Similarity in seasonal flow regimes,not regional environmental classifications explain synchrony in brown trout population dynamics in France

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Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species

Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool‐seq data to generate a de novo genome assembly for mining exons, upon which Pool‐seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual‐based single nucleotide polymorphisms [SNPs]) and from mapping the Pool‐seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F_ST) between the two introduced populations exceeds that of the naturally sympatric populations (F_ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ ( ≈ 0.002 and  ≈ 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high‐quality reference assembly from a divergent species. We conclude that the Pool‐seq‐only approach can be suitable for detecting and quantifying genome‐wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.     

Distribution and growth of brown trout in pristine headwaters of Central Europe

The majority of stream-dwelling salmonid populations in Europe are affected by artificial stocking and the fragmentation of riverine ecosystems. The present study was performed in the unique pristine headwaters of the Otava River in the Elbe catchment area of the Czech Republic. The aim was to investigate the spatial distribution and individual growth pattern of brown trout, Salmo trutta, populations. Twenty sites in two main streams and their tributaries were sampled twice a year (spring and autumn) during the period 2005–2011. The sampling sites were grouped into fourteen so-called synchronised population units within the boundaries of three populations, according to analyses of synchrony in population abundance. The individual growth of juveniles (age-0, age-1) varied between all three spatial units (sampling sites, synchronised population units and populations), while the individual growth of adults (age-2 and older) did not. The distinctiveness regarding individual growth and demographic independence among the synchronised population units and populations indicates their suitability for use as population units for management purposes.     

THE MAINTENANCE OF POLYGENIC VARIATION IN FINITE POPULATIONS

Models of the maintenance of genetic variance in a polygenic trait have usually assumed that population size is infinite and that selection is weak. Consequently, they will overestimate the amount of variation maintained in finite populations. I derive approximations for the equilibrium genetic variance, in finite populations under weak stabilizing selection for triallelic loci and for an infinite “rare alleles” model. These are compared to results for neutral characters, to the “Gaussian allelic” model, and to Wright's approximation for a biallelic locus under arbitrary selection pressures. For a variety of parameter values, the three-allele, Gaussian, and Wrightian approximations all converge on the neutral model when population size is small. As expected, far less equilibrium genetic variance can be maintained if effective population size, N, is on the order of a few hundred than if N is infinite. All of the models predict that comparisons among populations with N less than about 10⁴ should show substantial differences in . While it is easier to maintain absolute when alleles interact to yield dominance or overdominance for fitness, less additivity also makes more susceptible to differences in N. I argue that experimental data do not seem to reflect the predicted degree of relationship between N and . This calls into question the ability of mutation-selection balance or simple balancing selection to explain observed . The dependence of on N could be used to test the adequacy of mutation-selection balance models.     

Gastric evacuation in endangered Russian sturgeon (Acipenser gueldenstaedtii): Effects of body and meal sizes

This study aimed to parameterize the effects of body and meal sizes on the gastric evacuation (GE) of farmed Russian sturgeon (Acipenser gueldenstaedtii) fed on live food (whiting fish) or commercial pellets. The radiography technique was used to monitor the evacuation of food from the stomach into the intestine at postprandial time. Acipenser gueldenstaedtii of different body sizes (total length ranged 82–105 cm) were fed on meal sizes ranged from 23 to 72 g composed of either live food or commercial pellets (had a 20% of BaSO₄ as a radiopaque material). The square root model was found to adequality describe the process of GE in A. gueldenstaedtii independently of meal type and size. The effects of fish size on GER was described by simple power model and can be summarized by , where ρ_L was 0.000053 for live food and 0.000062 for commercial pellets (estimated from combined GE data), S_t is stomach contents (g), L is fish total length (cm) and t is time (h). The results of this study will provide a useful tool to estimate the stomach fullness of A. gueldenstaedtii at postprandial time t. Such information should assess the feeding strategy to minimize feed wastage and optimize the fish growth.     

Effects of trophic levels (chlorophyll and phosphorous content) in three different water bodies (urban lake,reservoir and aquaculture facility) on gill morphology of Nile tilapia (Oreochromis niloticus)

Histological and ultrastructural analyses of gills were observed in Nile tilapia collected from three different waterbodies in southeast Brazil: an urban lake in a park in the city of São Paulo, a reservoir in a rural city, and a commercial aquaculture facility. These waterbodies were analyzed and classified as hypereutrophic, eutrophic, and supereutrophic, respectively, with 310.00, 94.00, 28.00 of phosphate ( μg L^?1) and 65.49, 24.95, 12.83 of chlorophyll (μg L^?1). A significant difference in the histological alterations index (HAI) was observed only in fish from the urban lake, with the presence of cell hypertrophy, hyperplasia, aneurism, and other alterations. When compared to the other groups, a large quantity of rodlet cells was also observed in the urban group. These results demonstrate the correlation of eutrophic states of water with gill morphology. Also discussed is the premise that large amounts of organic material dissolved in water can alter the morphology of the fish gills.     

Lincoln estimates of mallard (Anas platyrhynchos) abundance in North America

Estimates of range‐wide abundance, harvest, and harvest rate are fundamental for sound inferences about the role of exploitation in the dynamics of free‐ranging wildlife populations, but reliability of existing survey methods for abundance estimation is rarely assessed using alternative approaches. North American mallard populations have been surveyed each spring since 1955 using internationally coordinated aerial surveys, but population size can also be estimated with Lincoln's method using banding and harvest data. We estimated late summer population size of adult and juvenile male and female mallards in western, midcontinent, and eastern North America using Lincoln's method of dividing (i) total estimated harvest, , by estimated harvest rate, , calculated as (ii) direct band recovery rate, , divided by the (iii) band reporting rate, . Our goal was to compare estimates based on Lincoln's method with traditional estimates based on aerial surveys. Lincoln estimates of adult males and females alive in the period June–September were 4.0 (range: 2.5–5.9), 1.8 (range: 0.6–3.0), and 1.8 (range: 1.3–2.7) times larger than respective aerial survey estimates for the western, midcontinent, and eastern mallard populations, and the two population estimates were only modestly correlated with each other (western: r = 0.70, 1993–2011; midcontinent: r = 0.54, 1961–2011; eastern: r = 0.50, 1993–2011). Higher Lincoln estimates are predictable given that the geographic scope of inference from Lincoln estimates is the entire population range, whereas sampling frames for aerial surveys are incomplete. Although each estimation method has a number of important potential biases, our review suggests that underestimation of total population size by aerial surveys is the most likely explanation. In addition to providing measures of total abundance, Lincoln's method provides estimates of fecundity and population sex ratio and could be used in integrated population models to provide greater insights about population dynamics and management of North American mallards and most other harvested species.     

A new method of sequential sampling to classify populations relative to a critical density

A method of sequential sampling for grading population level in relation to a critical density is proposed. The method is based on the relationship and can be used without restrictions on the distribution patterns. The formulae for simple random sampling as well as for two-stage sampling are given.     

A new proposal for measurement of the adjusted mean crowding through consideration of size variability in habitat units

The mean crowding has previously been measured under the assumption that all quadrats or habitat units have the same size, even though the actual habitat units such as seeds or leaves are generally variable in size. A new index, ‘adjusted mean crowding’, which is adjusted for this variability can be given as where Q is the total number of habitat units in the whole area, x_j the number of individuals in the jth habitat unit, and a_j is defined as the ‘relative size’ of the jth habitat unit, i.e. a_y=y_y/(∑y_j/Q) where y_j is the actually measured size of the jth habitat unit. It is expected that and for the uniform distribution and the random distribution ‘per unit size’, respectively. The comparison between and regressions ( analysis) for the egg distribution pattern of Callosobruchus chinensis or C. maculatus proved that the regression is biased by a positive correlation between the egg number per seed and seed size rather than by a density-dependent change in the ovipositional behavior.     

Anaesthesia and transport of juvenile tambaqui Colossoma macropomum (Cuvier, 1818) with tricaine methane‐sulphonate: Implications on secondary and oxidative stress responses

The aim of this study was to evaluate the anaesthetic efficacy and the effect of sedation with tricaine (TMS^®), also known as MS‐222, on secondary and oxidative stress parameters in juvenile tambaqui, Colossoma macropomum transported in hyperoxia for 2, 6 and 10 hr. Juveniles were placed in aquaria containing six different concentrations of buffered tricaine (150, 180, 210, 240, 270 and 300 mg/L) and the times for anaesthesia induction and recovery determined. Fish transported in hyperoxic conditions were investigated for glycemia, ionic concentration (K⁺, Ca⁺⁺, Na⁺) and osmolality, haematocrit (Ht) and haemoglobin concentration (Hb), partial pressure of gases (pCO₂ and pO₂), pH and bicarbonate concentration () in whole blood collected from caudal vasculature. Total antioxidant capacity against peroxyl radicals (ACAP), glutathione‐S‐transferase (GST) activity and lipid peroxidation levels (TBARS) were investigated in gills, brain and liver. All concentrations of TMS^® induced deep anaesthesia in juvenile tambaqui in this study. A concentration of 240 mg/L of TMS^® was sufficient to induce rapid anaesthesia (<3 min) with uneventful recovery (<5 min). In light of the secondary and oxidative stress responses of fish transported using TMS^®, which were generally not significantly different compared to responses of fish transported in anaesthetic‐free water, sedation with 20 mg/L is not advantageous and therefore is dispensable for the transport of this species for up to 10 hr.     

Effects of distance on detectability of Arctic waterfowl using double‐observer sampling during helicopter surveys

Aerial survey is an important, widely employed approach for estimating free‐ranging wildlife over large or inaccessible study areas. We studied how a distance covariate influenced probability of double‐observer detections for birds counted during a helicopter survey in Canada’s central Arctic. Two observers, one behind the other but visually obscured from each other, counted birds in an incompletely shared field of view to a distance of 200 m. Each observer assigned detections to one of five 40‐m distance bins, guided by semi‐transparent marks on aircraft windows. Detections were recorded with distance bin, taxonomic group, wing‐flapping behavior, and group size. We compared two general model‐based estimation approaches pertinent to sampling wildlife under such situations. One was based on double‐observer methods without distance information, that provide sampling analogous to that required for mark–recapture (MR) estimation of detection probability, , and group abundance, , along a fixed‐width strip transect. The other method incorporated double‐observer MR with a categorical distance covariate (MRD). A priori, we were concerned that estimators from MR models were compromised by heterogeneity in due to un‐modeled distance information; that is, more distant birds are less likely to be detected by both observers, with the predicted effect that would be biased high, and biased low. We found that, despite increased complexity, MRD models (ΔAICc range: 0–16) fit data far better than MR models (ΔAICc range: 204–258). However, contrary to expectation, the more naïve MR estimators of were biased low in all cases, but only by 2%–5% in most cases. We suspect that this apparently anomalous finding was the result of specific limitations to, and trade‐offs in, visibility by observers on the survey platform used. While MR models provided acceptable point estimates of group abundance, their far higher stranded errors (0%–40%) compared to MRD estimates would compromise ability to detect temporal or spatial differences in abundance. Given improved precision of MRD models relative to MR models, and the possibility of bias when using MR methods from other survey platforms, we recommend avian ecologists use MRD protocols and estimation procedures when surveying Arctic bird populations.     

Body shape and robustness response to water flow during development of brown trout Salmo trutta parr

Domesticated brown trout Salmo trutta parr were subjected to increased, variable flow under controlled experimental conditions. Using geometric morphometric analyses, (a mass–length index) and caudal fin area–body length ratio, this study assessed morphological responses in lateral body depth, growth and robustness and propulsive potential, respectively, of parr over the course of 32 weeks. Geometric morphometric analyses did not reveal an effect of exercise on either lateral body depth or caudal fin area. However, improved overall robustness and growth trajectories in exercised parr showed a positive adaptive response to the enriched habitat. Exercise and habitat heterogeneity thus have the potential to improve survivability of domesticated salmonids in the wild.     

Fine‐scale frequency differentiation along a herbivory gradient in the trichome dimorphism of a wild Arabidopsis

Geographic variation is commonly observed in plant resistance traits, where plant species might experience different selection pressure across a heterogeneous landscape. Arabidopsis halleri subsp. gemmifera is dimorphic for trichome production, generating two morphs, trichome‐producing (hairy) and trichomeless (glabrous) plants. Trichomes of A. halleri are known to confer resistance against the white butterfly, cabbage sawfly, and brassica leaf beetle, but not against flea beetles. We combined leaf damage, microclimate, and microsatellite loci data of 26 A. halleri populations in central Japan, to explore factors responsible for fine‐scale geographic variation in the morph frequency. We found that hairy plants were less damaged than glabrous plants within populations, but the among‐site variation was the most significant source of variation in the individual‐level damage. Fixation index () of a putative trichome locus exhibited a significant divergence along population‐level damage with an exception of an outlier population, inferring the local adaptation to herbivory. Notably, this outlier was a population wherein our previous study reported a balancing role of the brassica leaf beetle Phaedon brassicae on the morph frequency. This differentiation of the trichome locus was unrelated to neutral genetic differentiation (evaluated by of microsatellite loci) and meteorological factors (including temperature and solar radiation). The present findings, combined with those of our previous work, provide suggestive evidence that herbivore‐driven divergence and occasional outbreak of a specific herbivore have jointly contributed to the ecogeographic pattern in the frequency of two morphs.     

Identifying important conservation areas for the clouded leopard Neofelis nebulosa in a mountainous landscape: Inference from spatial modeling techniques

The survival of large carnivores is increasingly precarious due to extensive human development that causes the habitat loss and fragmentation. Habitat selection is influenced by anthropogenic as well as environmental factors, and understanding these relationships is important for conservation management. We assessed the environmental and anthropogenic variables that influence site use of clouded leopard Neofelis nebulosa in Bhutan, estimated their population density, and used the results to predict the species’ site use across Bhutan. We used a large camera‐trap dataset from the national tiger survey to estimate for clouded leopards, for the first time in Bhutan, (1) population density using spatially explicit capture–recapture models and (2) site‐use probability using occupancy models accounting for spatial autocorrelation. Population density was estimated at (0.10 SD) and (0.12 SE) per 100 km². Clouded leopard site use was positively associated with forest cover and distance to river while negatively associated with elevation. Mean site‐use probability (from the Bayesian spatial model) was (0.076 SD). When spatial autocorrelation was ignored, the probability of site use was overestimated, (0.066 SD). Predictive mapping allowed us to identify important conservation areas and priority habitats to sustain the future of these elusive, ambassador felids and associated guilds. Multiple sites in the south, many of them outside of protected areas, were identified as habitats suitable for this species, adding evidence to conservation planning for clouded leopards in continental South Asia.     

Synchronized mammalian cell culture: Part I—A physical strategy for synchronized cultivation under physiological conditions

Conventional analysis and optimization procedures of mammalian cell culture processes mostly treat the culture as a homogeneous population. Hence, the focus is on cell physiology and metabolism, cell line development, and process control strategy. Impact on cultivations caused by potential variations in cellular properties between different subpopulations, however, has not yet been evaluated systematically. One main cause for the formation of such subpopulations is the progress of all cells through the cell cycle. The interaction of potential cell cycle specific variations in the cell behavior with large‐scale process conditions can be optimally determined by means of (partially) synchronized cultivations, with subsequent population resolved model analysis. Therefore, it is desirable to synchronize a culture with minimal perturbation, which is possible with different yield and quality using physical selection methods, but not with frequently used chemical or whole‐culture methods. Conventional nonsynchronizing methods with subsequent cell‐specific, for example, flow cytometric analysis, can only resolve cell‐limited effects of the cell cycle. In this work, we demonstrate countercurrent‐flow centrifugal elutriation as a useful physical method to enrich mammalian cell populations within different phases of a cell cycle, which can be further cultivated for synchronized growth in bioreactors under physiological conditions. The presented combined approach contrasts with other physical selection methods especially with respect to the achievable yield, which makes it suitable for bioreactor scale cultivations. As shown with two industrial cell lines (CHO‐K1 and human AGE1.HN), synchronous inocula can be obtained with overall synchrony degrees of up to 82% in the G1 phase, 53% in the S phase and 60% in the phase, with enrichment factors ( ) of 1.71, 1.79, and 4.24 respectively. Cells are able to grow with synchrony in bioreactors over several cell cycles. This strategy, combined with population‐resolved model analysis and parameter extraction as described in the accompanying paper, offers new possibilities for studies of cell lines and processes at levels of cell cycle and population under physiological conditions. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:165–174, 2015     

ISOLATION BY DISTANCE IN EQUILIBRIUM AND NON-EQUILIBRIUM POPULATIONS

It is shown that for allele frequency data a useful measure of the extent of gene flow between a pair of populations is , which is the estimated level of gene flow in an island model at equilibrium. For DNA sequence data, the same formula can be used if F_ST is replaced by N_ST. In a population with restricted dispersal, analytic theory shows that there is a simple relationship between M? and geographic distance in both equilibrium and non-equilibrium populations and that this relationship is approximately independent of mutation rate when the mutation rate is small. Simulation results show that with reasonable sample sizes, isolation by distance can indeed be detected and that, at least in some cases, non-equilibrium patterns can be distinguished. This approach to analyzing isolation by distance is used for two allozyme data sets, one from gulls and one from pocket gophers.     

Integrating distance sampling with minimum counts to improve monitoring

Minimum counts are commonly used to estimate population size and trend for wildlife conservation and management; however, the scope of inference based on such data is limited by untestable assumptions regarding the detection process. Alternative approaches, such as distance sampling, occupancy surveys, and repeated counts, can be employed to produce detection-corrected estimates of population parameters. Unfortunately, these approaches can be more complicated and costly to implement, potentially limiting their use. We explored a conceptual framework linking datasets collected at different spatial scales under different survey designs, with the goal of improving inference. Specifically, we link landscape-scale distance sampling surveys with local-scale minimum counts in an integrated modeling framework to estimate mountain goat (Oreamnos americanus) abundance at both the local and regional scale in south-central Alaska, USA, and provide an estimate of detection probability (i.e., sightability) for the minimum counts. Estimated sightability for the minimum count surveys was 0.67 (95% credible interval [CrI] = 0.52–0.83) and abundance for the entire area was 5,600 goats (CV = 9%), both in broad agreement with estimates from previous studies. Abundance estimates at the local scale (i.e., individual min. count unit) were reasonably precise ( = 18%), suggesting the integrated approach can increase the amount of information produced at both spatial scales by linking minimum count approaches with more rigorous survey designs. We propose that our integrated approach may be implemented in the context of a modified split-panel monitoring design by altering survey protocols to include frequent minimum counts within local count units and intermittent but more rigorous survey designs with inference to the entire study area or population of interest. Doing so would provide estimates of abundance with appropriate measures of uncertainty at multiple spatial scales, thereby improving inference for population monitoring and management. © 2019 The Wildlife Society.     

Contemporary effective population and metapopulation size (Ne and meta‐Ne): comparison among three salmonids inhabiting a fragmented system and differing in gene flow and its asymmetries

We estimated local and metapopulation effective sizes ( and meta‐) for three coexisting salmonid species (Salmo salar, Salvelinus fontinalis, Salvelinus alpinus) inhabiting a freshwater system comprising seven interconnected lakes. First, we hypothesized that might be inversely related to within‐species population divergence as reported in an earlier study (i.e., F_ST: S. salar> S. fontinalis> S. alpinus). Using the approximate Bayesian computation method implemented in ONeSAMP, we found significant differences in () between species, consistent with a hierarchy of adult population sizes (). Using another method based on a measure of linkage disequilibrium (LDNE: ), we found more finite values for S. salar than for the other two salmonids, in line with the results above that indicate that S. salar exhibits the lowest among the three species. Considering subpopulations as open to migration (i.e., removing putative immigrants) led to only marginal and non‐significant changes in , suggesting that migration may be at equilibrium between genetically similar sources. Second, we hypothesized that meta‐ might be significantly smaller than the sum of local s (null model) if gene flow is asymmetric, varies among subpopulations, and is driven by common landscape features such as waterfalls. One ‘bottom‐up’ or numerical approach that explicitly incorporates variable and asymmetric migration rates showed this very pattern, while a number of analytical models provided meta‐ estimates that were not significantly different from the null model or from each other. Our study of three species inhabiting a shared environment highlights the importance and utility of differentiating species‐specific and landscape effects, not only on dispersal but also in the demography of wild populations as assessed through local s and meta‐s and their relevance in ecology, evolution and conservation.     

RISK OF POPULATION EXTINCTION FROM FIXATION OF NEW DELETERIOUS MUTATIONS

The fixation of new deleterious mutations is analyzed for a randomly mating population of constant size with no environmental or demographic stochasticity. Mildly deleterious mutations are far more important in causing loss of fitness and eventual extinction than are lethal and semilethal mutations in populations with effective sizes, N_e, larger than a few individuals. If all mildly deleterious mutations have the same selection coefficient, s against heterozygotes and 2s against homozygotes, the mean time to extinction, , is asymptotically proportional to for 4N_es > 1. Nearly neutral mutations pose the greatest risk of extinction for stable populations, because the magnitude of selection coefficient that minimizes is about ? = 0.4/N_e. The influence of variance in selection coefficients among mutations is analyzed assuming a gamma distribution of s, with mean and variance . The mean time to extinction increases with variance in selection coefficients if is near ?, but can decrease greatly if is much larger than ?. For a given coefficient of variation of , the mean time to extinction is asymptotically proportional to for . When s is exponentially distributed, (c = 1) is asymptotically proportional to . These results in conjunction with data on the rate and magnitude of mildly deleterious mutations in Drosophila melanogaster indicate that even moderately large populations, with effective sizes on the order of N_e = 10³, may incur a substantial risk of extinction from the fixation of new mutations.     

Detection of,and sampling procedures for,the citrus blackfly in urban southern Florida

The dispersion pattern of the citrus blackfly (CBF)Aleurocanthus woglumi Ashby on urban citrus trees was studied in southern Florida. There was no usable correlation (r²=0.41) between the % of older leaves infested with CBF versus that on the newest mature flush, but there was a strong correlation (r²=0.87) between the % of leaves in the newest mature flush infested with CBF and log_e, where is the number of egg spirals of CBF/leaf on the same leaves. CBF egg spirals are distributed among the flushes in groups rather than singly and the flushes are not over-dispersed. Visual surveys proved superior to sticky traps for the detection of CBF at low densities (<5% leaves infested) on citrus trees in an urban setting. A sampling procedure is described herein based upon visual surveys.