by Feulgen microdensitometry or flow cytometry. Each has several advantages but also important limitations. In this review, we provide a practical guide to the new technique of Feulgen image analysis densitometry. The review is designed for those interested in genome size measurements but not extensively experienced in histochemistry, densitometry, or microscopy. Therefore, relevant historical and technical background information is included. For easy reference, we provide recipes for required reagents, guidelines for cell staining, and a checklist of steps for successful image analysis. We hope that the accuracy, rapidity, and cost-effectiveness of Feulgen image analysis demonstrated here will stimulate further surveys of genome sizes in a variety of taxa.