The effect of prior experience on a prey’s current perceived risk

The prior experience of prey may influence how they assess the level of predation risk associated with an information source. Here, I present the results from a set of experiments that demonstrate how the prior experience of green frog (Rana clamitans) tadpoles can influence their risk assessment during exposure to the chemical cue of predatory larval dragonflies (Anax spp.) consuming conspecific tadpoles. At the short-term scale, green frog tadpoles perceived a higher level of risk when consecutive cue exposures overlapped, but only when the total chemical cue concentration was weak. Weaker chemical cue concentrations may be less reliable than stronger cue concentrations, and overlapping cue exposures may increase the degree of certainty that tadpoles have in their perceived risk. When consecutive cue exposures did not overlap, tadpoles assessed the risk associated with each cue exposure independently. Predator-conditioned tadpoles responded longer during exposure to the Anax chemical cue than nonconditioned tadpoles, which suggests that a tadpole’s long-term experience eventually does influence its risk assessment. In general, the results suggest that a prey’s prior experience may influence its current perceived risk by influencing either the degree of certainty in or the level of its perceived risk. Understanding how the prior experience of prey influences their current risk assessment requires that the rate of decay of the value of prior experience should be identified at two timescales as an indicator of the current level of predation risk.     

Tables for Testing the Equality of Two Proportions when Prior Information on their Common Value May be Available

In testing the equality of two proportions, one may define a rejection point T? such that if the test statistic T (in this paper, the ordinary Pearsonian chi-squared) exceeds T? then the hypothesis may safely be rejected, whatever the common value p of the two proportions may be; and similarly define an acceptance point A? such that if T ≦ T? then one may safely accept. These points may be refined if prior information is available, for example that p must lie in the central interval (c, 1 – c) or one of the extremal intervals (v, w) and (1 – w, 1 – v). Smallsample tables are provided both for the unrestricted case and for situations where one has such prior information.     

Energy expenditure and wing beat frequency in relation to body mass in free flying Barn Swallows (<Emphasis Type="Italic">Hirundo rustica</Emphasis>)

Many bird species steeply increase their body mass prior to migration. These fuel stores are necessary for long flights and to overcome ecological barriers. The elevated body mass is generally thought to cause higher flight costs. The relationship between mass and costs has been investigated mostly by interspecific comparison and by aerodynamic modelling. Here, we directly measured the energy expenditure of Barn Swallows (Hirundo rustica) flying unrestrained and repeatedly for several hours in a wind tunnel with natural variations in body mass. Energy expenditure during flight (e _f, in W) was found to increase with body mass (m, in g) following the equation e _f = 0.38 × m ^0.58. The scaling exponent (0.58) is smaller than assumed in aerodynamic calculations and than observed in most interspecific allometric comparisons. Wing beat frequency (WBF, in Hz) also scales with body mass (WBF = 2.4 × m ^0.38), but at a smaller exponent. Hence there is no linear relationship between e _f and WBF. We propose that spontaneous changes in body mass during endurance flights are accompanied by physiological changes (such as enhanced oxygen and nutrient supply of the muscles) that are not taken into consideration in standard aerodynamic calculations, and also do not appear in interspecific comparison.     

The predatory behavior of wintering <Emphasis Type="Italic">Accipiter</Emphasis> hawks: temporal patterns in activity of predators and prey

Studies focused on how prey trade-off predation and starvation risk are prevalent in behavioral ecology. However, our current understanding of these trade-offs is limited in one key respect: we know little about the behavior of predators. In this study, we provide some of the first detailed information on temporal patterns in the daily hunting behavior of bird-eating Accipiter hawks and relate that to their prey. During the winters of 1999–2004, twenty-one sharp-shinned hawks (A. striatus) and ten Cooper’s hawks (A. cooperii) were intensively radio tracked in rural and urban habitats in western Indiana, USA. Cooper’s hawks left roost before sunrise and usually returned to roost around sunset, while sharp-shinned hawks left roost at sunrise or later and returned to roost well before sunset. An overall measure of Cooper’s-hawk-induced risk (a composite variable of attack rate and activity patterns) generally reflected the timing of prey activity, with peaks occurring around sunrise and sunset. In contrast, risk induced by the smaller sharp-shinned hawk did not strongly reflect the activity of their prey. Specifically, an early morning peak in prey activity did not correspond to a period with intense hawk activity. The lack of early morning hunting by sharp-shinned hawks may reflect the high risk of owl-induced predation experienced by these hawks. The net effect of this intraguild predation may be to “free” small birds from much hawk-induced predation risk prior to sunrise. This realization presents an alternative to energetics as an explanation for the early morning peak in small bird activity during the winter.     

Predicting Bald Eagle Collision at Wind Energy Facilities

Bald eagles (Haliaeetus leucocephalus) are currently protected in the United States under the Bald and Golden Eagle Protection Act of 1940 and Migratory Bird Treaty Act of 1918. Given these protections and the increasing development of wind energy throughout the United States, it is important for regulators and the wind industry to understand the risk of bald eagle collisions with wind turbines. Prior probability distributions for eagle exposure rates and collision rates have been developed for golden eagles (Aquila chrysaetos) by the United States Fish and Wildlife Service (USFWS). Given similar information has not been available for bald eagles, the current recommendation by the USFWS is to use the prior probability distributions developed using data collected on golden eagles to predict take for bald eagles. But some evidence suggests that bald and golden eagles may be at different risk for collision with wind turbines and the prior probability distributions developed for golden eagles may not be appropriate for bald eagles. We developed prior probability distributions using data collected at MidAmerican Energy Company's operating wind energy facilities in Iowa, USA, from December 2014 to March 2017 for bald eagle exposure rates and collision rates. The prior probability distribution for collision rate developed for bald eagles has a lower mean collision rate and less variability relative to that developed for golden eagles. We determined that the prior probability distributions specific to bald eagles from these operating facilities are a better starting point for predicting take for bald eagles at operating wind energy facilities in an agricultural landscape than those developed for golden eagles. © 2021 The Wildlife Society.     

Rejoinder to “Predictively consistent prior effective sample sizes,” by Beat Neuenschwander,Sebastian Weber,Heinz Schmidli,and Anthony O'Hagan

Determining the sample size of an experiment can be challenging, even more so when incorporating external information via a prior distribution. Such information is increasingly used to reduce the size of the control group in randomized clinical trials. Knowing the amount of prior information, expressed as an equivalent prior effective sample size (ESS), clearly facilitates trial designs. Various methods to obtain a prior's ESS have been proposed recently. They have been justified by the fact that they give the standard ESS for one-parameter exponential families. However, despite being based on similar information-based metrics, they may lead to surprisingly different ESS for nonconjugate settings, which complicates many designs with prior information. We show that current methods fail a basic predictive consistency criterion, which requires the expected posterior-predictive ESS for a sample of size N to be the sum of the prior ESS and N. The expected local-information-ratio ESS is introduced and shown to be predictively consistent. It corrects the ESS of current methods, as shown for normally distributed data with a heavy-tailed Student-t prior and exponential data with a generalized Gamma prior. Finally, two applications are discussed: the prior ESS for the control group derived from historical data and the posterior ESS for hierarchical subgroup analyses.     

A large Alu-mediated deletion, identified by PCR, as the molecular basis for glycogen storage disease Type II (GSDII)

Glycogen storage disease type II (GSDII) is an autosomal recessive disorder resulting from inherited deficiency of the enzyme lysosomal acid α-glucosidase. Over 40 different mutations have been described but no large deletions have been previously identified. We now describe a homozygous large (9-kb) deletion extending from IVS15 to 4 kb downstream of the terminal exon (exon 20), detected by polymerase chain reaction (PCR)-based methods. The deletion was initially suspected because of failure to amplify a contiguous group of exons by PCR. We hypothesized an Alu/Alu recombination, based on our prior demonstration by Southern blotting of Alu elements in the regions potentially flanking the deletion. Additional sequence analysis of genomic fragments confirmed the presence of Alu elements and allowed the design of flanking primers for PCR amplification. Amplification resulted in a smaller than normal fragment (0.7 vs 10 kb) in homozygosity in the proband and in heterozygosity in her parents. Cloning and sequencing of the smaller than normal 0.7-kb deletion fragment revealed an Alu/Alu deletion junction. In heterozygosity this deletion would not be detected by currently standard PCR mutation detection methods. Based on other Alu-mediated deletions, this deletion is likely to be recurrent and should be screened for in all non-consanguineous GSDII patients, particularly when only one mutation has been identified and none of the 12 single-nucleotide polymorphisms in the deleted region are heterozygous. These observations also suggest that initial characterization of genes at disease-causing loci should include a search for Alu and other repetitive elements to facilitate subsequent PCR-based mutation analysis. Received: 24 August 1998 / Accepted: 13 November 1998     

Estimation of the Parameters of two Parallel Regression Lines Under Uncertain Prior Information

The problem of parallelism for bi‐linear regression lines arises in many real life investigations. For two linear regression models with normal errors, the estimation of the slope as well as the intercept parameters is considered when it is apriori suspected that the two lines are parallel. Three different estimators are defined by using both the sample data and the non‐sample uncertain prior information. The relative performances of the unrestricted, restricted and preliminary test estimators are investigated based on the analysis of the bias, and risk functions under quadratic loss. An example based on a medical study is used to illustrate the method.     

Consequences of larval intraspecific competition to stonefly growth and fecundity

Summary We conducted experiments in replicated circular streams to measure the effect of intraspecific larval density on growth rates, size at emergence, timing of emergence, and fecundity of two species of predatory stoneflies (Megarcys signata and Kogotus modestus, Perlodidae). Early instars of both species showed no significant effect of intraspecific larval density on mean growth rates, despite the observation that in the absence of competitors stoneflies ate on average, significantly more prey (Baetis bicaudatus, Ephemeroptera, Baetidae) than in the presence of competitors. However, larval size of stoneflies held at higher densities (two per chamber) diverged over time, resulting in a greater size variability (coefficient of variation) among Kogotus than in treatments with low densities of stoneflies (one per chamber). The effect of doubling the density of early-instar Megarcys larvae was also asymmetrical, resulting in one larger and one smaller individual. In contrast, doubling the density of last-instar stoneflies whose feeding rates declined significantly prior to emergence had few measurable consequences, except that male Megarcys, which continued to feed throughout the last instar, had lower average feeding rates in high-density than in low-density chambers, and emerged at a significantly smaller mean size. We conclude that competition between early-instar stonefly larvae results in an asymmetry of body sizes, but that competitive effects are reduced as larvae slow or cease feeding before emergence. Since larger females of both stonefly species produced more eggs, the probable cost to females of early-instar larval competition was a reduction in their potential contribution of offspring to the next generation. The cost of attaining a smaller body size for male stoneflies is unknown; but if, as in many other insects, larger males have greater reproductive success, larval competition may increase the opportunity for sexual selection among males. This hypothesis remains to be tested experimentally.     

On the Estimation of the Nearest Neighbour Distribution,G(t), for Point Processes

A new method is proposed for estimating G(t), the distribution function of the distance from an object to its nearest neighbour in a spatial point process. The new method makes more complete use of the information available and has a smaller mean squared error than that of the existing alternatives. The method appears equally effective with random, clustered and regular patterns.     

Cancer chemotherapy and somatic cell mutation

The occurrence of a second neoplasm is one of the major obstacles in cancer chemotherapy. The elucidation of the genotoxic effects induced by anti-cancer drugs is considered to be helpful in identifying the degree of cancer risk. Numerous investigations on cancer patients after chemotherapy have demonstrated: (i) an increase in the in vivo somatic cell mutant frequency (Mf) at three genetic loci, including hypoxanthine–guanine phosphoribosyl-transferase (hprt), glycophorin A (GPA), and the T-cell receptor (TCR), and (ii) alterations in the mutational spectra of hprt mutants. However, the time required for and the degree of such changes are quite variable among patients even if they have received the same chemotherapy, suggesting the existence of underlying genetic factor(s). Accordingly, some cancer patients prior to chemotherapy as well as patients with cancer-prone syndrome have been found to show an elevated Mf. Based on the information obtained from somatic cell mutation assays, an individualized chemotherapy should be considered in order to minimize the risk of a second neoplasm.     

Minichromosomes inDrosophila melanogaster derived from the transposing elementTE1

A minichromosome has originated from the transposing elementTE1. This autonomously replicating chromosome contains the structural genes white and roughest, from theDrosophila X chromosome. It arose within a stock carryingTE1 at 45F on chromosome2. In addition to thew andrst genes, the minichromosome may carry section 45C–45F from chromosome2. It is inherited by 33%–47% of the offspring. By this criterion it carries a centromere, although the origin of the centromere is unknown. From this minichromosome a still smaller one has originated, probably through the loss of all material from chromosome2 together with some heterochromatin. At the same time a duplication of white and roughest could have taken place. This chromosome has a strange morphology and is more frequently lost in meiosis than the larger one, but is still transmitted to about 29%–37% of the progeny of one parent heterozygous for the minichromosome. In both cases the flies have variegated eyes, probably as a result of position-effect variegation. The variegation pattern is influenced by factors in theX chromosome. The size of the smaller minichromosome is little more than 1 Mb as determined by pulsed field gel electrophoresis.     

THE MEAN INNER RADIUS OF SUN AND SHADE ILEX OPACA LEAVES

The mean inner radius of thickness M, a shape measure defined as the mean of the shortest distances d to the border from all internal points P_i of an object, was applied in its dimensionless form D₀M to Ilex opaca sun and shade leaves. This measure has the following attributes: 1) ubiquitous input; 2) the point function f(P) = d is always single valued; 3) it is an intrinsic measure; 4) it is nondirectional; 5) the same definition may be used for any dimension number and be extended to other functions of d. Since Ilex opaca is found in hot, sunny environments, one might predict its sun leaves to be smaller in area and “narrower” in shape (lower D₀M) than shade leaves, making them better convective coolers. Although sun leaves of Ilex opaca have been shown to be smaller in area, their D₀M was unexpectedly greater than shade leaves.     

Effects of two blood-feeding regimes on mortality and female reproduction in a laboratory colony of stable flies,Stomoxys calcitrans

Abstract. Stable flies (Stomoxys calcitrans L.) deprived of a bloodmeal until 3 days post-emergence had higher mortality rates than control flies fed from the day of emergence. Fat bodies of deprived females required one more bloodmeal to reach maximum size, and maximum size was smaller, than fat bodies of control females. Ovarian development did not commence prior to feeding in deprived flies, and proceeded more slowly thereafter, resulting in a one bloodmeal delay in egg maturation in deprived flies. Deprived females produced fewer (54.7, SD 2.8) eggs than controls (75.9, SD 3.7) and eggs from deprived females were smaller (mean length 684.0 μrn) than control females' eggs (mean length 1165.7 μm).     

Estimating overdispersion in sparse multinomial data

Multinomial data arise in many areas of the life sciences, such as mark-recapture studies and phylogenetics, and will often by overdispersed, with the variance being higher than predicted by a multinomial model. The quasi-likelihood approach to modeling this overdispersion involves the assumption that the variance is proportional to that specified by the multinomial model. As this approach does not require specification of the full distribution of the response variable, it can be more robust than fitting a Dirichlet-multinomial model or adding a random effect to the linear predictor. Estimation of the amount of overdispersion is often based on Pearson's statistic X² or the deviance D. For many types of study, such as mark-recapture, the data will be sparse. The estimator based on X² can then be highly variable, and that based on D can have a large negative bias. We derive a new estimator, which has a smaller asymptotic variance than that based on X², the difference being most marked for sparse data. We illustrate the numerical difference between the three estimators using a mark-recapture study of swifts and compare their performance via a simulation study. The new estimator has the lowest root mean squared error across a range of scenarios, especially when the data are very sparse.     

Protein Architecture Chronology Deduced From Structures of Amino Acid Synthases

Abstract

Inferring the protein architecture chronology is one of central topics in origin of life study and has been given much attention. Based on an amino acid evolutionary model that late amino acids were bio-synthesized prior to early counterparts, we addressed the issue by examining the structures of amino acid synthases. Despite the limited structural information on amino acid synthases, our deduction revealed that α/β was the oldest protein class, which is in good agreement with the prior fold-usage-based conclusion.     

A genetic component of extinction risk in mammals

Genetic factors may play an important role in species extinction but their actual effect remains poorly understood, particularly because of a strong and potentially masking effect expected from ecological traits. We investigated the role of genetics in mammal extinction taking both ecological and genetic factors into account. As a proxy for the role of genetics we used the ratio of the rates of nonsynonymous (amino acid changing) to synonymous (leaving the amino acid unchanged) nucleotide substitutions, K_a / K_s. Because most nonsynonymous substitutions are likely to be slightly deleterious and thus selected against, this ratio is a measure of the inefficiency of selection: if large (but less than 1), it implies a low efficiency of selection against nonsynonymous mutations. As a result, nonsynonymous mutations may accumulate and thus contribute to extinction. As a proxy for the role of ecology we used body mass W, with which most extinction‐related ecological traits strongly correlate. As a measure of extinction risk we used species’ affiliation with the five levels of extinction threat according to the IUCN Red List of Threatened Species. We calculated K_a / K_s for mitochondrial protein‐coding genes of 211 mammalian species, each of which was characterized by body mass and the level of threat. Using logistic regression analysis, we then constructed a set of logistic regression models of extinction risk on ln(K_a / K_s) and lnW. We found that K_a / K_s and body mass are responsible for a 38% and a 62% increase in extinction risk, respectively. Given that the standard error of these values is 13%, the contribution of genetic factors to extinction risk in mammals is estimated to be one‐quarter to one‐half of the total of ecological and genetic effects. We conclude that the effect of genetics on extinction is significant, though it is almost certainly smaller than the effect of ecological traits. Synthesis Mutation provides the material for evolution. However, most mutations that play a role in evolution are slightly deleterious and thus may contribute to extinction. We assess the role of mitochondrial DNA mutations in mammalian extinction risk and find it to be one‐quarter to one‐half of the total of mutation and body mass effects, where body mass represents an integral measure of extinction‐related ecological traits. Genetic factors may be all the more important, because ecological traits associated with large body mass would both promote and protect from extinction, while mutation accumulation caused by low effective population size seems to have no counterbalance.     

The development of seedlings from fragments of monoembryonic seeds as an important survival strategy for Eugenia (Myrtaceae) tree species

The uncommon ability of monoembryonic seeds of Eugenia to develop seedlings after cutting or even after the removal of more than half of their storage tissue has recently been reported. Some Eugenia species are included among those at risk of disappearing, so the regeneration of plantlets from fragments of seeds could be an important mechanism both for the production of more than one normal seedling per seed and to understand the survival strategies of these species. Because the period in which this ability is present has not been studied, we analyzed the regenerative capacity of seeds of five Brazilian native species of Eugenia, considering two levels of maturity and three germination phases. Mature seeds have a greater potential to regenerate than immature ones; germinating seeds showed that the longer the root protrusion, the smaller the potential to regenerate new seedlings. However, our results clearly demonstrate that the ability to regenerate new roots or complete seedlings is present during a long period from the beginning of development until the late phases of germination. Cutting is potentially important to obtain plants on a larger scale. Because of intense predation of these seeds, this ability could be linked to an essential strategy for survival even after the removal of more than half of the storage tissues. As an alternative strategy to orthodox seeds, whose preservation is based on tolerance to desiccation, the recalcitrant seeds of Eugenia probably adopted the great reserve quantity and the regenerative capacity, allowing them to undergo successive germinations.     

Improved Identification of Parameters in the Wolgograd Growth Model for Sugar Beets

Starting point of the investigations is the time-invariant Wolgograd model applied to a sample of sugar beets. To overcome the weak multicollinearity of the model in its logarithmic form, a ridge-type estimator is applied which uses prior information on the unknown regression coefficients. This is done by introducing the biased minimax-linear estimator. To judge the goodness of the estimates there are calculated the minimax risks of the MILE and the OLSE as well as the estimated maximal crop yields.     

On the inadmissibility of Watterson's estimator

We consider the estimation of the scaled mutation parameter θ, which is one of the parameters of key interest in population genetics. We provide a general result showing when estimators of θ can be improved using shrinkage when taking the mean squared error as the measure of performance. As a consequence, we show that Watterson’s estimator is inadmissible, and propose an alternative shrinkage-based estimator that is easy to calculate and has a smaller mean squared error than Watterson’s estimator for all possible parameter values 0<θ<∞. This estimator is admissible in the class of all linear estimators. We then derive improved versions for other estimators of θ, including the MLE. We also investigate how an improvement can be obtained both when combining information from several independent loci and when explicitly taking into account recombination. A simulation study provides information about the amount of improvement achieved by our alternative estimators.