Respirometer in a box: development and use of a portable field respirometer for estimating oxygen consumption of large-bodied fishes

This study developed a portable, low-cost field respirometer for measuring oxygen consumption rates of large-bodied fishes. The respirometer performed well in laboratory tests and was used to measure the oxygen consumption rates ( O₂) of bull sharks Carcharhinus leucas (mean: 249.21 ± 58.10 mg O₂ kg⁻¹ h⁻¹ at 27.05°C). Interspecific comparisons and assessments of oxygen degradation curves indicated that the respirometer provided reliable measurements of O₂. This system presents a field-based alternative to laboratory respirometers, opening opportunities for studies on species in remote localities, increasing the ability to validate physiological field studies.     

The effects of hurricanes on the stochastic population growth of the endemic epiphytic orchid Broughtonia cubensis living in Cuba

We carried out a posthurricane evaluation of Broughtonia cubensis (Lindl.) Cogn., an endemic Cuban epiphytic orchid, after Hurricane Ivan (2004). We studied the transient responses in the stochastic dynamics of the species at three different sites over 13 successive years (2006–2019), monitored plot inventories (464 individuals in 10 transects) and built stochastic population models. The deterministic stochastic growth rate values () did not significantly differ (F = 2.76; p > 0.076) among the three sites over the 2006–2019 period. The long-term stochastic growth rate was 0.973 [0.932, 1.034]. The matrix elements that had the largest effect on were the transition to and stasis within the largest size class. Transient responses explained an average of 86% of the variation in the observed population growth rates , compared to 4% of the variation in the vital rates . Because transient dynamics are dependent on the population size composition, we ran extinction risk analyses under two scenarios: a population composed mainly of juveniles and another composed mainly of adults. There was little risk of falling below the quasi-extinction threshold before 25 year for both juveniles and adults. However, the risk of quasi-extinction was almost certain for both size classes by 80 year. We also simulated the effect of increasing the hurricane occurrence probability over 80 year on the population. There was little risk of extinction before 20 year in the baseline model, but there was a significant risk of extinction within 5 year when 90% of the individuals were affected by a new hurricane event.     

Age,growth and reproductive life-history characteristics infer a high population productivity for the sustainably fished protogynous hermaphroditic yellowspotted rockcod (Epinephelus areolatus) in north-western Australia

The yellowspotted rockcod, Epinephelus areolatus, is a small-sized grouper that is widely distributed throughout the Indo-Pacific, where it forms a valuable component of the harvest derived from multispecies fisheries along continental and insular shelves. Samples of E. areolatus were collected from 2012 to 2018 from commercial catches and research surveys in the Kimberley, Pilbara and Gascoyne regions of north-western Australia to improve the understanding of the life history, inherent vulnerability and stock status of this species. Histological analysis of gonads (n = 1889) determined that E. areolatus was a monandric protogynous hermaphrodite. Non-functional spermatogenic crypts were dispersed within the ovaries of 23% of mature functioning females; nonetheless, these crypts were not observed during the immature female phase. The length and age at which 50% of females matured were 266 mm total length (L_T) and 2.7 years, respectively. The spawning period was protracted over 10–12 months of the year with biannual peaks at the start of spring and autumn (i.e., September and March) when the photoperiod was at its mid-range (i.e., 12.1 h). Estimates of the lengths and ages at which 50% of E. areolatus change sex from female to male were very similar (i.e., <5% difference) between the Kimberley and Pilbara regions, i.e., of 364 and 349 mm L_T and of 7.9 and 7.3 years, respectively. A maximum age of 19 years was observed in all three regions, but there was significant regional variation in growth. These variations in growth were not correlated with latitude; instead a parabolic relationship was evident, where the smallest mean length-at-age and fastest growth rates (k) occurred in the mid-latitudes of the Pilbara region. In the Kimberley and Pilbara regions, individuals were not fully selected by commercial fish traps until 5–6 years of age, hence, several years after reaching maturity. These life-history characteristics infer a high population productivity, which underpins the sustainable harvest of this species, despite comprising the largest catches of all epinephelids in the multispecies tropical fisheries across north-western Australia.     

Spatial pattern of distribution and reproductive strategy of vermiculate electric-rays Narcine vermiculatus

In the study, the authors evaluate the spatial distribution pattern of vermiculate electric-ray Narcine vermiculatus using geostatistical techniques to predict its spatial distribution and indicate its reproduction strategy. From January 2008 to December 2009, 3333 specimens of vermiculate electric-ray were caught. Total length (L_T), sex, maturity stage, catch location and depth were recorded for each specimen. The L_T of vermiculate electric-ray ranged from 6.7–24.6 cm. The authors estimate an irregular spatial structure, with a high-density patch ( 53 ind. ha⁻¹) located on the east coast, which concentrates 65.2% of the specimens. The high-density patch consists mainly of large juveniles (13.3–19.5 cm L_T), sub-adults (14.0–19.8 cm L_T) and young adults (14.7–21.3 cm L_T). Data indicate that adults migrate to the high-density patch to reproduce. Males reached maturity at 14.5 cm L_T, whereas females reached maturity at 19.3 cm L_T. Vitellogenesis in female vermiculate electric-ray begins in June; ovulation, mating, fertilization and gestation in October and birth begins in February. This indicates an annual cycle with vitellogenesis and consecutive gestation, in females synchronized in reproduction. Fecundity was 1–8 ( 4), and the sex ratio of embryos was 1:1. The birth occurred between February and April, with an average size at parturition of 6.3 cm L_T. Incidental capture of sub-adults and adults of N. vermiculatus by bottom trawls threatens the survival of this species.     

An estimator of the Opportunity for Selection that is independent of mean fitness

Variation among individuals in number of offspring (fitness, k) sets an upper limit to the evolutionary response to selection. This constraint is quantified by Crow's Opportunity for Selection (I), which is the variance in relative fitness (I = σ²_k/(u_k)²). Crow's I has been widely used but remains controversial because it depends on mean offspring number in a sample (). Here, I used a generalized Wright-Fisher model that allows for unequal probabilities of producing offspring to evaluate behavior of Crow's I and related indices under a wide range of sampling scenarios. Analytical and numerical results are congruent and show that rescaling the sample variance (s²_k) to its expected value at a fixed removes dependence of I on mean offspring number, but the result still depends on choice of . A new index is introduced, Δ_I = Π– E(Î_drift) = Π– 1/, which makes Î independent of sample without the need for variance rescaling. Δ_I has a straightforward interpretation as the component of variance in relative fitness that exceeds that expected under a null model of random reproductive success. Δ_I can be used to directly compare estimates of the Opportunity for Selection for samples from different studies, different sexes, and different life stages.     

Valid oxygen uptake measurements: using high r2 values with good intentions can bias upward the determination of standard metabolic rate

This analysis shows good intentions in the selection of valid and precise oxygen uptake (O₂) measurements by retaining only slopes of declining dissolved oxygen level in a respirometer that have very high values of the coefficient of determination, r², are not always successful at excluding nonlinear slopes. Much worse, by potentially removing linear slopes that have low r² only because of a low signal-to-noise ratio, this procedure can overestimate the calculation of standard metabolic rate (SMR) of the fish. To remedy this possibility, a few simple diagnostic tools are demonstrated to assess the appropriateness of a given minimum acceptable r², such as calculating the proportion of rejected O₂ determinations, producing a histogram of the r² values and a plot of r² as a function of O₂. The authors offer solutions for cases when many linear slopes have low r². The least satisfactory but easiest to implement is lowering the minimum acceptable r². More satisfactory solutions involve processing (smoothing) the raw signal of dissolved oxygen as a function of time to improve the signal-to-noise ratio and the r²s.     

Inverse problem approach to regularized regression models with application to predicting recovery after stroke

Regression modelling is a powerful statistical tool often used in biomedical and clinical research. It could be formulated as an inverse problem that measures the discrepancy between the target outcome and the data produced by representation of the modelled predictors. This approach could simultaneously perform variable selection and coefficient estimation. We focus particularly on a linear regression issue, , where is the parameter of interest and its components are the regression coefficients. The inverse problem finds an estimate for the parameter , which is mapped by the linear operator to the observed outcome data . This problem could be conveyed by finding a solution in the affine subspace . However, in the presence of collinearity, high-dimensional data and high conditioning number of the related covariance matrix, the solution may not be unique, so the introduction of prior information to reduce the subset and regularize the inverse problem is needed. Informed by Huber's robust statistics framework, we propose an optimal regularizer to the regression problem. We compare results of the proposed method and other penalized regression regularization methods: ridge, lasso, adaptive-lasso and elastic-net under different strong hypothesis such as high conditioning number of the covariance matrix and high error amplitude, on both simulated and real data from the South London Stroke Register. The proposed approach can be extended to mixed regression models. Our inverse problem framework coupled with robust statistics methodology offer new insights in statistical regression and learning. It could open a new research development for model fitting and learning.     

Enhanced temporal and spatial resolution in super-resolution covariance imaging algorithm with deconvolution optimization

Based on the numerical analysis that covariance exhibits superior statistical precision than cumulant and variance, a new SOFI algorithm by calculating the n orders covariance for each pixel is presented with an almost -fold resolution improvement, which can be enhanced to 2ⁿ via deconvolution. An optimized deconvolution is also proposed by calculating the (n + 1) order SD associated with each n order covariance pixel, and introducing the results into the deconvolution as a damping factor to suppress noise generation. Moreover, a re-deconvolution of the covariance image with the covariance-equivalent point spread function is used to further increase the final resolution by above 2-fold. Simulated and experimental results show that this algorithm can significantly increase the temporal–spatial resolution of SOFI, meanwhile, preserve the sample's structure. Thus, a resolution of 58 nm is achieved for 20 experimental images, and the corresponding acquisition time is 0.8 seconds.     

Optimal rotation of insecticides to prevent the evolution of resistance in a structured environment

Several strategies have been used in insecticide resistance management to prevent the evolution of resistance, but the spatial aspects of insecticide application are crucially important among these strategies. Here, we consider a structured environment that consists of on-farm and off-farm fields where crops are planted periodically in on-farm fields during cultivation periods. We define the basic reproduction rate () of resistance as the expected number of offspring of a resistant individual divided by that of a susceptible individual under the condition that the proportion of resistance is extremely small; it is measured as the quantity per cycle of the cultivation period. We calculate using realistic dose-survival curves under a given fitness cost of resistance genes. The evolution of resistance occurs if and only if the value is larger than 0. Then, we propose a procedure for calculating the optimal design of rotational spraying that prevents the evolution of resistance, that is, the evolutionary stable strategy (ESS) for farmers, satisfying the mortality required for managing the abundance of insects. We consider the following controllable factors in calculating the optimal design: the dose of insecticide, the number of sprays, the number of different types of insecticides and potentially, the size of on-farm fields.     

Determination of the diameter of simulated human capillaries using shifted position-diffuse reflectance imaging

Multiple diseases are associated with a wide spectrum of microvascular dysfunctions, microangiopathies and microcirculation disorders. Monitoring the microcirculation could thus be useful to diagnose many local and systemic circulatory disorders and to supervise critically ill patients. Many of the scores currently available to help identify the condition of a microcirculation disorder are invasive or leave scope for interpretation. Thus, the present study aims to investigate with Monte-Carlo simulations (as numerical solutions of the radiative transfer equation) whether shifted position-diffuse reflectance imaging (SP-DRI), a non-invasive diagnostic technique, reveals information on the capillary diameter to assess the state of the microcirculation. To quantify the SP-DRI signal, the modulation parameter K is introduced. It proves to correlate almost perfectly with the capillary diameter (), making it a valid parameter for reliably assessing microcirculation. SP-DRI is emerging as an important milestone on the way to early and conveniently diagnosing microcirculation associated diseases.     

Developmental changes in oxygen consumption and hypoxia tolerance in the heat and hypoxia-adapted tabasco line of the Nile tilapia Oreochromis niloticus,with a survey of the metabolic literature for the genus Oreochromis

The genus Oreochromis is among the most popular of the tilapiine cichlid tribe for aquaculture. However, their temperature and hypoxia tolerance, if tested at all, is usually tested at temperatures of 20–25°C, rather than at the considerably higher temperatures of 30–35°C typical of tropical aquaculture. We hypothesized that both larvae and adults of the heat and hypoxia-adapted Tabasco-line of the Nile tilapia Oreochromis niloticus would be relatively hypoxia-tolerant. Oxygen consumption rate (), Q₁₀ and aquatic surface respiration (ASR) was measured using closed respirometry at 2 (c. 0.2 g), 30 (c. 2–5 g), 105 c. (10–15 g) and 240 (c. 250 g) days of development, at 25°C, 30°C and 35°C. at 30°C was inversely related to body mass: c. 90 μM O₂ g⁻¹/h in larvae down to c. 1 μM O₂ g⁻¹/h in young adults. Q₁₀ for was typical for fish over the range 25–35°C of 1.5–2.0. ASR was exhibited by 50% of the fish at pO₂ of 15–50 mmHg in a temperature-dependent fashion. However, the largest adults showed notable ASR only when pO₂ fell to below 10 mmHg. Remarkably, p_crit for was 12–17 mmHg at 25–30°C and still only 20–25 mmHg across development at 35°C. These values are among the lowest measured for teleost fishes. Noteworthy is that all fish maintain equilibrium, ventilated their gills and showed routine locomotor action for 10–20 min after ceased at near anoxia and when then returned to oxygenated waters, all fish survived, further indicating a remarkable hypoxic tolerance. Remarkably, data assembled for from >30 studies showed a > x2000 difference, which we attribute to calculation or conversion errors. Nonetheless, p_crit was very low for all Oreochromis sp. and lowest in the heat and hypoxia-adapted Tabasco line.     

Estimating the decision curve and its precision from three study designs

The decision curve plots the net benefit of a risk model for making decisions over a range of risk thresholds, corresponding to different ratios of misclassification costs. We discuss three methods to estimate the decision curve, together with corresponding methods of inference and methods to compare two risk models at a given risk threshold. One method uses risks (R) and a binary event indicator (Y) on the entire validation cohort. This method makes no assumptions on how well-calibrated the risk model is nor on the incidence of disease in the population and is comparatively robust to model miscalibration. If one assumes that the model is well-calibrated, one can compute a much more precise estimate of based on risks R alone. However, if the risk model is miscalibrated, serious bias can result. Case–control data can also be used to estimate if the incidence (or prevalence) of the event () is known. This strategy has comparable efficiency to using the full data, and its efficiency is only modestly less than that for the full data if the incidence is estimated from the mean of Y. We estimate variances using influence functions and propose a bootstrap procedure to obtain simultaneous confidence bands around the decision curve for a range of thresholds. The influence function approach to estimate variances can also be applied to cohorts derived from complex survey samples instead of simple random samples.     

Excess post‐hypoxic oxygen consumption in Atlantic cod Gadus morhua

Atlantic cod Gadus morhua experienced oxygen deficit () when exposed to oxygen levels below their critical level (c. 73% of p_crit) and subsequent excess post‐hypoxic oxygen consumption (C_EPHO) upon return to normoxic conditions, indicative of an oxygen debt. The mean ± s.e . C_EPHO: was 6·9 ± 1·5, suggesting that resorting to anaerobic energy production in severe hypoxia is energetically expensive.     

Anthropogenic Disturbance and Population Viability of Woodland Caribou in Ontario

One of the most challenging tasks in wildlife conservation and management is to clarify how spatial variation in land cover due to anthropogenic disturbance influences wildlife demography and long-term viability. To evaluate this, we compared rates of survival and population growth by woodland caribou (Rangifer tarandus caribou) from 2 study sites in northern Ontario, Canada that differed in the degree of anthropogenic disturbance because of commercial logging and road development, resulting in differences in predation risk due to gray wolves (Canis lupus). We used an individual-based model for population viability analysis (PVA) that incorporated adaptive patterns of caribou movement in relation to predation risk and food availability to predict stochastic variation in rates of caribou survival. Field estimates of annual survival rates for adult female caribou in the unlogged ( 0.90) and logged ( 0.76) study sites recorded during 2010–2014 did not differ significantly (P > 0.05) from values predicted by the individual-based PVA model (unlogged: = 0.87; logged: 0.79). Outcomes from the individual-based PVA model and a simpler stage-structured matrix model suggest that substantial differences in adult survival largely due to wolf predation are likely to lead to long-term decline of woodland caribou in the commercially logged landscape, whereas the unlogged landscape should be considerably more capable of sustaining caribou. Estimates of population growth rates (λ) for the 2010–2014 period differed little between the matrix model and the individual-based PVA model for the unlogged (matrix model = 1.01; individual-based model = 0.98) and logged landscape (matrix model = 0.88; individual-based model = 0.89). We applied the spatially explicit PVA model to assess the viability of woodland caribou across 14 woodland caribou ranges in Ontario. Outcomes of these simulations suggest that woodland caribou ranges that have experienced significant levels of commercial forestry activities in the past had annual growth rates <0.89, whereas caribou ranges that had not experienced commercial forestry operations had population growth rates >0.96. These differences were strongly related to regional variation in wolf densities. Our results suggest that increased wolf predation risk due to anthropogenic disturbance is of sufficient magnitude to cause appreciable risk of population decline in woodland caribou in Ontario. © 2020 The Authors. The Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.     

Quantitative genetics of temperature performance curves of Neurospora crassa

Earth's temperature is increasing due to anthropogenic CO emissions; and organisms need either to adapt to higher temperatures, migrate into colder areas, or face extinction. Temperature affects nearly all aspects of an organism's physiology via its influence on metabolic rate and protein structure, therefore genetic adaptation to increased temperature may be much harder to achieve compared to other abiotic stresses. There is still much to be learned about the evolutionary potential for adaptation to higher temperatures, therefore we studied the quantitative genetics of growth rates in different temperatures that make up the thermal performance curve of the fungal model system Neurospora crassa. We studied the amount of genetic variation for thermal performance curves and examined possible genetic constraints by estimating the G -matrix. We observed a substantial amount of genetic variation for growth in different temperatures, and most genetic variation was for performance curve elevation. Contrary to common theoretical assumptions, we did not find strong evidence for genetic trade-offs for growth between hotter and colder temperatures. We also simulated short-term evolution of thermal performance curves of N. crassa, and suggest that they can have versatile responses to selection.     

Relationship of current management practices to movements of Piping Plover broods in an Atlantic Coast population

Mobility of precocial chicks facilitates self-feeding and escape from predators, but also allows chicks to move into potentially dangerous areas. At Cape Hatteras National Seashore and Pea Island National Wildlife Refuge, North Carolina, precocial Piping Plovers (Charadrius melodus) are managed with vehicle and pedestrian exclusion buffers to reduce potential anthropogenic disturbance and mortality. From 2015 to 2018, we monitored 23 broods from hatching until fledging age (25 days), and recorded brood locations, chick behavior, and potentially disruptive predators, people, or vehicles. We estimated straight-line hourly movement rates relative to brood habitat selection, behavior, and potential disturbance stimuli, daily movement distances, and 95% minimum convex polygon home range areas of broods through the pre-fledging period. Daily brood movements , range = 0–327.3 m/d) varied by age and year. Hourly movements also varied , range = 0.04–1450.9 m/h), but were not well described by the factors we tested. Daily and hourly movements were generally shorter than current management buffer sizes, broods were always observed within protective buffers, and were rarely disturbed by human activity or possible predators. Home range sizes of broods ( increased as broods aged. Our results show that movements by plover broods can be variable and relatively unpredictable across temporal and spatial scales, but the low rate of brood disturbance suggests effective management of anthropogenic disturbance. We recommend that under current conditions, regular monitoring by managers should continue to ensure that the size and location of implemented buffers track actual brood use without exposing broods to risks from human beach users.     

Dual‐ and single‐shot susceptibility ratio measurements with circular polarizations in second‐harmonic generation microscopy

Polarization‐resolved second‐harmonic generation (P‐SHG) microscopy is a technique capable of characterizing nonlinear optical properties of noncentrosymmetric biomaterials by extracting the nonlinear susceptibility tensor components ratio , with z‐axis parallel and x‐axis perpendicular to the C₆ symmetry axis of molecular fiber, such as a myofibril or a collagen fiber. In this paper, we present two P‐SHG techniques based on incoming and outgoing circular polarization states for a fast extraction of : A dual‐shot configuration where the SHG circular anisotropy generated using incident right‐ and left‐handed circularly‐polarized light is measured; and a single‐shot configuration for which the SHG circular anisotropy is measured using only one incident circular polarization state. These techniques are used to extract the of myosin fibrils in the body wall muscles of Drosophila melanogaster larva. The results are in good agreement with values obtained from the double Stokes‐Mueller polarimetry. The dual‐ and single‐shot circular anisotropy measurements can be used for fast imaging that is independent of the in‐plane orientation of the sample. They can be used for imaging of contracting muscles, or for high throughput imaging of large sample areas.     

Precision of the age–length increments of three cyprinids: effects of fish number and sub‐sampling strategy

The effects of number of fish that are aged and scale sub‐sampling strategies on the precision of estimates of mean age–length increments from populations of Rutilus rutilus, Leuciscus leuciscus and Leuciscus cephalus were tested. Analyses used data derived from river fish communities in eastern England, U.K.. Regarding the number of fishes analysed in each age group, for each species and mean fork‐length increment at age, significant relationships were detected between sample size (n) and the coefficient of variation of the mean (Z) and mean length increment and measured variance (s²). This enabled calculation of the number of scales for producing a mean length increment at age according to . Outputs indicated that the number of scales requiring ageing increased substantially as precision increased, but with little variation between species per age category. Ageing between seven and 12 scales per age group would thus provide estimates at 10% precision. As the ages of fishes are not known in advance of scale ageing, the effect of scale sub‐sampling regime on precision was also tested using randomized strategies of 10 fish per 5 mm, five per 5 mm, three per 5 mm, 10 per 10 mm, five per 10 mm and three per 10 mm. These were applied to the datasets and the consequences of their reduction in the number of scales for precision were determined using . When compared to no sub‐sampling, three per 10 mm always significantly reduced data precision, whereas 10 per 5 mm never significantly reduced precision. These outputs can thus be applied to the design of fish sampling protocols where age and growth estimates are required, with the randomized sub‐sampling likely to be the most useful strategy.     

Important role of genetic drift in rapid polygenic adaptation

We analyzed a model to determine the factors that facilitate or limit rapid polygenic adaptation. This model includes population genetic terms of mutation and both directional and stabilizing selection on a highly polygenic trait in a diploid population of finite size. First, we derived the equilibrium distribution of the allele frequencies of the multilocus model by diffusion approximation. This formula describing the equilibrium allele frequencies as a mutation‐selection‐drift balance was examined by computer simulation using parameter values inferred for human height, a well‐studied polygenic trait. Second, assuming that a sudden environmental shift of the fitness optimum occurs while the population is in equilibrium, we analyzed the adaptation of the trait to the new optimum. The speed at which the trait mean approaches the new optimum increases with the equilibrium genetic variance. Thus, large population size and/or large mutation rate may facilitate rapid adaptation. Third, the contribution of an individual locus i to polygenic adaptation depends on the compound parameter , where is the effect size, the equilibrium frequency of the trait‐increasing allele of this locus, and . Thus, only loci with large values of this parameter contribute coherently to polygenic adaptation. Given that mutation rates are relatively small, this is more likely in large populations, in which the effects of drift are limited.