Modelling survival and allele complementation in the evolution of genomes with polymorphic loci

We have simulated the evolution of sexually reproducing populations composed of individuals represented by diploid genomes. A series of eight bits formed an allele occupying one of 128 loci of one haploid genome (chromosome). The environment required a specific activity of each locus, this being the sum of the activities of both alleles located at the corresponding loci on two chromosomes. This activity is represented by the number of bits set to zero. In a constant environment the best fitted individuals were homozygous with alleles’ activities corresponding to half of the environment requirement for a locus (in diploid genome two alleles at corresponding loci produced a proper activity). Changing the environment under a relatively low recombination rate promotes generation of more polymorphic alleles. In the heterozygous loci, alleles of different activities complement each other fulfilling the environment requirements. Nevertheless, the genetic pool of populations evolves in the direction of a very restricted number of complementing haplotypes and a fast changing environment kills the population. If simulations start with all loci heterozygous, they stay heterozygous for a long time.     

The new clinical standard of integrated quadruple stress echocardiography with ABCD protocol

Background

The detection of regional wall motion abnormalities is the cornerstone of stress echocardiography. Today, stress echo shows increasing trends of utilization due to growing concerns for radiation risk, higher cost and stronger environmental impact of competing techniques. However, it has also limitations: underused ability to identify factors of clinical vulnerability outside coronary artery stenosis; operator-dependence; low positivity rate in contemporary populations; intermediate risk associated with a negative test; limited value of wall motion beyond coronary artery disease. Nevertheless, stress echo has potential to adapt to a changing environment and overcome its current limitations.

Integrated-quadruple stress-echo

Four parameters now converge conceptually, logistically, and methodologically in the Integrated Quadruple (IQ)-stress echo. They are: 1- regional wall motion abnormalities; 2-B-lines measured by lung ultrasound; 3-left ventricular contractile reserve assessed as the stress/rest ratio of force (systolic arterial pressure by cuff sphygmomanometer/end-systolic volume from 2D); 4- coronary flow velocity reserve on left anterior descending coronary artery (with color-Doppler guided pulsed wave Doppler). IQ-Stress echo allows a synoptic functional assessment of epicardial coronary artery stenosis (wall motion), lung water (B-lines), myocardial function (left ventricular contractile reserve) and coronary small vessels (coronary flow velocity reserve in mid or distal left anterior descending artery). In “ABCD” protocol, A stands for Asynergy (ischemic vs non-ischemic heart); B for B-lines (wet vs dry lung); C for Contractile reserve (weak vs strong heart); D for Doppler flowmetry (warm vs cold heart, since the hyperemic blood flow increases the local temperature of the myocardium). From the technical (acquisition/analysis) viewpoint and required training, B-lines are the kindergarten, left ventricular contractile reserve the primary (for acquisition) and secondary (for analysis) school, wall motion the university, and coronary flow velocity reserve the PhD program of stress echo.

Conclusion

Stress echo is changing. As an old landline telephone with only one function, yesterday stress echo used one sign (regional wall motion abnormalities) for one patient with coronary artery disease. As a versatile smart-phone with multiple applications, stress echo today uses many signs for different pathophysiological and clinical targets. Large scale effectiveness studies are now in progress in the Stress Echo2020 project with the omnivorous “ABCD” protocol.

     

Parameters adaptation in the populations models

Ecology-evolutionary models of low dimensions were developed on the basis of competitive selection criteria. Dynamics of variables (number of individuals) and the search of evolutionary-stable values of parameters (biological characterictics of populations) were monitored in the suggested models. If the environmental temperature is changing periodically, the average (a) and width (d) of temperature tolerance range appears to be the important parameters. By model experiments it was established that stable values of temperature (a), favorable for development of highly specialized algae (d is low) were close to minimum and maximum of temperature curve. And for the low specialized algae (d is high) this values were close to the average temperature of environment. In a similar manner, a set of evolutionally stable parameters (a, d) was established for either of the two interacted populations (competitors and "predator-prey"). The hypotheses concerning it's geometric structure and the process of coevolution is formulated.     

Increase in body size is correlated to warmer winters in a passerine bird as inferred from time series data

Climate change is expected to affect natural populations in many ways. One way of getting an understanding of the effects of a changing climate is to analyze time series of natural populations. Therefore, we analyzed time series of 25 and 20 years, respectively, in two populations of the citril finch (Carduelis citrinella) to understand the background of a dramatic increase in wing length in this species over this period, ranging between 1.3 and 2.9 phenotypic standard deviations. We found that the increase in wing length is closely correlated to warmer winters and in one case to rain in relation to temperature in the summer. In order to understand the process of change, we implemented seven simulation models, ranging from two nonadaptive models (drift and sampling), and five adaptive models with selection and/or phenotypic plasticity involved and tested these models against the time series of males and females from the two population separately. The nonadaptive models were rejected in each case, but the results were mixed when it comes to the adaptive models. The difference in fit of the models was sometimes not significant indicating that the models were not different enough. In conclusion, the dramatic change in mean wing length can best be explained as an adaptive response to a changing climate.     

A simple fitness proxy for structured populations with continuous traits, with case studies on the evolution of haplo-diploids and genetic dimorphisms

For structured populations in equilibrium with everybody born equal, ln(R (0)) is a useful fitness proxy for evolutionarily steady strategy (ESS) and most adaptive dynamics calculations, with R (0) the average lifetime number of offspring in the clonal and haploid cases, and half the average lifetime number of offspring fathered or mothered for Mendelian diploids. When individuals have variable birth states, as is, for example, the case in spatial models, R (0) is itself an eigenvalue, which usually cannot be expressed explicitly in the trait vectors under consideration. In that case, Q(Y| X):=-det (I-L(Y| X)) can often be used as fitness proxy, with L the next-generation matrix for a potential mutant characterized by the trait vector Y in the (constant) environment engendered by a resident characterized by X. If the trait space is connected, global uninvadability can be determined from it. Moreover, it can be used in all the usual local calculations like the determination of evolutionarily singular trait vectors and their local invadability and attractivity. We conclude with three extended case studies demonstrating the usefulness of Q: the calculation of ESSs under haplo-diploid genetics (I), of evolutionarily steady genetic dimorphisms (ESDs) with a priori proportionality of macro- and micro-gametic outputs (an assumption that is generally made but the fulfilment of which is a priori highly exceptional) (II), and of ESDs without such proportionality (III). These case studies should also have some interest in their own right for the spelled out calculation recipes and their underlying modelling methodology.     

On optimal size and number of reserves for metapopulation persistence

Habitat fragmentation is generally considered to be detrimental to the persistence of natural populations. In nature management, one therefore tends to prefer few large nature reserves over many small nature reserves having equal total area. This paper examines whether this preference is warranted in a metapopulation framework with circular reserves (patches) by formulating the dependence of metapopulation persistence on the size and number of reserves, both of which depend on reserve radius if the total area is kept constant. Two measures of metapopulation persistence are used: R(0), the number of patches colonized by an occupied patch during its lifetime as an occupied patch, and T(e), the expected time to extinction. These two measures are functions of the extinction and colonization rates of the metapopulation. Several mechanisms for the extinction and colonization processes are formulated from which the dependence of these rates on reserve radius is calculated. It turns out that T(e)generally increases with reserve radius for all mechanisms, which supports the preference of few large reserves. However, R(0)supports this preference only in the case of some special, rather unrealistic, mechanisms. In many other, more realistic, cases an intermediate reserve size exists for which metapopulation persistence measured by R(0)is optimal.     

How much evolutionary advantage does sex confer?

In discussing the long term advantage of sex, Crow & Kimura (1965) andMaynard Smith (1971) have argued that the advantage of a reproductive system allowing recombination (sex) is greatest for large populations. However the validity of this conclusion depends upon the model used for evolution. We propose two simple models: the bootstrap model, where the number of loci at which favourable mutations may take place remains constant over long time periods; and the environment-led model, where evolution is at a constant rate dictated by the environment (and does not depend on the organism's ability to evolve). While the bootstrap model leads to conclusions similar to those mentioned above, the conclusions for environment-led evolution are the opposite: as the size of the population decreases the advantage for sex increases.     

Fixation probabilities when generation times are variable: the burst death model

Estimating the fixation probability of a beneficial mutation has a rich history in theoretical population genetics. Typically, to attain mathematical tractability, we assume that generation times are fixed, while the number of offspring per individual is stochastic. However, fixation probabilities are extremely sensitive to these assumptions regarding life history. In this article, we compute the fixation probability for a "burst-death" life-history model. The model assumes that generation times are exponentially distributed, but the number of offspring per individual is constant. We estimate the fixation probability for populations of constant size and for populations that grow exponentially between periodic population bottlenecks. We find that the fixation probability is, in general, substantially lower in the burst-death model than in classical models. We also note striking qualitative differences between the fates of beneficial mutations that increase burst size and mutations that increase the burst rate. In particular, once the burst size is sufficiently large relative to the wild type, the burst-death model predicts that fixation probability depends only on burst rate.     

Sedimentation in the seasonal cycle of unicellular algae. Model analysis]

The efficiency of quick sedimentation (quicker then at normal condition) of unicellular algae at the end of seasonal cycle was studied in Okhotsk Sea. Model researches were based on the effect of competition of two algae populations. Analytical investigations of simplified variant of mathematical model and computing experiments showed that cell sedimentation and falling into the unfavorable (dark and cold) environment could be compensated by the increase in survival under these "negative" conditions. Vertical mixing of water has effect. Generally, mechanism of convective mixing is one of the factors that helps competing populations of unicellular algae to exist under conditions of changing environment.     

Testing Models of Insulin Binding in Rat Adipocytes using Network Thermodynamic Computer Simulations

Abstract

Many different models have been proposed to explain the complex binding behavior of insulin to its receptor, but a systematic comparison of models with experimental results is lacking. We have used network thermodynamic computer simulations to compare models of insulin binding against the results of several experimental tests designed to differentiate between the models. Six models of insulin binding were tested (simple, diffusion-reaction, conversion, dissociation, heterogeneous site, and two-step intramembrane) against results reported in the literature for isolated rat adipocytes. Although still a matter of experimental controversy, the criteria selected for modeling were curvilinear Scatchard plots, bi-or multi-exponential dissociation, insulin-accelerated dissociation, lack of dependence of the overall dissociation constant on receptor number, and receptor reserve. Using a given set of parameter values most appropriate for each model, none was able to account for all of the observed experimental results. This indicates both the complexity of the binding reaction and the need for further model development. The approach of using computer simulations to systematically test models against experimental results affords not only insight into the critical features of a model enabling it to pass a test, but also indicates potential experiments which might differentiate between models.     

Genetic consequences of ecological reserve design guidelines: An empirical investigation

We assessed the geneticdiversity consequences of applying ecologicalreserve design guidelines to four federally-listedglobally-rare plant species. Consequences weremeasured using two metrics: proportion of allalleles and of common alleles included inreserves. Common alleles were defined as those alleleshaving a frequency of 0.05 in at least onepopulation. Four conservation professionalsapplied ecological reserve guidelines to choosespecific populations of each species forinclusion in reserves of size 1 to N – 1, whereN is the total number of populations of each species.Information regarding genetic diversity was notused in selecting populations. The resulting reservedesigns were compared to random designs, andthe agreement among experts was assessed usingKendall's coefficient of concordance.Application of ecological reserve design guidelines provedmostly ineffective in capturing more geneticdiversity than is captured selectingpopulations randomly. Meeting establishedtargets for genetic diversity, such as one advocated by theCenter for Plant Conservation, required largernumbers of populations than are suggested to besufficient. Relative performance of expertdesigns differed among species and wasdependent on whether the proportion of allalleles or of common alleles was used as a measure ofdiversity. Furthermore there was no significantconcordance among experts in order in whichpopulations were incorporated into reserves asexperts differed in priority they placed onindividual guidelines.     

Spatial population dynamics and the design of marine reserves

The failure of many fisheries world-wide, and the concern about marine biodiversity, has sparked a growing interest in the spatial aspects of harvested populations. If a population conforms to the Ideal Free Distribution and that one of the habitats is set aside as a reserve free from harvesting, the design of reserves may be problematic. If a substantial proportion of the unharvested population is to be preserved, then the reserve area must be unrealistically large, or have a much higher expected fitness than the unprotected area. Interestingly, the optimal harvest rate will be unaffected by both the size of the reserve and the quality of it relative to the harvested area. Even if the Ideal Free Distribution model is extended to include simple age-structure and "spillover" of recruits from the reserve, these conclusions largely remain intact. In a model that also includes spillover, the habitat quality of the reserve may also affect the catch.     

A strategy to increase cooperation in the volunteer's dilemma: reducing vigilance improves alarm calls

One of the most common examples of cooperation in animal societies is giving the alarm in the presence of a predator. A reduction in individual vigilance against predators when group size increases (the "group size effect") is one of the most frequently reported relationships in the study of animal behavior, and is thought to be due to relaxed selection, either because more individuals can detect the predator more easily (the "many eyes" effect) or because the risk of predator attack is diluted on more individuals (the "selfish herd" effect). I show that these hypotheses are not theoretically grounded: because everybody relies on someone else to raise the alarm, the probability that at least one raises the alarm declines with group size; therefore increasing group size does not lead to relaxed selection. Game theory shows, instead, that increasing the risk that the predator is not reported (by reducing vigilance) induces everybody to give the alarm more often. The group size effect, therefore, can be due to strategic behavior to improve the production of a public good. This shows how a selfish behavior can lead to a benefit for the group, and suggests a way to solve social dilemmas in the absence of relatedness and repeated interactions.     

Evolution of dispersal in density regulated populations: A haploid model

The evolution of dispersal is explored in a density-dependent framework. Attention is restricted to haploid populations in which the genotypic fitnesses at a single diallelic locus are decreasing functions of the changing number of individuals in the population. It is shown that migration between two populations in which the genotypic response to density is reversed can maintain both alleles when the intermigration rates are constant or nondecreasing functions of the population densities. There is always a unique symmetric interior equilibrium with equal numbers but opposite gene frequencies in the two populations, provided the system is not degenerate. Numerical examples with exponential and hyperbolic fitnesses suggest that this is the only stable equilibrium state under constant positive migration rates (m) less than . Practically speaking, however, there is only convergence after a reasonable number of generations for relatively small migration rates ( ). A migration-modifying mutant at a second, neutral locus, can successfully enter two populations at a stable migration-selection balance if and only if it reduces the intermigration rates of its carriers at the original equilibrium population size. Moreover, migration modification will always result in a higher equilibrium population size, provided the system approaches another symmetric interior equilibrium. The new equilibrium migration rate will be lower than that at the original equilibrium, even when the modified migration rate is a nondecreasing function of the population sizes. Therefore, as in constant viability models, evolution will lead to reduced dispersal.     

Statolith morphometrics as a tool to distinguish among populations of three cubozoan species

Timely identification of endangered populations is vital to save them from extirpation. Here we tested whether six commonly used early-warning metrics are useful predictors of impending extirpation in laboratory rotifer (Brachionus calyciflorus) populations. To this end, we cultured nine rotifer clones in a constant laboratory environment, in which the rotifer populations were known to grow well, and in a deteriorating environment, in which the populations eventually perished. We monitored population densities in both environments until the populations in the deteriorating environment had gone extinct. We then used the population-density time series to compute the early-warning metrics and the temporal trends in these metrics. We found true positives (i.e. correct signals) in only two metrics, the standard deviation and the coefficient of variation, but the standard deviation also generated a false positive. Moreover, the signal produced by the coefficient of variation appeared when the populations in the deteriorating environment were about to cross the critical threshold and began to decline. As such, it cannot be regarded as an early-warning signal. Together, these findings support the growing evidence that density-based generic early-warning metrics—against their intended use—might not be universally suited to identify populations that are about to collapse.     

Experimental evidence for the adaptive value of sexual reproduction

It is generally believed that recombination by sexual reproduction is unfavourable in constant environments but is of adaptive value under changing environmental conditions. To test this theory, experimental populations of yeast (Saccharomyces cerevisiae) were set up and maintained at different levels of environmental heterogeneity. Recombination was estimated by determining sporulation rates. Sporulation rates first increased in populations living in highly variable environments, but after some time began to decrease. The decrease started last and was slowest in populations which were maintained under the same conditions for a sufficiently long time, to allow some adaptation of the gene pool to the respective environment. Patterns of genotypic variability could not be interpreted in such simple terms, but there was a statistically significant correlation between sporulation rate and genotypic variability. This correlation is to be expected because recombination generates genotypic variability. Summing up, recombination by sexual reproduction is advantageous in changing environments if the population can track the changes in the environment by changing its genotypic structure.     

Lack of evolutionary stasis during alternating replication of an arbovirus in insect and mammalian cells

The evolution of vesicular stomatitis virus (VSV) in a constant environment, consisting of either mammalian or insect cells, has been compared to the evolution of the same viral population in changing environments consisting in alternating passages in mammalian and insect cells. Fitness increases were observed in all cases. An initial fitness loss of VSV passaged in insect cells was noted when fitness was measured in BHK-21 cells, but this effect could be attributed to a difference of temperature during VSV replication at 37 degrees C in BHK-21 cells. Sequencing of nucleotides 1-4717 at the 3' end of the VSV genome (N, P, M and G genes) showed that at passage 80 the number of mutations accumulated during alternated passages (seven mutations) is similar or larger than that observed in populations evolving in a constant environment (two to four mutations). Our results indicate that insect and mammalian cells can constitute similar environments for viral replication. Thus, the slow rates of evolution observed in natural populations of arboviruses are not necessarily due to the need for the virus to compromise between adaptation to both arthropod and vertebrate cell types.     

Selection for altruism through random drift in variable size populations

ABSTRACT: BACKGROUND: Altruistic behavior is defined as helping others at a cost to oneself and a lowered fitness. The lower fitness implies that altruists should be selected against, which is in contradiction with their widespread presence is nature. Present models of selection for altruism (kin or multilevel) show that altruistic behaviors can have 'hidden' advantages if the 'common good' produced by altruists is restricted to some related or unrelated groups. These models are mostly deterministic, or assume a frequency dependent fitness. RESULTS: Evolutionary dynamics is a competition between deterministic selection pressure and stochastic events due to random sampling from one generation to the next. We show here that an altruistic allele extending the carrying capacity of the habitat can win by increasing the random drift of "selfish" alleles. In other terms, the fixation probability of altruistic genes can be higher than those of a selfish ones, even though altruists have a smaller fitness. Moreover when populations are geographically structured, the altruists advantage can be highly amplified and the fixation probability of selfish genes can tend toward zero. The above results are obtained both by numerical and analytical calculations. Analytical results are obtained in the limit of large populations. CONCLUSIONS: The theory we present does not involve kin or multilevel selection, but is based on the existence of random drift in variable size populations. The model is a generalization of the original Fisher-Wright and Moran models where the carrying capacity depends on the number of altruists.     

Spillover Effects of a Community-Managed Marine Reserve

The value of no-take marine reserves as fisheries-management tools is controversial, particularly in high-poverty areas where human populations depend heavily on fish as a source of protein. Spillover, the net export of adult fish, is one mechanism by which no-take marine reserves may have a positive influence on adjacent fisheries. Spillover can contribute to poverty alleviation, although its effect is modulated by the number of fishermen and fishing intensity. In this study, we quantify the effects of a community-managed marine reserve in a high poverty area of Northern Mozambique. For this purpose, underwater visual censuses of reef fish were undertaken at three different times: 3 years before (2003), at the time of establishment (2006) and 6 years after the marine reserve establishment (2012). The survey locations were chosen inside, outside and on the border of the marine reserve. Benthic cover composition was quantified at the same sites in 2006 and 2012. After the reserve establishment, fish sizes were also estimated. Regression tree models show that the distance from the border and the time after reserve establishment were the variables with the strongest effect on fish abundance. The extent and direction of the spillover depends on trophic group and fish size. Poisson Generalized Linear Models show that, prior to the reserve establishment, the survey sites did not differ but, after 6 years, the abundance of all fish inside the reserve has increased and caused spillover of herbivorous fish. Spillover was detected 1km beyond the limit of the reserve for small herbivorous fishes. Six years after the establishment of a community-managed reserve, the fish assemblages have changed dramatically inside the reserve, and spillover is benefitting fish assemblages outside the reserve.     

Temporal quota corrections based on timing of harvest in a small game species

Theoretical models have shown that the effect of removing a given proportion of the population can be profoundly different if the harvest takes place late in the season compared to early. We explore the effect of these differences using theoretical models based on the concept of demographic value and empirical data on seasonal patterns of natural mortality risk in two contrasting populations of willow ptarmigan in Norway. Based on the theoretical models, we found that changes in the timing of harvest have a much stronger effect in populations with relatively low annual survival compared to populations characterized by longevity typical for species with slow life histories. Also, the timing of harvest is more influential in cases with constant mortality hazards compared to a situation with density-dependent natural mortality. Empirical data from two study populations of willow ptarmigan showed large deviations from the theoretical predictions of models with both constant and density-dependent mortality hazards. There were also large differences in both the temporal pattern and magnitude of annual survival between the two ptarmigan populations (54 vs 26% annual survival). Site differences illustrate the importance of knowledge of both the magnitude and temporal pattern of natural mortality hazard to be able to correctly predict the effect of changing the timing of harvest in a population. In the two ptarmigan populations, we show how harvest quotas can be adjusted in accordance to the empirical estimates of natural mortality risk and how this determines the effects of shifting from harvesting early to late in the annual cycle.