Determinants of distribution and abundance in the clouded apollo butterfly: a landscape ecological approach

Recent studies on the determinants of distribution and abundance of animals at landscape level have emphasized the usefulness of the metapopulation approach, in which patch area and habitat connectivity have often proved to explain satisfactorily existing patch occupancy patterns. A different approach is needed to study the common situation in which suitable habitat is difficult to determine or does not occur in well‐defined habitat patches. We applied a landscape ecological approach to study the determinants of distribution and abundance of the threatened clouded apollo Parnassius mnemosyne butterfly within an area of 6 km² of agricultural landscape in south‐western Finland. The relative role of 24 environmental variables potentially affecting the distribution and abundance of the butterfly was studied using a spatial grid system with 2408 grid squares of 0.25 ha, of which 349 were occupied by the clouded apollo. Both the probability of butterfly presence and abundance in a 0.25 ha square increased with the presence of the larval host plant Corydalis solida the cover of semi‐natural grassland, the amount of solar radiation and spalial autocorrelation in butterfly occurrence. Additionally, butterfly abundance increased with overall mean patch size and decreased with maximum slope angle and wind speed. Two advantages of the employment of a spatial grid system included the avoidance of a subjective definition of suitable habitat patches and an evaluation of the relative significance of different components of habitat quality at the same time with habitat availability and connectivity. The large variation in habitat quality was influenced by the abundance of the larval host plant and adult nectar sources but also by climatological. topographical and structural factors. The application of a spatial grid system as used here has potential for a wide use in studies on landscape‐level distribution and abundance patterns in species with complex habitat requirements and habitat availability patterns.     

Intraseasonal asynchrony as a factor boosting isolation within a metapopulation: The case of the clouded apollo

This article discusses the influence of phenology-related intraseasonal asynchrony on metapopulation dynamics and stability. As the part played by intraseasonal asynchrony is as yet unclear and poorly described, greater account of it should be taken in both metapopulation research and conservation practice. The subpopulations of the Parnassius mnemosyne metapopulation studied here are strongly isolated because of the phenological shift between them, despite the relatively small physical distances between them. This isolation is the result of a significant temporal shift in the species' flight periods in the main metapopulation centers: in som e seasons its flight times in the different subpopulations did not overlap at all. The predicted results of such strong intraseasonal asynchrony are not altogether clear. On the one hand, they reduce the vulnerability of the entire metapopulation to the effects of short-term random disasters. On the other, the ever-greater isolation of subpopulations may cause the metapopulation to becom e a nonequilibrium one, which will have a serious impact on its long-term survival.     

An empirical model for predicting microhabitat of 0+ juvenile fishes in a lowland river catchment

Summary Species-habitat relationships are an important aspect of fish life history, particularly in early ontogeny. To address the lack of information on the microhabitat use/requirements of European coarse fishes, particularly 0-group fishes in riverine systems, an empirical model was generated from data collected in the River Great Ouse catchment (UK). During 7 weeks in autumn 1990, data on young-of-the-year (0+) juvenile fishes and 15 environmental variables were collected at 2800 stratified, random point samples within 130 study sites (streams, rivers, side-channels, backwaters). Of 24 species of 0+ fish, only 10 were captured in 3% of non-null samples. Association analysis and canonical correspondence analysis of the samples-by-species (967×10) and samples-by-variables (967×15) data matrices revealed that the shallow, narrow, lotic, stony-pebbly channel microhabitat of riffles and runs was preferred by the progeny of substrate-spawning, substrate/plant-spawning and nest-guarding fishes. Moderately deeper and wider, sinuous channels, with slowto-moderate water velocities and medium-sized substrata were also favourable to progeny of substrate spawners. Assemblages of 0+ fish in deeper, wider, silted, trapezoidal-shaped channels with slow-to-lentic flowing water, i.e. channelised and regulated, were dominated by ubiquitous (plant/substrate) spawners.     

Effect of non-linearity in predicting doppler waveforms through a novel model

Background  

In pregnancy, the uteroplacental vascular system develops de novo locally in utero and a systemic haemodynamic & bio-rheological alteration accompany it. Any abnormality in the non-linear vascular system is believed to trigger the onset of serious morbid conditions like pre-eclampsia and/or intrauterine growth restriction (IUGR). Exact Aetiopathogenesis is unknown. Advancement in the field of non-invasive doppler image analysis and simulation incorporating non-linearities may unfold the complexities associated with the inaccessible uteroplacental vessels. Earlier modeling approaches approximate it as a linear system.     

An epidemic model in a patchy environment

An epidemic model is proposed to describe the dynamics of disease spread among patches due to population dispersal. We establish a threshold above which the disease is uniformly persistent and below which disease-free equilibrium is locally attractive, and globally attractive when both susceptible and infective individuals in each patch have the same dispersal rate. Two examples are given to illustrate that the population dispersal plays an important role for the disease spread. The first one shows that the population dispersal can intensify the disease spread if the reproduction number for one patch is large, and can reduce the disease spread if the reproduction numbers for all patches are suitable and the population dispersal rate is strong. The second example indicates that a population dispersal results in the spread of the disease in all patches, even though the disease can not spread in each isolated patch.     

Sexually antagonistic co‐evolution: a model and an empirical test

Models reveal that sexually antagonistic co‐evolution exaggerates female resistance and male persistence traits. Here we adapt an established model by including directional sexual selection acting against persistence. We find similar equilibria to previous models showing that sexually antagonistic co‐evolution can be limited by counteracting sexual, as well as, natural selection. We tested the model using empirical data for the seaweed fly, Coelopa ursina, in which body size acts as a persistence and a resistance trait. Our model can generate continuous co‐evolutionary cycles and stable equilibria, however, all simulations using empirically derived parameter estimates reach stable equilibria. Thus, stable equilibria might be more common in nature than continuous co‐evolutionary cycles, suggesting that sexual conflict is unlikely to promote speciation. The model predicts male biased sexual size dimorphism for C. ursina, comparable with empirically observed values. Male persistence is shown to be more sensitive than female resistance to changes in model parameters.     

An empirical test for a zone of canalization in thermal reaction norms

Theoretical models on the evolution of phenotypic plasticity predict a zone of canalization where reaction norms cross, and genetic variation is minimized in the environment a population most frequently encounter. Empirical tests of this prediction are largely missing, in particular for life‐history traits. We addressed this prediction by quantifying thermal reaction norms of three life‐history traits (somatic growth rate, age and size at maturation) of a Norwegian population of Daphnia magna and testing for the occurrence of an intermediate temperature (T_m) at which genetic variance in the traits is minimized. Size at maturation changed relatively little with temperature compared to the other traits, and there was no genetic variance in the shape of the reaction norm. Consequently, age at maturation and somatic growth rate were strongly negatively correlated. Both traits showed a strong genotype–environment interaction, and the estimated T_m was 14 °C for both age at maturation and growth rate. This value of T_m corresponds well with mean summer temperatures experienced by the population and suggests that the population has evolved under stabilizing selection in temperatures that fluctuate around this mean temperature. These results suggest local adaptation to temperature in the studied population and allow predicting evolutionary trajectories of thermal reaction norms under changing thermal regimes.     

Density dependence in resource exploitation: empirical test of Levins' metapopulation model

Levins' model of metapopulation dynamics is modified to incorporate variable degrees of density dependence in the per capita exploitation of resource patches. We demonstrate a simple means of testing for this density dependence in a sample of metapopulations, each at its equilibrium balance of local colonization to extinction. The fraction of habitable unoccupied patches equilibrates to a constant number under the null model of density independent colonization, and to a constant proportion under strong density dependence. We compare the null model to two density dependent alternatives, using data on exploitation of nest boxes by collared flycatchers Ficedula albicollis . The analysis shows how predicted trends in the equilibrium unoccupied fraction are similar for both spatial interference and net immigration. This needs to be recognized, since the null hypothesis of a constant unused resource applies also to the dynamics of consumable resources, where it is expressed in a constant stock of uneaten prey at the dynamic equilibrium of predators to prey.     

An empirical test of partner choice mechanisms in a wild legume-rhizobium interaction

Mutualisms can be viewed as biological markets in which partners of different species exchange goods and services to their mutual benefit. Trade between partners with conflicting interests requires mechanisms to prevent exploitation. Partner choice theory proposes that individuals might foil exploiters by preferentially directing benefits to cooperative partners. Here, we test this theory in a wild legumerhizobium symbiosis. Rhizobial bacteria inhabit legume root nodules and convert atmospheric dinitrogen (N2) to a plant available form in exchange for photosynthates. Biological market theory suits this interaction because individual plants exchange resources with multiple rhizobia. Several authors have argued that microbial cooperation could be maintained if plants preferentially allocated resources to nodules harbouring cooperative rhizobial strains. It is well known that crop legumes nodulate non-fixing rhizobia, but allocate few resources to those nodules. However, this hypothesis has not been tested in wild legumes which encounter partners exhibiting natural, continuous variation in symbiotic benefit. Our greenhouse experiment with a wild legume, Lupinus arboreus, showed that although plants frequently hosted less cooperative strains, the nodules occupied by these strains were smaller. Our survey of wild-grown plants showed that larger nodules house more Bradyrhizobia, indicating that plants may prevent the spread of exploitation by favouring better cooperators.     

Glandular regulation of interstitial diffusion: a model and simulation of a novel physiological mechanism

In endocrine glands, vigorous and coordinated responses are often elicited by modest changes in the concentration of the agonist molecule. The mammalian parathyroid gland is a representative case. Small (5%) changes in serum calcium result in 10-fold (1,000%) changes in glandular parathyroid hormone (PTH) release. In vitro, single isolated cells are observed to secrete fewer hormones than cells residing within a connected group, suggesting that a network has emergent regulatory properties. In PTH-secreting tumors, however, the ability to respond quickly to changes in calcium is strongly damped. A unifying hypothesis that accounts for these phenomena is realized by extracellular modulation of calcium diffusivity. A theoretical model and computational experiments demonstrate qualitative agreement with published experimental results. Our results suggest that, in addition to the cellular mechanisms, endocrine glandular networks may have regulatory prowess at the level of interstitial transport.     

Population diffusion in a two-patch environment

A model of a single-species population diffusing in a two-patch environment is proposed. It is shown that there exists a positive, monotonic, continuous steady-state solution with continuous flux, in the cases of both reservoir and no-flux boundary conditions, that is asymptotically stable. In the case of patches with equal carrying capacities, it is shown that the uniform steady state is globally asymptotically stable.     

A diffusion model for population growth in random environment

The growth of a population in a randomly varying environment is modeled by replacing the Malthusian growth rate with a delta-correlated normal process. The population size is then shown to be a random process, lognormally distributed, obeying a diffusion equation of the Fokker-Planck type. The first passage time p.d.f. through any arbitrarily assigned value and the probability of absorption are derived. The asymptotic behavior of the population size is investigated.     

Hindered diffusion in agarose gels: test of effective medium model.

The diffusivities of uncharged macromolecules in gels (D) are typically lower than in free solution (D infinity), because of a combination of hydrodynamic and steric factors. To examine these factors, we measured D and D infinity for dilute solutions of several fluorescein-labeled macromolecules, using an image-based fluorescence recovery after photobleaching technique. Test macromolecules with Stokes-Einstein radii (rs) of 2.1-6.2 nm, including three globular proteins (bovine serum albumin, ovalbumin, lactalbumin) and four narrow fractions of Ficoll, were studied in agarose gels with agarose volume fractions (phi) of 0.038-0.073. The gels were characterized by measuring the hydraulic permeability of supported agarose membranes, allowing calculation of the Darcy permeability (kappa) for each gel sample. It was found that kappa, which is a measure of the intrinsic hydraulic conductance of the gel, decreased by an order of magnitude as phi was increased over the range indicated. The diffusivity ratio D/D infinity, which varied from 0.20 to 0.63, decreased with increases in rs or phi. Thus as expected, diffusional hindrances were the most severe for large macromolecules and/or relatively concentrated gels. According to a recently proposed theory for hindered diffusion through fibrous media, the diffusivity ratio is given by the product of a hydrodynamic factor (F) and a steric factor (S). The functional form is D/D infinity = F(rs/k1/2) S(f), where f = [(rs+rf)/rf]2 phi and rf is the fiber radius. Values of D/D infinity calculated from this effective medium theory, without use of adjustable parameters, were in much better agreement with the measured values than were predictions based on other approaches. The strengths and limitations of the effective medium theory for predicting diffusivities in gels are discussed.     

An empirical test of the midpoint rooting method

The outgroup method is widely used to root phylogenetic trees. An accurate root indication, however, strongly depends on the availability of a proper outgroup. An alternate rooting method is the midpoint rooting (MPR). In this case, the root is set at the midpoint between the two most divergent operational taxonomic units. Although the midpoint rooting algorithm has been extensively used, the efficiency of this method in retrieving the correct root remains untested. In the present study, we empirically tested the success rate of the MPR in obtaining the outgroup root for a given phylogenetic tree. This was carried out by eliminating outgroups in 50 selected data sets from 33 papers and rooting the trees with the midpoint method. We were thus able to compare the root position retrieved by each method. Data sets were separated into three categories with different root consistencies: data sets with a single outgroup taxon (54% success rate for MPR), data sets with multiple outgroup taxa that showed inconsistency in root position (82% success rate), and data sets with multiple outgroup taxa in which root position was consistent (94% success rate). Interestingly, the more consistent the outgroup root is, the more successful MPR appears to be. This is a strong indication that the MPR method is valuable, particularly for cases where a proper outgroup is unavailable.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 669–674.     

Transient SI and the dynamics of self-incompatibility alleles: a simulation model and empirical test

A stochastic computer simulation model was created to compare the combined effects of selection and genetic drift on the dynamics of S-alleles under full sporophytic self-incompatibility (SI) versus transient SI, a form of partial SI in which flowers become self-compatible as they age. S-alleles were lost more rapidly with transient than with full SI, as is expected with weakened frequency-dependent selection. Based on these results, equilibrium S-allele diversity is expected to be lower with partial SI for populations of comparable size and migration rates. Consistent with model results, a comparison of the proportion of incompatible crosses in full diallel experiments for a fully SI and a transiently SI species in the annual genus Leptosiphon suggests that S-allele diversity is lower in the partially SI species. Results of the simulation model indicate that the transmission advantage of self-fertilization can have complex effects on S-allele dynamics in partial SI systems.     

A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples

MOTIVATION: The classification of samples using gene expression profiles is an important application in areas such as cancer research and environmental health studies. However, the classification is usually based on a small number of samples, and each sample is a long vector of thousands of gene expression levels. An important issue in parametric modeling for so many gene expression levels is the control of the number of nuisance parameters in the model. Large models often lead to intensive or even intractable computation, while small models may be inadequate for complex data.Methodology: We propose a two-step empirical Bayes classification method as a solution to this issue. At the first step, we use the model-based cluster algorithm with a non-traditional purpose of assigning gene expression levels to form abundance groups. At the second step, by assuming the same variance for all the genes in the same group, we substantially reduce the number of nuisance parameters in our statistical model. RESULTS: The proposed model is more parsimonious, which leads to efficient computation under an empirical Bayes estimation procedure. We consider two real examples and simulate data using our method. Desired low classification error rates are obtained even when a large number of genes are pre-selected for class prediction.     

Forecasting the elimination of active trachoma: An empirical model

BackgroundGreat progress has been made toward the elimination of trachoma as a public-health problem. Mathematical and statistical models have been used to forecast when the program will attain the goal of the elimination of active trachoma, defined as prevalence of trachomatous inflammation—follicular in 1–9 year olds (TF_1–9) <5%. Here we use program data to create an empirical model predicting the year of attaining global elimination of TF_1–9.Methodology/Principal findingsWe calculated the mean number of years (95% CI) observed for an implementation unit (IU) to move from a baseline TF_1–9 prevalence ≥5% to the elimination threshold, based on the region (Ethiopia vs. non-Ethiopia) and baseline prevalence category. Ethiopia IUs had significantly different rates of reaching the TF_1–9 elimination threshold after a trachoma impact survey (TIS) compared to non-Ethiopia IUs across all baseline categories. We used those estimates to predict when remaining active trachoma-endemic IUs (TF_1–9 ≥5%) would have their last round of mass drug administration (MDA) based on the mean number of years required and number of MDA rounds already completed. Our model predicts that elimination of TF_1–9 will be achieved in 2028 in Ethiopia (95% CI: 2026–2033) and 2029 outside of Ethiopia (95% CI: 2023–2034), with some IUs in East Africa predicted to be the last requiring MDA globally.Conclusions/SignificanceOur empirical estimate is similar to those resulting from previous susceptible-infectious-susceptible (SIS) and mathematical models, suggesting that the forecast achievement of TF_1–9 elimination is realistic with the caveat that although disease elimination progress can be predicted for most IUs, there is an important minority of IUs that is not declining or has not yet started trachoma elimination activities. These IUs represent an important barrier to the timely global elimination of active trachoma.     

Competition for females on leks when male competitive abilities differ: empirical test of a model

Leks are mating arenas visited by females seeking copulationsand can be thought of as patches differing in female encounterrate. Recently, the ideal free distribution model of unequalcompetitors with interference has been applied to explain maledistributions between leks. This model predicts that the malesof highest competitive ability should be present on the lekswith the highest female encounter rates and should be most successful.I tested the predictions from the model with empirical datafrom the ruff, Philomachus pugnax. Contrary to the predictionsfrom the model, low-ranking males preferentially visited theleks with highest female encounter rates, where the degree ofmale aggression was greatest Furthermore, there was no generalrelationship between female encounter rate and male success,and the empirical data again refute the predictions from themodel. The results illustrate the problem of using male per-capitasuccess when predicting individual behavior. Several more generalproblems with applying the ideal free distribution of unequalcompetitors model to competition for mates are also discussed.     

FMSM: a novel computational model for predicting potential miRNA biomarkers for various human diseases

Background

MicroRNA (miRNA) plays a key role in regulation mechanism of human biological processes, including the development of disease and disorder. It is necessary to identify potential miRNA biomarkers for various human diseases. Computational prediction model is expected to accelerate the process of identification.

Results

Considering the limitations of previously proposed models, we present a novel computational model called FMSM. It infers latent miRNA biomarkers involved in the mechanism of various diseases based on the known miRNA-disease association network, miRNA expression similarity, disease semantic similarity and Gaussian interaction profile kernel similarity. FMSM achieves reliable prediction performance in 5-fold and leave-one-out cross validations with area under ROC curve (AUC) values of 0.9629+/??0.0127 and 0.9433, respectively, which outperforms the state-of-the-art competitors and classical algorithms. In addition, 19 of top 25 predicted miRNAs have been validated to have associations with Colonic Neoplasms in case study.

Conclusions

A factored miRNA similarity based model and miRNA expression similarity substantially contribute to the well-performing prediction. The list of the predicted most latent miRNA biomarkers of various human diseases is publicized. It is anticipated that FMSM could serve as a useful tool guiding the future experimental validation for those promising miRNA biomarker candidates.