Can measures of prey availability improve our ability to predict the abundance of large marine predators?

Apex marine predators can structure marine communities, so factors underlying their abundance are of broad interest. However, such data are almost completely lacking for large sharks. We assessed the relationship between tiger shark abundance, water temperature, and the availability of a variety of known prey over 5 years in Western Australia. Abundance of sharks in four size categories and the density of prey (cormorants, dugongs, sea snakes, sea turtles) were indexed using daily catch rates and transects, respectively. Across all sizes, thermal conditions were a determinant of abundance, with numerical peaks coinciding with periods of high water temperature. However, for sharks exceeding 300 cm total length, the inclusion of dugong density significantly improved temperature-based models, suggesting that use of particular areas by large tiger sharks is influenced by availability of this sirenian. We conclude that large marine predator population models may benefit from the inclusion of measures of prey availability, but only if such measures consider prey types separately and account for ontogenetic shifts in the diet of the predator in question. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Which factors influence the ability of a computational model to predict the in vivo deformation behaviour of skeletal muscle?

Deep tissue injury (DTI) is a severe form of pressure ulcer where tissue damage starts in deep tissues underneath intact skin. Tissue deformation may play an important role in the aetiology, which can be investigated using an experimental–numerical approach. Recently, an animal-specific finite element model has been developed to simulate experiments in which muscle tissue was compressed with an indenter. In this study, the material behaviour and boundary conditions were adapted to improve the agreement between model and experiment and to investigate the influence of these adaptations on the predicted strain distribution. The use of a highly nonlinear material law and including friction between the indenter and the muscle both improved the quality of the model and considerably influenced the estimated strain distribution. With the improved model, the required sample size to detect significant differences between loading conditions can be diminished, which is clearly relevant in experiments involving animals.     

Does the strength of cross‐ecosystem trophic cascades vary with ecosystem size? A test using a natural microcosm

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A further cost for the sicker sex? Evidence for male‐biased parasite‐induced vulnerability to predation

Males are typically the sicker sex. Data from multiple taxa indicate that they are more likely to be infected with parasites, and are less “tolerant,” or less able to mitigate the fitness costs of a given infection, than females. One cost of infection for many animals is an increased probability of being captured by a predator. A clear, hitherto untested, prediction is therefore that this parasite‐induced vulnerability to predation is more pronounced among males than females. We tested this prediction in the sexually size dimorphic guppy, Poecilia reticulata, in which females are typically larger than males. We either sham or experimentally infected guppies with Gyrodactylus turnbulli, elicited their escape response using an established protocol and measured the distance they covered during 60 ms. To discriminate between the effects of body size and those of other inherent sex differences, we size‐matched fish across treatment groups. Infection with G. turnbulli reduced the distance covered during the escape response of small adults by 20.1%, whereas that of large fish was unaffected. This result implies that parasite‐induced vulnerability to predation is male‐biased in the wild: although there was no difference in escape response between our experimentally size‐matched groups of males and females, males are significantly smaller across natural guppy populations. These results are consistent with Bateman's principle for immunity: Natural selection for larger body sizes and longevity in females seems to have resulted in the evolution of increased infection tolerance. We discuss the potential implications of sex‐ and size‐biased parasite‐induced vulnerability to predation for the evolutionary ecology of this host–parasite interaction in natural communities.     

Cryptic speciation in the Acari: a function of species lifestyles or our ability to separate species?

There are approximately 55,000 described Acari species, accounting for almost half of all known Arachnida species, but total estimated Acari diversity is reckoned to be far greater. One important source of currently hidden Acari diversity is cryptic speciation, which poses challenges to taxonomists documenting biodiversity assessment as well as to researchers in medicine and agriculture. In this review, we revisit the subject of biodiversity in the Acari and investigate what is currently known about cryptic species within this group. Based on a thorough literature search, we show that the probability of occurrence of cryptic species is mainly related to the number of attempts made to detect them. The use of, both, DNA tools and bioassays significantly increased the probability of cryptic species detection. We did not confirm the generally-accepted idea that species lifestyle (i.e. free-living vs. symbiotic) affects the number of cryptic species. To increase detection of cryptic lineages and to understand the processes leading to cryptic speciation in Acari, integrative approaches including multivariate morphometrics, molecular tools, crossing, ecological assays, intensive sampling, and experimental evolution are recommended. We conclude that there is a demonstrable need for future investigations focusing on potentially hidden mite and tick species and addressing evolutionary mechanisms behind cryptic speciation within Acari.     

What factors potentially influence the ability of phylogenetic distance to predict trait dispersion in a temperate forest?

Although phylogenetic‐based approaches have been frequently used to infer ecological processes, they have been increasingly criticized in recent years. To date, the factors that affect phylogenetic signals and further the ability of phylogenetic distance to predict trait dispersion have been assumed but not empirically tested. Therefore, we investigate which factors potentially influence the ability of phylogenetic distance to predict trait dispersion. We quantified the phylogenetic and trait dispersions across size classes and spatial scales in a 9‐ha old‐growth temperate forest dynamics plot in northeastern China. Phylogenetic signals at the community level were generally lower than those at the species pool level, and phylogenetically clustered communities showed lower phylogenetic signals than did overdispersed communities. This pattern might explain the other three findings of our study. First, phylogenetically overdispersed communities performed better at predicting trait dispersion than did clustered communities. Second, the mean pairwise distance (MPD)‐based metric exhibited a stronger correlation with trait dispersion than did the mean nearest taxon distance (MNTD)‐based metric. Finally, the MNTD‐based metric showed that the prediction accuracy for trait dispersion decreased with increasing spatial scales, whereas its effects were weak on the MPD‐based metric. In addition, phylogeny could not determine the dispersions of all functional axes but was able to predict certain traits depending on whether they were evolutionarily conserved. These results were conserved when we removed the effects of space and environment. Our findings highlighted that using phylogenetic distance as a proxy of trait similarity might work in a temperate forest depending on the species in local communities sampled from total pool as well as the traits measured. Utilizing these rules, we should rethink the conclusions of previous studies that were based on phylogenetic‐based approaches.     

Do zwitterions contribute to the ionic strength of a solution?

Capillary electrophoresis has been used to determine whether zwitterions contribute to the ionic strength of a solution, by measuring the mobility of a double-stranded DNA oligomer in cacodylate-buffered solutions containing various concentrations of the ionic salt tetraethylammonium chloride (TEA(+)Cl(-)) or the zwitterion tricine(+/-). The mobility of the DNA decreased as the square root of ionic strength, as expected from the Debye-Hückel-Onsager theory of electrophoresis, when TEA(+)Cl(-) was added to the buffer. However, the mobility was independent of the concentration of added tricine(+/-). Hence, zwitterions do not contribute to the ionic strength of a solution.     

Does the location of a mutation determine the ability to form amyloid fibrils?

We have previously reported studies of fibril formation by a set of protein G B1 domain (beta1) variants, with mutations located around the central parallel beta-strands. In this study, we designed multiple mutations in the edge strands of beta1 to create proteins with a stability range comparable to that of the set of central mutants. All the edge variants are able to form amyloid fibrils when they are incubated at their melting temperatures. This result suggests that overall protein stability is the key determinant for amyloid formation and not the specific location of destabilizing mutations. The edge strand and variants cross-seed with each other and with members of the central variant family. Interesting fibrillar morphology was observed in some cross-seeding cases and its implications for a better understanding of nucleation and elongation events are discussed.     

Use of meta‐analysis to predict degradation of carbaryl and malathion in freshwater for exposure assessment

Carbaryl (1‐naphthyl methylcarbamate) and malathion (diethyl mercaptosuccinate, S‐ester with O, O‐dimethyl phosphorodithioate) are insecticides used to control grasshopper infestations on rangeland. Insecticides used to control grasshopper infestations pose a hazard to aquatic organisms because although no‐spray buffer zones are observed around aquatic habitats, pesticide may be deposited by drift or mobilized from upland areas by runoff. A number of processes may affect the fate of carbaryl and malathion in the aquatic environment, but no method is available for estimating degradation over the range of conditions that occur in the field. We used results of published studies in meta‐analyses to estimate degradation models that predict half‐life of carbaryl and malathion in freshwater over temperature and pH ranges relevant to western grasshopper‐management programs. Estimated degradation models were:

In (half‐life carbaryl) = 24.3 ‐ 2.36(pH) ‐ 0.0788(t)

and In (half‐life malathion) = 5.98 + 2.84(pH) ‐ 0.326(pH ²) ‐ 0.202(t) + 0.00135(t ²)

where half‐life has units of hours, and temperature (t) has units °C. Both models accounted for a significant amount of total variation (P<0.0001) and had r²>0.97. Accuracy of these degradation models was evaluated by comparing predicted degradation of carbaryl and malathion to field and laboratory data. We suggest that use of these degradation models be restricted to conditions where water has 7 ≤. pH ≤. 10 for carbaryl, and 7 ≤ pH ≤ 8.2 for malathion.     

Does predation by the introduced rainbow trout cascade down to detritus and algae in a forested small stream in Patagonia?

Cascade effects of an exotic predator, the rainbow trout (Oncorhynchus mykiss), on periphyton and leaf litter were analysed in a headwater, forested stream of Andean Patagonia (Argentina). We conducted seasonal field sampling and two field experiments measuring leaf litter mass, periphyton biomass and macroinvertebrate biomass in relation to the presence and absence of rainbow trout. In the field survey, the presence of trout influenced resource mass: leaf litter (60% decrease in summer, P = 0.024) and periphyton (tenfold increase in chlorophyll a, P < 0.001) were affected, which were mediated by a decrease in the biomass of shredders (95% decrease in summer, P < 0.001) and scrapers (90% decrease, P < 0.001). There was an effect on leaf litter biomass only in the summer, whereas fish presence reduced periphyton biomass all year except in the winter. In the field experiments, we observed that leaf litter breakdown and periphyton development were effectively controlled by consumers in the absence of fish. In contrast, the presence of fish caused a release of herbivory and detritivory resulting in a significant increase in periphyton biomass (100% increase, P < 0.001) and a decrease in leaf litter decay (40% decrease, P < 0.001). Our results suggest that in low order streams and in the presence of visual predators, trophic cascades may operate both on detritus and algae, but with different timing.     

Evolution of trophic transmission in parasites: the need to reach a mating place?

Although numerous parasite species have a simple life cycle (SLC) and complete their life cycle in one host, there are other parasite species that exploit several host species successively. From an evolutionary perspective, understanding the mix of adaptive and contingent forces shaping the transition from an ancestral single‐host state to such a complex life cycle (CLC) has proved an intriguing challenge. In this paper, we propose a new hypothesis, which states that CLCs involving trophic transmission (i.e. transmission to a predator) evolved because they are an efficient way for parasites to meet a sexual partner, assuming that selective benefits are associated with cross‐fertilization. Predators that eat a lot of prey in a relatively short time interval act to concentrate isolated parasites. We use an optimality model to develop our hypothesis and discuss further directions of potential research.     

Nickel is a specific antagonist for the catabolism of activated α2-macroglobulin

The multifunctional low density lipoprotein receptor-related protein/α₂-macroglobulin receptor (LRP) binds and degrades several ligands involved in protease and lipoprotein metabolism. We previously reported that nickel (Ni²⁺) specifically inhibits the binding of activated α₂-macroglobulin (α₂M^*) at 4°C to LRP and had no effect on the binding of other ligands to the receptor (Hussain et al. (1995) Biochem. 34, 16074–16081). In the current investigation, we have examined the effect of Ni²⁺ on the catabolism of ¹²⁵I-labeled α₂M^*, receptor-associated protein (RAP) and lactoferrin at physiologic temperatures by fibroblasts. Nickel completely inhibited the degradation of α₂M^* over a wide range of concentrations (0.3–2.4 nM); 50% inhibition for the degradation of 1.2 nM α₂M^* was observed at 0.5 mM Ni²⁺. Furthermore, nickel inhibited the binding, internalization and degradation of ¹²⁵I-α₂M^* in a dose- and time- dependent manner. In contrast, the degradation of several concentrations of ¹²⁵I-RAP by fibroblasts was not affected by different amounts of Ni²⁺ for various times. Similarly, Ni²⁺ did not inhibit the degradation of lactoferrin either before or after treating the cells with heparitinase to remove cell-surface proteoglycans. The degradation of lactoferrin was, however, inhibited by the RAP indicating that lactoferrin degradation was mediated by the LRP. These data suggest that Ni²⁺ is a specific inhibitor for the degradation of α₂M^*.     

Accounting for Partial Sleep Deprivation and Cumulative Sleepiness in the Three‐Process Model of Alertness Regulation

Mathematical models designed to predict alertness or performance have been developed primarily as tools for evaluating work and/or sleep‐wake schedules that deviate from the traditional daytime orientation. In general, these models cope well with the acute changes resulting from an abnormal sleep but have difficulties handling sleep restriction across longer periods. The reason is that the function representing recovery is too steep—usually exponentially so—and with increasing sleep loss, the steepness increases, resulting in too rapid recovery. The present study focused on refining the Three‐Process Model of alertness regulation. We used an experiment with 4 h of sleep/night (nine participants) that included subjective self‐ratings of sleepiness every hour. To evaluate the model at the individual subject level, a set of mixed‐effect regression analyses were performed using subjective sleepiness as the dependent variable. These mixed models estimate a fixed effect (group mean) and a random effect that accounts for heterogeneity between participants in the overall level of sleepiness (i.e., a random intercept). Using this technique, a point was sought on the exponential recovery function that would explain maximum variance in subjective sleepiness by switching to a linear function. The resulting point explaining the highest amount of variance was 12.2 on the 1–21 unit scale. It was concluded that the accumulation of sleep loss effects on subjective sleepiness may be accounted for by making the recovery function linear below a certain point on the otherwise exponential function.     

Accounting for the capacity of common and rare species to contribute to diversity spatial patterns: Is it a sampling issue or a biological effect?

The contribution of common species to overall species richness in many cases is greater than that of rare species. However, the explanation of this phenomenon remains vague. One hypothesis is that this is a sampling issue and not a biological one. Therefore standardization methods like the information index and empirical variance have been proposed. But, these standardizations do not explicitly compare the significance of the dataset size of the common and rare sub-assemblage. Here, we investigate the role of dataset size in accounting for the capacity of common and rare species to contribute to diversity spatial patterns. We used a dataset of 5148 vascular plant species recorded in 16,439 sample plots in the Greek Natura 2000 network. Species were ranked according to the number of sample plots they occupied in ascending (rare to common), descending (common to rare) and random order. We analyzed the correlation between the richness of each sub-assemblage and total species richness. When comparing among sub-assemblages with equal number of species, common species are clearly the better predictors of total species richness. But, when comparing among sub-assemblages with equal number of occurrence records, the patterns changed. Common and rare species contribution to the overall richness pattern was comparable, with rare species contributing slightly less than widespread species in some cases and the opposite in other cases. However in all cases, sub-assemblages of random species remarkably outperformed the equal sized sub-assemblages of common or rare species. Our results suggest that common and rare species are biased samples of the community and that equal sized random samples are more representative; thus the greater contribution of common species than rare species to biodiversity patterns might be more a sampling issue than a biological effect of commonness or rarity.     

Toxicological screening of chemical emissions from municipal solid waste landfills. application of a predictive framework to a state‐of‐the‐art facility

A screening‐level risk assessment was used to identify chemicals of potential health concern emitted during the normal operation of an hypothetical state‐of‐the‐art municipal solid waste landfill. Data on the amount of contaminants (carcinogens, non‐carcinogenic systemic toxicants, odorous compounds, and particulate‐bound metals) were obtained from existing facilities and used to estimate ground‐level air concentrations of airborne chemicals at the point of maximum impact (property line) and at year 20 (year of maximum emissions from the landfill). Concentrations of leachate components present in the corresponding underlying aquifer were also estimated. Intakes of chemicals experienced by a series of human receptors were then computed using either single‐media or multi‐media algorithms. Carcinogens of concern were selected as those contributing to a lifetime excess cancer risk (LECR) greater than 10^‐6; for non‐carcinogenic systemic toxicants and odorous volatiles an Exposure Ratio (ER=intake or concentration/RfD, RfC, odor threshold) greater than 0.1 was used as cut‐off. The results obtained identified a final set of air emission components (n = 25) constituted mainly of carcinogenic and odorous substances whereas 2 leachate components were retained. Additional analysis using more refined risk‐based approaches are necessary to verify the relevance of these projections.     

Time to the MRCA of a sample in a Wright–Fisher model with variable population size

Determining the expected distribution of the time to the most recent common ancestor of a sample of individuals may deliver important information about the genetic markers and evolution of the population. In this paper, we introduce a new recursive algorithm to calculate the distribution of the time to the most recent common ancestor of the sample from a population evolved by any conditional multinomial sampling model. The most important advantage of our method is that it can be applied to a sample of any size drawn from a population regardless of its size growth pattern. We also present a very efficient method to implement and store the genealogy tree of the population evolved by the Galton–Watson process. In the final section we present results applied to a simulated population with a single bottleneck event and to real populations of known size histories.     

Monitoring population size of mammals using a spotlight-count-based abundance index: How to relate the number of counts to the precision?

Abundance indices are widely used to study changes in population size in wildlife management. However, a truly appropriate measure of precision is often lacking in such studies. Statistically, the two crucial issues regarding the use of an abundance index are sampling and observability, which lead one to consider two kinds of errors, namely sampling and observation errors. The purpose of this methodological paper is to relate the number of counts to the precision of an abundance index by introducing the Hansen–Hurwitz–Bershad model which takes into account both sampling and observation errors. We illustrate this statistical approach in the case of a European rabbit (Oryctolagus cuniculus) abundance index based on spotlight counts, for two fixed spatial sampling units located in different ecological contexts. We show (i) that the usual sampling variance estimator is a downward-biased estimator of the total variance of the abundance index, (ii) that the bias of the usual variance estimator does not decrease when increasing the sampling size, (iii) that correlated observation errors may have a dramatic impact on the total variance, especially when the sampling size increases. The acknowledgement that the (pure) sampling variance underestimates the total variance because of observation errors is a statistical result that is neither widely known nor appreciated by most wildlife ecologists. The magnitude of this underestimation may be important and, therefore, observation errors cannot be always considered as a priori negligible in assessing the precision of a count-based abundance index.