Influence of climate and abundance on migration timing of adult Atlantic salmon (Salmo salar) among rivers in Newfoundland and Labrador

Evidence mounts for the influence of climate variability on temporal trends in the phenology of many organisms including various species of fish. Accordingly, we examined variation in adult Atlantic salmon Salmo salar run timing in thirteen Newfoundland and Labrador rivers where returns were monitored at fishways or fish‐counting fences. Run timing varied significantly among rivers with the median date of return differing by up to 5 weeks. Duration of runs was generally short with most adults returning over a period of three to 5 weeks. A mixed model analysis incorporating a first‐order autoregressive error structure was used to generalise changes in run timing among all monitored rivers. Results indicated that the median date of return has advanced by almost 12 days over a 35‐year interval from 1978 to 2012, while several individual rivers have advanced by almost 21 days. The influence of climate on median timing was evident when the simultaneous effects of both climate and salmon abundance were controlled. We found earlier runs associated with overall warmer climate conditions on the Newfoundland and Labrador Shelf. Results contrast with those from the north‐east Atlantic where Atlantic salmon are returning later in some rivers coincident with warming climate conditions.     

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.

     

Ecoviability for ecosystem‐based fisheries management

Reconciling food security, economic development and biodiversity conservation is a key challenge, especially in the face of the demographic transition characterizing many countries in the world. Fisheries and marine ecosystems constitute a difficult application of this bio‐economic challenge. Many experts and scientists advocate an ecosystem approach to manage marine socio‐ecosystems for their sustainability and resilience. However, the ways by which to operationalize ecosystem‐based fisheries management (EBFM) remain poorly specified. We propose a specific methodological framework—viability modelling—to do so. We show how viability modelling can be applied using four contrasted case‐studies: two small‐scale fisheries in South America and Pacific and two larger‐scale fisheries in Europe and Australia. The four fisheries are analysed using the same modelling framework, structured around a set of common methods, indicators and scenarios. The calibrated models are dynamic, multispecies and multifleet and account for various sources of uncertainty. A multicriteria evaluation is used to assess the scenarios’ outcomes over a long time horizon with different constraints based on ecological, social and economic reference points. Results show to what extent the bio‐economic and ecosystem risks associated with the adoption of status quo strategies are relatively high and challenge the implementation of EBFM. In contrast, strategies called ecoviability or co‐viability strategies, that aim at satisfying the viability constraints, reduce significantly these ecological and economic risks and promote EBFM. The gains associated with those ecoviability strategies, however, decrease with the intensity of regulations imposed on these fisheries.     

Geosmin depuration from European eel (Anguilla anguilla) is not affected by the water renewal rate of depuration tanks

This study established that geosmin depuration from European eel is not affected by the water renewal rate of depuration tanks. A general fish bioaccumulation model extended with terms that account for effects of tank water renewal rate and system losses of chemicals, predicted strong effects of the water renewal rate of depuration tanks on geosmin depuration from European eel. Model predictions were validated in a depuration experiment with geosmin‐loaded European eel (n = 95) with a mean (SD) individual weight of 134.4 (5.0) g and a mean (SD) lipid content of 33.7 (2.8) % (w/w). Fish were depurated for 24, 48 or 72 h at three different tank water renewal rates (0.3, 3.3 and 33 day^?1). Treatments were installed by three different mean (SD) water flow rates (13.8 (1.3), 143.5 (9.2) and 1511 (80) L kg fish^?1 day^?1) over 30‐L tanks. Eels eliminated geosmin from their bodies, but unlike the model predicted, this was independent of the water renewal rate of the depuration tanks. Although being eliminated from the fish, geosmin hardly appeared and certainly did not accumulate in the water of the depuration tanks as the model predicted. This observation may be explained by geosmin being eliminated from eel as metabolite rather than the parent compound. Geosmin elimination from eel seems not to occur according to the generally accepted passive diffusion mechanism for excretion of lipophilic chemicals, and geosmin biotransformation by the eel seems indicated. Clearly geosmin depuration from European eel cannot be enhanced by increasing water renewal rates of depuration tanks.     

Hybrid breeding for biomass yield in winter triticale: II. Combining ability and hybrid prediction

Accurate hybrid prediction and knowledge about the relative contribution of general (GCA) and specific combining ability (SCA) are of utmost importance for efficient hybrid breeding. We therefore evaluated 91 triticale single-cross hybrids in field trials at seven environments for plant height, heading time, fresh biomass, dry matter content and dry biomass. Fresh and dry biomass showed the highest proportion (23%) of variance due to SCA. Prediction accuracies based on GCA were slightly higher than based on mid-parent values. Utilizing parental kinship information yielded the highest prediction accuracies when both parental lines have been tested in other hybrid combinations, but still moderate-to-low prediction accuracies for two untested parents. Thus, hybrid prediction for biomass traits in triticale is currently promising based on mid-parent values as emphasized by our simulation study, but can be expected to shift to GCA-based prediction with an increasing importance of GCA due to selection in hybrid breeding. Moreover, the performance of potential hybrids between newly developed lines can be predicted with moderate accuracy using genomic relationship information.     

EFFECTS OF FLUID AND COMPUTED TOMOGRAPHIC TECHNICAL FACTORS ON CONSPICUITY OF CANINE AND FELINE NASAL TURBINATES

Turbinate destruction is an important diagnostic criterion in canine and feline nasal computed tomography (CT). However decreased turbinate visibility may also be caused by technical CT settings and nasal fluid. The purpose of this experimental, crossover study was to determine whether fluid reduces conspicuity of canine and feline nasal turbinates in CT and if so, whether CT settings can maximize conspicuity. Three canine and three feline cadaver heads were used. Nasal slabs were CT‐scanned before and after submerging them in a water bath; using sequential, helical, and ultrahigh resolution modes; with images in low, medium, and high frequency image reconstruction kernels; and with application of additional posterior fossa optimization and high contrast enhancing filters. Visible turbinate length was measured by a single observer using manual tracing. Nasal density heterogeneity was measured using the standard deviation (SD) of mean nasal density from a region of interest in each nasal cavity. Linear mixed‐effect models using the R package ‘nlme’, multivariable models and standard post hoc Tukey pair‐wise comparisons were performed to investigate the effect of several variables (nasal content, scanning mode, image reconstruction kernel, application of post reconstruction filters) on measured visible total turbinate length and SD of mean nasal density. All canine and feline water‐filled nasal slabs showed significantly decreased visibility of nasal turbinates (P < 0.001). High frequency kernels provided the best turbinate visibility and highest SD of aerated nasal slabs, whereas medium frequency kernels were optimal for water‐filled nasal slabs. Scanning mode and filter application had no effect on turbinate visibility.     

Assessing the influence of mechanical ventilation on blood gases and blood pressure in rattlesnakes

ObjectiveTo characterize the impact of mechanical positive pressure ventilation on heart rate (HR), arterial blood pressure, blood gases, lactate, glucose, sodium, potassium and calcium concentrations in rattlesnakes during anesthesia and the subsequent recovery period.Study designProspective, randomized trial.AnimalsTwenty one fasted adult South American rattlesnakes (Crotalus durissus terrificus).MethodsSnakes were anesthetized with propofol (15 mg kg⁻¹) intravenously, endotracheally intubated and assigned to one of four ventilation regimens: Spontaneous ventilation, or mechanical ventilation at a tidal volume of 30 mL kg⁻¹ at 1 breath every 90 seconds, 5 breaths minute⁻¹, or 15 breaths minute⁻¹. Arterial blood was collected from indwelling catheters at 30, 40, and 60 minutes and 2, 6, and 24 hours following induction of anesthesia and analyzed for pH, PaO₂, PaCO₂, and selected variables. Mean arterial blood pressure (MAP) and HR were recorded at 30, 40, 60 minutes and 24 hours.ResultsSpontaneous ventilation and 1 breath every 90 seconds resulted in a mild hypercapnia (PaCO₂ 22.4 ± 4.3 mmHg [3.0 ± 0.6 kPa] and 24.5 ± 1.6 mmHg [3.3 ± 0.2 kPa], respectively), 5 breaths minute⁻¹ resulted in normocapnia (14.2 ± 2.7 mmHg [1.9 ± 0.4 kPa]), while 15 breaths minute⁻¹ caused marked hypocapnia (8.2 ± 2.5 mmHg [1.1 ± 0.3 kPa]). Following recovery, blood gases of the four groups were similar from 2 hours. Anesthesia, independent of ventilation was associated with significantly elevated glucose, lactate and potassium concentrations compared to values at 24 hours (p < 0.0001). MAP increased significantly with increasing ventilation frequency (p < 0.001). HR did not vary among regimens.Conclusions and clinical relevanceMechanical ventilation had a profound impact on blood gases and blood pressure. The results support the use of mechanical ventilation with a frequency of 1–2 breaths minute⁻¹ at a tidal volume of 30 mL kg⁻¹ during anesthesia in fasted snakes.     

Comparison of the effects of propofol or alfaxalone for anaesthesia induction and maintenance on respiration in cats

ObjectiveTo compare the effects of propofol and alfaxalone on respiration in cats.Study designRandomized, ‘blinded’, prospective clinical trial.AnimalsTwenty cats undergoing ovariohysterectomy.MethodsAfter premedication with medetomidine 0.01 mg kg⁻¹ intramuscularly and meloxicam 0.3 mg kg⁻¹ subcutaneously, the cats were assigned randomly into two groups: group A (n = 10) were administered alfaxalone 5 mg kg⁻¹ minute⁻¹ followed by 10 mg kg⁻¹ hour⁻¹ intravenously (IV) and group P (n = 10) were administered propofol 6 mg kg⁻¹ minute⁻¹ followed by 12 mg kg⁻¹hour⁻¹ IV for induction and maintenance of anaesthesia, respectively. After endotracheal intubation, the tube was connected to a non-rebreathing system delivering 100% oxygen. The anaesthetic maintenance drug rate was adjusted (± 0.5 mg kg⁻¹ hour⁻¹) every 5 minutes according to a scoring sheet based on physiologic variables and clinical signs. If apnoea > 30 seconds, end-tidal carbon dioxide (Pe′CO₂) > 7.3 kPa (55 mmHg) or arterial haemoglobin oxygen saturation (SpO₂) < 90% occurred, manual ventilation was provided. Methadone was administered postoperatively. Data were analyzed using independent-samples t-tests, Fisher's exact test, linear mixed-effects models and binomial test.ResultsManual ventilation was required in two and eight of the cats in group A and P, respectively (p = 0.02). Two cats in both groups showed apnoea. Pe′CO₂ > 7.3 kPa was recorded in zero versus four and SpO₂ < 90% in zero versus six cats in groups A and P respectively. Induction and maintenance dose rates (mean ± SD) were 11.6 ± 0.3 mg kg⁻¹ and 10.7 ± 0.8 mg kg⁻¹ hour⁻¹ for alfaxalone and 11.7 ± 2.7 mg kg⁻¹ and 12.4 ± 0.5 mg kg⁻¹ hour⁻¹ for propofol.Conclusion and clinical relevanceAlfaxalone had less adverse influence on respiration than propofol in cats premedicated with medetomidine. Alfaxalone might be better than propofol for induction and maintenance of anaesthesia when artificial ventilation cannot be provided.