MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Theoretical Population Biology' source. Thu, 09 Feb 2012 14:32:17 +0100 http://www.medworm.com/index.php?rid=5672539&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22306589%26dopt%3DAbstract Authors: Aoki K, Wakano JY, Lehmann L Abstract Individual learning (e.g., trial-and-error) and social learning (e.g., imitation) are alternative ways of acquiring and expressing the appropriate phenotype in an environment. The optimal choice between using individual learning and/or social learning may be dictated by the life-stage or age of an organism. Of special interest is a learning schedule in which social learning precedes individual learning, because such a schedule is apparently a necessary condition for cumulative culture. Assuming two obligatory learning stages per discrete generation, we obtain the evolutionarily stable learning schedules for the three situations where the environment is constant, fluctuates between generations, or fluctuates within generations. During e... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5672539 Fri, 27 Jan 2012 05:00:00 +0100 5672539 http://www.medworm.com/index.php?rid=5672538&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22306590%26dopt%3DAbstract Authors: Finkelstein M Abstract We consider hazard (mortality) rates in heterogeneous populations consisting of ordered (in the defined stochastic sense) subpopulations. This setting can be interpreted via the fixed frailty models with one or more frailty parameters. The shape of the hazard rate is of main interest in this paper. Specifically, the deceleration and leveling off in the hazard rates (mortality plateaus) are discussed and some examples of lifetime distributions that can result in asymptotically flat hazard rates are considered. These examples are based on vitality models when an organism's initial vitality (resource) is 'consumed' in the course of life in accordance with a simple stochastic process (e.g., the Wiener process with drift or the gamma process). PMID: 2... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5672538 Fri, 27 Jan 2012 05:00:00 +0100 5672538 http://www.medworm.com/index.php?rid=5656188&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22285149%26dopt%3DAbstract Authors: Stech H, Peckham B, Pastor J Abstract This paper presents the derivation and partial analysis of a general producer-consumer model. The model is stoichiometric in that it includes the growth constraints imposed by species-specific biomass carbon to nutrient ratios. The model unifies the approaches of other studies in recent years, and is calibrated from an extensive review of the algae-Daphnia literature. Numerical simulations and bifurcation analysis are used to examine the impact of energy enrichment under nutrient and stoichiometric constraints. Our results suggest that the variety of system responses previously cited for related models can be attributed to the size of the total system nutrient pool, which is here assumed fixed. New, more complicated bifurcation sequenc... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5656188 Fri, 20 Jan 2012 05:00:00 +0100 5656188 http://www.medworm.com/index.php?rid=5656187&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22285150%26dopt%3DAbstract Authors: Wang Y, Wu H, Sun S Abstract Interactions between pollinators, nectar robbers, defensive plants and non-defensive plants are characterized by evolutionary games, where payoffs for the four species are represented by population densities at steady states in the corresponding dynamical systems. The plant-robber system is described by a predator-prey model with the Holling II functional response, while the plant-pollinator system is described by a cooperative model with the Beddington-DeAngelis functional response. By combining dynamics of the models with properties of the evolutionary games, we show mechanisms by which pollination mutualisms could persist in the presence of nectar robbers. The analysis leads to an explanation for persistence of plant-pollinator-robber system... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5656187 Fri, 20 Jan 2012 05:00:00 +0100 5656187 http://www.medworm.com/index.php?rid=5656189&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22273833%26dopt%3DAbstract We report the emergence of a circular dynamics in the diffusion process, with an intrinsic frequency, near the endemic steady state. The endemic steady state is represented by a stable node in the deterministic dynamics. As a NESS phenomenon, the circular motion is caused by the intrinsic heterogeneity within the subgroups, leading to a broken symmetry and time irreversibility. PMID: 22273833 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5656189 Mon, 16 Jan 2012 05:00:00 +0100 5656189 http://www.medworm.com/index.php?rid=5656190&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22269092%26dopt%3DAbstract Authors: Vogl C, Clemente F Abstract We analyze a decoupled Moran model with haploid population size N, a biallelic locus under mutation and drift with scaled forward and backward mutation rates θ(1)=μ(1)N and θ(0)=μ(0)N, and directional selection with scaled strength γ=sN. With small scaled mutation rates θ(0) and θ(1), which is appropriate for single nucleotide polymorphism data in highly recombining regions, we derive a simple approximate equilibrium distribution for polymorphic alleles with a constant of proportionality. We also put forth an even simpler model, where all mutations originate from monomorphic states. Using this model we derive the sojourn times, conditional on the ancestral and fixed allele, and under equilibrium the distributions of fixed and polymorphic ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5656190 Fri, 13 Jan 2012 05:00:00 +0100 5656190 http://www.medworm.com/index.php?rid=5619196&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22248701%26dopt%3DAbstract We present a simple method to simulate dynamical networks of sexual partnerships. We inform the model using survey data on sexual attitudes and lifestyles, and investigate how the duration of infectiousness changes the effective contact network over which disease may spread. We then simulate several control strategies: screening, vaccination and behavioural interventions. Previous theory and research has advanced the importance of core groups for spread and control of STD. Our work is consistent with the importance of core groups, but extends this idea to consider how the duration of infectiousness associated with a particular pathogen interacts with host behaviours to define these high risk subpopulations. Characteristics of the parts of the network accessible to the pathogen, which repre... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5619196 Sun, 08 Jan 2012 05:00:00 +0100 5619196 http://www.medworm.com/index.php?rid=5619197&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22227065%26dopt%3DAbstract Authors: Wikström A, Ripa J, Jonzén N Abstract Understanding the processes generating fluctuations of natural populations lies at the very heart of academic ecology. It is also very important for applications such as fisheries management and pest control. We are interested in the effect of harvesting on population fluctuations and for that purpose we develop and analyze an age-structured model where recruitment is a stochastic process and the adult segment of the population is harvested. When a constant annual harvest is taken the coefficient of variation of the adult population increases for most parameter values due to the age truncation effect, i.e. an increased variability in a juvenescent population due to the removal of older individuals. However, if a constant proportion o... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5619197 Tue, 27 Dec 2011 05:00:00 +0100 5619197 http://www.medworm.com/index.php?rid=5576697&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22212374%26dopt%3DAbstract Authors: Mougi A Abstract Population dynamics and evolutionary dynamics can occur on similar time scales, and a coupling of these two processes can lead to novel population dynamics. Recent theoretical studies of coevolving predator-prey systems have concentrated more on the stability of such systems than on the characteristics of cycles when they are unstable. Here I explore the characteristics of the cycles that arise due to coevolution in a system in which prey can increase their ability to escape from predators by becoming either significantly larger or significantly smaller in trait value (i.e., a bidirectional trait axis). This is a reasonable model of body size evolution in some systems. The results show that antiphase population cycles and cryptic cycles (large population ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5576697 Thu, 22 Dec 2011 05:00:00 +0100 5576697 http://www.medworm.com/index.php?rid=5557932&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22209755%26dopt%3DAbstract Authors: Kucharski AJ, Gog JR Abstract When multiple infections are possible during an individual's lifetime, such as with influenza, a host's history of infection and immunity will determine the result of future exposures. In turn, the suite of varying individual infection histories will shape the population level dynamics of the disease. Exploring the consequences of precisely how immunity is acquired using mathematical models has proven challenging though: if n strains have circulated previously, there are 2(n) different combinations of past infection to consider. However, by using an age-structured mathematical model of a disease with multiple strains, we can examine the population immune profile without having to explicitly keep track of all possible infection histories. This ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5557932 Thu, 22 Dec 2011 05:00:00 +0100 5557932 http://www.medworm.com/index.php?rid=5557931&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22210390%26dopt%3DAbstract Authors: Heled J Abstract The study of sequence diversity under phylogenetic models is now classic. Theoretical studies of diversity under the Kingman coalescent appeared shortly after the introduction of the coalescent. In this paper we revisit this topic under the multispecies coalescent, an extension of the single population model to multiple populations. We derive exact formulas for the sequence dissimilarity of two sequences drawn at random under a basic multispecies setup. The multispecies model uses three parameters-the species tree birth rate under the pure birth process (Yule), the species effective population size and the mutation rate. We also discuss the effects of relaxing some of the model assumptions. PMID: 22210390 [PubMed - as supplied by publisher] (Source: Th... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5557931 Wed, 21 Dec 2011 05:00:00 +0100 5557931 http://www.medworm.com/index.php?rid=5557930&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22210391%26dopt%3DAbstract Authors: Chasnov JR Abstract Under haploid selection, a multi-locus, diallelic, two-niche Levene (1953) model is studied. Viability coefficients with symmetrically opposing directional selection in each niche are assumed, and with a further simplification that the most and least favored haplotype in each niche shares no alleles in common, and that the selection coefficients monotonically increase or decrease with the number of alleles shared. This model always admits a fully polymorphic symmetric equilibrium, which may or may not be stable. We show that a stable symmetric equilibrium can become unstable via either a supercritical or subcritical pitchfork bifurcation. In the supercritical bifurcation, the symmetric equilibrium bifurcates to a pair of stable fully polymorphic asymmet... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5557930 Wed, 21 Dec 2011 05:00:00 +0100 5557930 http://www.medworm.com/index.php?rid=5557933&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22200649%26dopt%3DAbstract This article is concerned with the choice of structural prior density for use in a fully Bayesian approach to pedigree inference. It is found that the choice of prior has considerable influence on the accuracy of the estimation. To guide this choice, a scale invariance property is introduced. Under a structural prior with this property, the marginal prior distribution of the local properties of a pedigree node (number of parents, offspring, etc.) does not depend on the number of nodes in the pedigree. Such priors are found to arise naturally by an application of the Minimum Description Length (MDL) principle, under which construction of a prior becomes equivalent to the problem of determining the length of a code required to encode a pedigree, using the principles of information theory. Tw... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5557933 Mon, 19 Dec 2011 05:00:00 +0100 5557933 http://www.medworm.com/index.php?rid=5544809&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22198521%26dopt%3DAbstract Authors: Desai MM, Nicolaisen LE, Walczak AM, Plotkin JB Abstract In the absence of selection, the structure of equilibrium allelic diversity is described by the elegant sampling formula of Ewens. This formula has helped to shape our expectations of empirical patterns of molecular variation. Along with coalescent theory, it provides statistical techniques for rejecting the null model of neutrality. However, we still do not fully understand the statistics of the allelic diversity expected in the presence of natural selection. Earlier work has described the effects of strongly deleterious mutations linked to many neutral sites, and allelic variation in models where offspring fitness is unrelated to parental fitness, but it has proven difficult to understand allelic diversity in the p... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5544809 Fri, 16 Dec 2011 05:00:00 +0100 5544809 http://www.medworm.com/index.php?rid=5526519&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22186167%26dopt%3DAbstract Authors: Anazawa M Abstract This paper provides first-principles derivations of population models for competition involving multiple resources with different competition types, based on resource partitioning between individuals. The following two cases are investigated. The first is the case in which the resource competed for and its competition type change depending on life stages from scramble to contest competition, or from contest to scramble competition. The second is the case in which individuals compete for two resources simultaneously with scramble and contest types, respectively. In both cases, population models are derived analytically, and in particular, the Hassell model is derived in the second case. The nature of reproduction curves and the stability properties of thr... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5526519 Tue, 13 Dec 2011 05:00:00 +0100 5526519 http://www.medworm.com/index.php?rid=5526520&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178687%26dopt%3DAbstract Authors: Metcalf CJ, Lessler J, Klepac P, Morice A, Grenfell BT, Bjørnstad ON Abstract The usage of structured population models can make substantial contributions to public health, particularly for infections where clinical outcomes vary over age. There are three theoretical challenges in implementing such analyses: (i) developing an appropriate framework that models both demographic and epidemiological transitions; (ii) parameterizing the framework, where parameters may be based on data ranging from the biological course of infection, basic patterns of human demography, specific characteristics of population growth, and details of vaccination regimes implemented; (iii) evaluating public health strategies in the face of changing human demography. We illustrate the general approac... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5526520 Fri, 09 Dec 2011 05:00:00 +0100 5526520 http://www.medworm.com/index.php?rid=5526521&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178309%26dopt%3DAbstract We present a methodology to calculate the hazard rate for situations with time-varying gene flow from a crop to a large recipient wild population. As an illustration, several types of time-inhomogeneity are examined, including deterministic periodicity as well as random variation. Furthermore, we examine the effects of an extended fitness bottleneck of hybrids and backcrosses in combination with time-varying gene flow. It is found that bottlenecks decrease the hazard rate, but also slow down and delay its changes in reaction to changes in gene flow. Furthermore, we find that random variation in gene flow generates a lower hazard rate than analogous deterministic variation. We discuss the implications of our findings for crop management and introgression risk assessment. PMID: 22178309 ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5526521 Thu, 08 Dec 2011 05:00:00 +0100 5526521 http://www.medworm.com/index.php?rid=5506933&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22155293%26dopt%3DAbstract We present a new approach to estimate the rate and selective advantage of beneficial mutations that underlie the adaptation of asexual populations. We base our approach on the analysis of experiments that track the effect of newly arising beneficial mutations on the dynamics of a neutral marker in evolving bacterial populations and develop efficient estimators of mutation rate and selective advantage. Using extensive simulations, we evaluate the accuracy of our estimators and conclude that they are quite robust to the use of relatively low experimental replication. To validate the predictions of our model, we compare theoretical and experimentally determined estimates of the selective advantage of the first beneficial mutation to fix in a series of ten replicate populations. We find that o... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5506933 Sat, 03 Dec 2011 05:00:00 +0100 5506933 http://www.medworm.com/index.php?rid=5506932&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22155588%26dopt%3DAbstract Authors: Chen H Abstract The allele frequency spectrum is a series of statistics that describe genetic polymorphism, and is commonly used for inferring population genetic parameters and detecting natural selection. Population genetic theory on the allele frequency spectrum for a single population has been well studied using both coalescent theory and diffusion equations. Recently, the theory was extended to the joint allele frequency spectrum (JAFS) for three populations using diffusion equations and was shown to be very useful in inferring human demographic history. In this paper, I show that the JAFS can be analytically derived with coalescent theory for a basic model of two isolated populations and then extended to multiple populations and various complex scenarios, such as thos... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5506932 Fri, 02 Dec 2011 05:00:00 +0100 5506932 http://www.medworm.com/index.php?rid=5506934&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22142718%26dopt%3DAbstract Authors: Rebarber R, Tenhumberg B, Townley S Abstract Many stage-structured density dependent populations with a continuum of stages can be naturally modeled using nonlinear integral projection models. In this paper, we study a trichotomy of global stability result for a class of density dependent systems which include a Platte thistle model. Specifically, we identify those systems parameters for which zero is globally asymptotically stable, parameters for which there is a positive asymptotically stable equilibrium, and parameters for which there is no asymptotically stable equilibrium. PMID: 22142718 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5506934 Mon, 28 Nov 2011 05:00:00 +0100 5506934 http://www.medworm.com/index.php?rid=5506935&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22120126%26dopt%3DAbstract Authors: Chatterjee K, Reiter JG, Nowak MA Abstract Many scenarios in the living world, where individual organisms compete for winning positions (or resources), have properties of auctions. Here we study the evolution of bids in biological auctions. For each auction, n individuals are drawn at random from a population of size N. Each individual makes a bid which entails a cost. The winner obtains a benefit of a certain value. Costs and benefits are translated into reproductive success (fitness). Therefore, successful bidding strategies spread in the population. We compare two types of auctions. In "biological all-pay auctions", the costs are the bid for every participating individual. In "biological second price all-pay auctions", the cost for everyone other than the winner is the ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5506935 Sat, 19 Nov 2011 05:00:00 +0100 5506935 http://www.medworm.com/index.php?rid=5506936&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22100752%26dopt%3DAbstract Authors: Griswold CK, Eisner DJ Abstract In this paper we present a model that maps epistatic effects onto a genealogical tree for a haploid population. Prior work has demonstrated that genealogical structure causes the genotypic values of individuals to covary. Our results indicate that epistasis can reduce genotypic covariance that is caused by genealogical structure. Genotypic effects (both additive and epistatic) occur along the branches of a genealogical tree, from the base of the tree to its tips. Epistasis reduces genotypic covariance because there is a reweighting of the contribution of branches to the states of genotypes compared to the additive case. Branches near the tips of a genealogical tree contribute proportionally more genetic effects with epistasis than without ep... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5506936 Sat, 12 Nov 2011 05:00:00 +0100 5506936 http://www.medworm.com/index.php?rid=5412885&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22079669%26dopt%3DAbstract Authors: Morozov A, Sen M, Banerjee M Abstract In this paper, we revisit the stabilizing role that predator dispersal and aggregation have in the top-down regulation of predator-prey systems in a heterogeneous environment. We consider an environment consisting of sites interconnected by dispersal, and propose a novel mechanism of stabilization for the case with a non-sigmoid functional response of predators. We assume that the carrying capacity of the prey is infinitely large in each site, and show that successful top-down regulation of this otherwise globally unstable system is made possible through an interplay between the unevenness of prey fitness across the sites and the rapid food-dependent migration of predators. We argue that this mechanism of stabilization is different fro... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5412885 Fri, 04 Nov 2011 04:00:00 +0100 5412885 http://www.medworm.com/index.php?rid=5412884&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22079670%26dopt%3DAbstract Authors: Tachiki Y, Iwasa Y Abstract Many long-lived plants such as trees show masting or intermittent and synchronized reproduction. In a coupled chaos system describing the dynamics of individual-plant resource budgets, masting occurs when the resource depletion coefficient k (ratio of the reproductive expenditure to the excess resource reserve) is large. Here, we mathematically studied the condition for masting evolution. In an infinitely large population, we obtained a deterministic dynamical system, to which we applied the pairwise invasibility plot and convergence stability of evolutionary singularity analyses. We prove that plants reproducing at the same rate every year are not evolutionarily stable. The resource depletion coefficient k increases, and the system oscillates w... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5412884 Fri, 04 Nov 2011 04:00:00 +0100 5412884 http://www.medworm.com/index.php?rid=5294189&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21801738%26dopt%3DAbstract Authors: Proulx SR Abstract Several groups have recently modeled evolutionary transitions from an ancestral allele to a beneficial allele separated by one or more intervening mutants. The beneficial allele can become fixed if a succession of intermediate mutants are fixed or alternatively if successive mutants arise while the previous intermediate mutant is still segregating. This latter process has been termed stochastic tunneling. Previous work has focused on the Moran model of population genetics. I use elementary methods of analyzing stochastic processes to derive the probability of tunneling in the limit of large population size for both Moran and Wright-Fisher populations. I also show how to efficiently obtain numerical results for finite populations. These results show that ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5294189 Sat, 08 Oct 2011 01:40:31 +0100 5294189 http://www.medworm.com/index.php?rid=5273116&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21945887%26dopt%3DAbstract Authors: Arbilly M, Motro U, Feldman MW, Lotem A Abstract A long standing question in evolutionary biology concerns the maintenance of adaptive combinations of traits in the presence of recombination. This problem may be solved if positive epistasis selects for reducing the rate of recombination between such traits, but this requires sufficiently strong epistasis. Here we use a model that we developed previously to analyze a frequency-dependent strategy game in asexual populations, to study how adaptive combinations of traits may be maintained in the presence of recombination when epistasis is too weak to select for genetic linkage. Previously, in the asexual case, our model demonstrated the evolution of adaptive associations between social foraging strategies and learning rules. W... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5273116 Wed, 14 Sep 2011 04:00:00 +0100 5273116 http://www.medworm.com/index.php?rid=5241037&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21925527%26dopt%3DAbstract Authors: Agranovich A, Vider-Shalit T, Louzoun Y Abstract Following cell entry, viruses can be detected by cytotoxic T lymphocytes. These cytotoxic T lymphocytes can induce host cell apoptosis and prevent the propagation of the virus. Viruses with fewer epitopes have a higher survival probability, and are selected through evolution. However, mutations have a fitness cost and on evolutionary periods viruses maintain some epitopes. The number of epitopes in each viral protein is a balance between the selective advantage of having fewer epitopes and the reduced fitness following the epitope removing mutations. We discuss a bioinformatic analysis of the number of epitopes in various viral proteins and propose an optimization framework to explain these numbers. We show, using a genomic ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5241037 Fri, 02 Sep 2011 04:00:00 +0100 5241037 http://www.medworm.com/index.php?rid=5215738&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21888925%26dopt%3DAbstract Authors: Masel J, Lyttle DN Abstract Clonal reproduction of diploids leads to an increase in heterozygosity over time. A single round of selfing will then create new homozygotic genotypes. Given the same allele frequencies, heritable genetic variation is larger when there are more extreme, i.e. homozygotic genotypes. So after a long clonal expansion, one round of selfing increases heritable genetic variation, but any fully or partially recessive deleterious alleles simultaneously impose a fitness cost. Here we calculate that the cost of selfing in the yeast Saccharomyces is experienced only by a minority of zygotes. This allows a round of selfing to act as an evolutionary capacitor to unlock genetic variation previously found in a cryptic heterozygous form. We calculate the evoluti... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5215738 Wed, 24 Aug 2011 04:00:00 +0100 5215738 http://www.medworm.com/index.php?rid=5189503&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21884715%26dopt%3DAbstract Authors: Garay J, Varga Z Abstract We consider a survival game of gregarious individuals, in which the aim of the players is survival to reproductive age under predator attacks. The survivor's dilemma (shortly: SVD) game consists in the following: a group member either surely survives alone by fleeing, while its defensive mate may be killed; or tries to save its mate's life, risking to get killed. The dilemma is that, in every single attack, fleeing ensures maximal survival probability, but if its mate survives by fighting both, and they remain together, its risk to be killed at the next attack will be lower. We show that, if defense is successful enough, then the one-attack game is a prisoner's dilemma (PD), where fleeing is the strict ESS. We have additively decomposed the SVD ga... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5189503 Mon, 22 Aug 2011 23:00:00 +0100 5189503 http://www.medworm.com/index.php?rid=5171312&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21867722%26dopt%3DAbstract Authors: Rinaldi S Abstract A minimal model for the interactions of trees, insects, and their enemies suggests a simple formula for splitting all forests where insect outbreaks can occur into two categories: where outbreaks are periodic and endogenously generated and where outbreaks are triggered by exogenous factors and are, in general, recurrent but aperiodic. The formula is in full agreement with all field studies in which various phenomena triggering insect outbreaks have been identified. The observed consequences of introductions and removals of insects are also well predicted by the minimal model. But, even more surprisingly, the model allows a simple and explicit condition for the synchronization of outbreaks in spatially extended forests to be derived analytically. This con... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5171312 Mon, 15 Aug 2011 23:00:00 +0100 5171312 http://www.medworm.com/index.php?rid=5147441&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21855559%26dopt%3DAbstract Authors: Geoghegan JL, Spencer HG Abstract There is increasing evidence that epigenetic modifications can be passed from one generation to the next. The population-level consequence of these discoveries, however, remains largely unexplored. In this paper, we introduce and analyze some simple models of constant viability selection acting on such heritable epigenetic variation. These "population-epigenetic" models are analogous to those of traditional population genetics, and are a preliminary step in quantifying the effect of non-genomic transgenerational inheritance, aiming to improve our understanding of how this sort of environmental response may affect evolution. PMID: 21855559 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5147441 Mon, 08 Aug 2011 23:00:00 +0100 5147441 http://www.medworm.com/index.php?rid=5089965&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21801738%26dopt%3DAbstract Authors: Proulx SR Several groups have recently modeled evolutionary transitions from an ancestral allele to a beneficial allele separated by one or more intervening mutants. The beneficial allele can become fixed if a succession of intermediate mutants are fixed or alternatively if successive mutants arise while the previous intermediate mutant is still segregating. This latter process has been termed stochastic tunneling. Previous work has focused on the Moran model of population genetics. I use elementary methods of analyzing stochastic processes to derive the probability of tunneling in the limit of large population size for both Moran and Wright-Fisher populations. I also show how to efficiently obtain numerical results for finite populations. These results show that the probabili... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5089965 Fri, 22 Jul 2011 23:00:00 +0100 5089965 http://www.medworm.com/index.php?rid=5089961&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21801739%26dopt%3DAbstract Authors: Bürger R, Akerman A Population subdivision and migration are generally considered to be important causes of linkage disequilibrium (LD). We explore the combined effects of recombination and gene flow on the amount of LD, the maintenance of polymorphism, and the degree of local adaptation in a subdivided population by analyzing a diploid, deterministic continent-island model with genic selection on two linked loci (i.e., no dominance or epistasis). For this simple model, we characterize explicitly all possible equilibrium configurations. Simple and intuitive approximations for many quantities of interest are obtained in limiting cases, such as weak migration, weak selection, weak or strong recombination. For instance, we derive explicit expressions for the measures D(=p(AB)-p(... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5089961 Fri, 22 Jul 2011 23:00:00 +0100 5089961 http://www.medworm.com/index.php?rid=5039123&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21767557%26dopt%3DAbstract We present an epidemiological example and evaluate the system for third and fourth moments compared with Monte Carlo simulations. PMID: 21767557 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5039123 Thu, 14 Jul 2011 23:00:00 +0100 5039123 http://www.medworm.com/index.php?rid=5039124&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21763708%26dopt%3DAbstract Authors: Zhang C, Zhang J, Xie G, Wang L We study the evolution of cooperation in spatial prisoner's dilemma games, whereby each player extends its interaction scope by trying to interact with a certain number of encounters randomly chosen from its non-neighbors, in addition to its permanently linked nearest neighbors. Furthermore, the non-neighbors treat the initiative interactions in two scenarios: definitely accepting that from the cooperators, whereas guardedly interacting with defectors with an acceptance probability which may take arbitrary value in [0,1]. Importantly, our results reveal that the proposed encounter mechanism is a potent extrinsic factor that is able to boost cooperation when appropriately adjusting the values of the encounter number and acceptance probability, th... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5039124 Thu, 07 Jul 2011 23:00:00 +0100 5039124 http://www.medworm.com/index.php?rid=5039125&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21763337%26dopt%3DAbstract Authors: Macbeth GM, Broderick D, Ovenden JR, Buckworth RC Genotypes produced from samples collected non-invasively in harsh field conditions often lack the full complement of data from the selected microsatellite loci. The application to genetic mark-recapture methodology in wildlife species can therefore be prone to misidentifications leading to both 'true non-recaptures' being falsely accepted as recaptures (Type I errors) and 'true recaptures' being undetected (Type II errors). Here we present a new likelihood method that allows every pairwise genotype comparison to be evaluated independently. We apply this method to determine the total number of recaptures by estimating and optimising the balance between Type I errors and Type II errors. We show through simulation that the standar... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=5039125 Tue, 05 Jul 2011 23:00:00 +0100 5039125 http://www.medworm.com/index.php?rid=4997163&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21718713%26dopt%3DAbstract Authors: Der R, Epstein CL, Plotkin JB The Wright-Fisher model of allele dynamics forms the basis for most theoretical and applied research in population genetics. Our understanding of genetic drift, and its role in suppressing the deterministic forces of Darwinian selection has relied on the specific form of sampling inherent to the Wright-Fisher model and its diffusion limit. Here we introduce and analyze a broad class of forward-time population models that share the same mean and variance as the Wright-Fisher model, but may otherwise differ. The proposed class unifies and further generalizes a number of population-genetic processes of recent interest, including the Λ and Cannings processes. Even though these models all have the same variance effective population size, they encode a... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4997163 Sun, 26 Jun 2011 23:00:00 +0100 4997163 http://www.medworm.com/index.php?rid=4997166&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21708180%26dopt%3DAbstract Authors: Chisholm R Previous research into the neutral theory of biodiversity has focused mainly on equilibrium solutions rather than time-dependent solutions. Understanding the time-dependent solutions is essential for applying neutral theory to ecosystems in which time-dependent processes, such as succession and invasion, are driving the dynamics. Time-dependent solutions also facilitate tests against data that are stronger than those based on static equilibrium patterns. Here I investigate the time-dependent solutions of the classic spatially implicit neutral model, in which a small local community is coupled to a much larger metacommunity through immigration. I present explicit general formulas for the eigenvalues, left eigenvectors and right eigenvectors of the transition matrix t... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4997166 Thu, 23 Jun 2011 23:00:00 +0100 4997166 http://www.medworm.com/index.php?rid=4997165&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21712051%26dopt%3DAbstract Authors: Eshel I, Sansone E, Shaked A The phenomenon of group escape cannot be explained by an argument of risk dilution, applied to gregarious behaviour of passive prey whose risk of predation is equally shared by all group members (Hamilton, 1971). Instead, individuals at the tail of an escaping group suffer the bulk of the group's predation risk, and thus have the highest incentive to desert it. Just because of this, desertion, in this case, may serve as a signal of vulnerability for the pursuing predator. Under wide conditions, it is therefore shown that the predator is always expected to prefer the chasing of a deserter, whenever it is observed. Consequently, an individual who finds himself at the tail of the herd must compare the risk of remaining there with that of deserting the... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4997165 Mon, 20 Jun 2011 23:00:00 +0100 4997165 http://www.medworm.com/index.php?rid=4997164&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21718712%26dopt%3DAbstract Authors: Fusco D, Uyenoyama MK Adaptation to local conditions within demes balanced by migration can maintain polymorphisms for variants that reduce fitness in certain ecological contexts. Here, we address the effects of such polymorphisms on the rate of introgression of neutral marker genes, possibly genetically linked to targets of selection. Barriers to neutral gene flow are expected to increase with linkage to targets of local selection and with differences between demes in the frequencies of locally adapted alleles. This expectation is borne out under purifying and disruptive selection, regimes that promote monomorphism within demes. In contrast, overdominance within demes induces minimal barriers to neutral introgression even in the face of very large differences between demes in... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4997164 Mon, 20 Jun 2011 23:00:00 +0100 4997164 http://www.medworm.com/index.php?rid=4997167&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21704051%26dopt%3DAbstract Authors: Wakano JY, Kawasaki K, Shigesada N, Aoki K Individual learning and social learning are two primary abilities supporting cultural evolution. Conditions for their evolution have mostly been studied by investigating gene frequency dynamics, which essentially implies constant population size. Predictions from such "static" models may only be of partial relevance to the evolution of advanced individual learning in modern humans, because modern humans have experienced rapid population growth and range expansion during "out-of-Africa." Here we model the spatial population dynamics of individual and social learners by a reaction-diffusion system. One feature of our model is the inclusion of the possibility that social learners may fail to find an exemplar to copy in regions where the ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4997167 Wed, 15 Jun 2011 23:00:00 +0100 4997167 http://www.medworm.com/index.php?rid=4947217&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21640742%26dopt%3DAbstract Authors: Boca SM, Rosenberg NA We consider the properties of the F(st) measure of genetic divergence between an admixed population and its parental source populations. Among all possible populations admixed among an arbitrary set of parental populations, we show that the value of F(st) between an admixed population and a specific source population is maximized when the admixed population is simply the most distant of the other source populations. For the case with only two parental populations, as a function of the admixture fraction, we further demonstrate that this F(st) value is monotonic and convex, so that F(st) is informative about the admixture fraction. We illustrate our results using example human population-genetic data, showing how they provide a framework in which to interp... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4947217 Tue, 24 May 2011 23:00:00 +0100 4947217 http://www.medworm.com/index.php?rid=4897849&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21609727%26dopt%3DAbstract Authors: Beltrán-Sánchez H, Soneji S For over forty years, demographers have worked intensely to develop methods that assess a gain in life expectancy from a reduction in mortality, either hypothetical or observed. This considerable body of research was motivated by assessing the gains in life expectancy when mortality declined in a particular manner and determining the contribution of a cause of death in observed changes in life expectancy over time. As yet, there has been no framework unifying this important demographic work. In this paper, we provide a unifying framework for assessing the change in life expectancy given a change in age- and cause-specific mortality. We consider both conceptualizations of mortality change-counterfactual assessment of a hypothetical change and a ret... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4897849 Wed, 11 May 2011 23:00:00 +0100 4897849 http://www.medworm.com/index.php?rid=4897850&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21600234%26dopt%3DAbstract Authors: Missov TI, Finkelstein M Statistical analysis of data on the longest living humans leaves room for speculation whether the human force of mortality is actually leveling off. Based on this uncertainty, we study a mixture failure model, introduced by Finkelstein and Esaulova (2006) that generalizes, among others, the proportional hazards and accelerated failure time models. In this paper we first, extend the Abelian theorem of these authors to mixing distributions, whose densities are functions of regular variation. In addition, taking into account the asymptotic behavior of the mixture hazard rate prescribed by this Abelian theorem, we prove three Tauberian-type theorems that describe the class of admissible mixing distributions. We illustrate our findings with examples of pop... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4897850 Mon, 09 May 2011 23:00:00 +0100 4897850 http://www.medworm.com/index.php?rid=4851398&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21570994%26dopt%3DAbstract Authors: Guillon JM, Bottein J Sex-biased dispersal occurs in all seed plants and many animal species. Theoretical models have shown that sex-biased dispersal can lead to evolutionarily stable biased sex ratios. Here, we use a spatially explicit chessboard model to simulate the evolution of sex ratio in response to sex-biased dispersal range and sex-biased dispersal rate. Two life cycles are represented in the model: one in which both sexes disperse before mating (DDM), the other in which males disperse before mating and mated females or zygotes disperse after mating (DMD). Model parameters include factors like dispersal rate, dispersal range, number of individuals per patch, and habitat heterogeneity. When dispersal range is sex biased, we find that, in a homogeneous environment, the ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4851398 Thu, 05 May 2011 23:00:00 +0100 4851398 http://www.medworm.com/index.php?rid=4851396&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21575649%26dopt%3DAbstract Authors: Song S, Dey DK, Holsinger KE Microsatellite loci are widely used for investigating patterns of genetic variation within and among populations. Those patterns are in turn determined by population sizes, migration rates, and mutation rates. We provide exact expressions for the first two moments of the allele frequency distribution in a stochastic model appropriate for studying microsatellite evolution with migration, mutation, and drift under the assumption that the range of allele sizes is bounded. Using these results, we study the behavior of several measures related to Wright's F(ST), including Slatkin's R(ST). Our analytical approximations for F(ST) and R(ST) show that familiar relationships between N(e)m and F(ST) or R(ST) hold when the migration and mutation rates are smal... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4851396 Thu, 05 May 2011 23:00:00 +0100 4851396 http://www.medworm.com/index.php?rid=4851397&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21570995%26dopt%3DAbstract Authors: Eldon B The ratio of singletons to the total number of segregating sites is used to estimate a reproduction parameter in a population model of large offspring numbers without having to jointly estimate the mutation rate. For neutral genetic variation, the ratio of singletons to the total number of segregating sites is equivalent to the ratio of total length of external branches to the total length of the gene genealogy. A multinomial maximum likelihood method that takes into account more frequency classes than just the singletons is developed to estimate the parameter of another large offspring number model. The performance of these methods with regard to sample size, mutation rate, and bias, is investigated by simulation. The expected value of the ratio of the total length of... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4851397 Wed, 04 May 2011 23:00:00 +0100 4851397 http://www.medworm.com/index.php?rid=4851399&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21550359%26dopt%3DAbstract Authors: Jenkins PA, Song YS The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to be polymorphic. This distribution is widely used in population genetic inferences, including statistical tests of neutrality in which a skew in the observed frequency spectrum across independent sites is taken as a signature of departure from neutral evolution. Theoretical aspects of the frequency spectrum have been well studied and several interesting results are available, but they are usually under the assumption that a site has undergone at most one mutation event in the history of the sample. Here, we extend previous theoretical results by allowing for at most two mutation events per sit... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4851399 Wed, 27 Apr 2011 23:00:00 +0100 4851399 http://www.medworm.com/index.php?rid=4798253&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21514313%26dopt%3DAbstract Authors: Szpiech ZA, Rosenberg NA Private microsatellite alleles tend to be found in the tails rather than in the interior of the allele size distribution. To explain this phenomenon, we have investigated the size distribution of private alleles in a coalescent model of two populations, assuming the symmetric stepwise mutation model as the mode of microsatellite mutation. For the case in which four alleles are sampled, two from each population, we condition on the configuration in which three distinct allele sizes are present, one of which is common to both populations, one of which is private to one population, and the third of which is private to the other population. Conditional on this configuration, we calculate the probability that the two private alleles occupy the two tails of ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4798253 Thu, 14 Apr 2011 23:00:00 +0100 4798253 http://www.medworm.com/index.php?rid=4745396&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21510965%26dopt%3DAbstract Authors: Ricotta C, Szeidl L, Moretti M, Blasi C Functional diversity is generally regarded as the constituent of biological diversity that considers how the species functional traits affect ecosystem processes. Due to its ecological relevance, a number of indices of functional diversity have been proposed to date based on distinct objectives and motivations. Such proliferation of indices can be at least partially overcome by a more fundamental mathematical approach. In this paper we propose an intrinsic ordering approach for abundance-weighted measures of functional diversity that is similar to the Lorenz curves used by ecologists for ordering evenness measures. We then discuss the relevance of a number of functional diversity indices that have a behavior compatible with the proposed ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4745396 Mon, 11 Apr 2011 23:00:00 +0100 4745396 http://www.medworm.com/index.php?rid=4745395&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21510966%26dopt%3DAbstract Authors: Elhanati Y, Schuster S, Brenner N Interactions between microorganisms can have a crucial effect on their population dynamics. Typically, interactions are mediated through the environment by molecules and proteins that are products of cell metabolism and physiology; they therefore reflect the internal dynamics of the single cell. In this work we aim to integrate single-cell properties of gene expression that affect indirect interactions between microorganisms under challenging conditions, into a quantitative model of population dynamics. Specifically we address the problem of a microbial population secreting a protein that can actively extract a growth-limiting resource, such as a simple sugar or iron, from the environment. The genes coding for the protein can undergo random ep... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4745395 Mon, 11 Apr 2011 23:00:00 +0100 4745395 http://www.medworm.com/index.php?rid=4745397&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21463645%26dopt%3DAbstract Authors: Steinsaltz D, Tuljapurkar S, Horvitz C We consider stochastic matrix models for population driven by random environments which form a Markov chain. The top Lyapunov exponent a, which describes the long-term growth rate, depends smoothly on the demographic parameters (represented as matrix entries) and on the parameters that define the stochastic matrix of the driving Markov chain. The derivatives of a-the "stochastic elasticities"-with respect to changes in the demographic parameters were derived by Tuljapurkar (1990). These results are here extended to a formula for the derivatives with respect to changes in the Markov chain driving the environments. We supplement these formulas with rigorous bounds on computational estimation errors, and with rigorous derivations of both the... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4745397 Fri, 01 Apr 2011 23:00:00 +0100 4745397 http://www.medworm.com/index.php?rid=4635858&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21426909%26dopt%3DAbstract Authors: Zivković D, Stephan W The allele frequency spectrum has attracted considerable interest for the simultaneous inference of the demographic and adaptive history of populations. In a recent study, Evans et al. (2007) developed a forward diffusion equation describing the allele frequency spectrum, when the population is subject to size changes, selection and mutation. From the diffusion equation, the authors derived a system of ordinary differential equations (ODEs) for the moments in a Wright-Fisher diffusion with varying population size and constant selection. Here, we present an explicit solution for this system of ODEs with variable population size, but without selection, and apply this result to derive the expected spectrum of a sample for time-varying population size. We us... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4635858 Sat, 19 Mar 2011 00:00:00 +0100 4635858 http://www.medworm.com/index.php?rid=4635857&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21426910%26dopt%3DAbstract Authors: Gyllenberg M, Kisdi E, Utz M We find the evolutionarily stable dispersal behaviour of a population that inhabits a heterogeneous environment where patches differ in safety (the probability that a juvenile individual survives until reproduction) and productivity (the total competitive weight of offspring produced by the local individual), assuming that these characteristics do not change over time. The body condition of clonally produced offspring varies within and between families. Offspring compete for patches in a weighted lottery, and dispersal is driven by kin competition. Survival during dispersal may depend on body condition, and competitive ability increases with increasing body condition. The evolutionarily stable strategy predicts that families abandon patches which a... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4635857 Sat, 19 Mar 2011 00:00:00 +0100 4635857 http://www.medworm.com/index.php?rid=4635859&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21420994%26dopt%3DAbstract Authors: Zhu S, Degnan JH, Steel M The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions concerning the probability that pre-specified groups of taxa form monophyletic groups (clades) in the tree. We extend earlier work to derive exact formulae for the probability of finding one or more groups of taxa as clades in a rooted tree, or as 'clans' in an unrooted tree. Our findings are relevant for calculating the statistical significance of observed monophyly and reciprocal monophyly in phylogenetics. PMID: 21420994 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4635859 Fri, 18 Mar 2011 00:00:00 +0100 4635859 http://www.medworm.com/index.php?rid=4635860&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21397621%26dopt%3DAbstract Authors: Tamura K, Ihara Y Evolution of communication is conceptualized as a coevolutionary process in which evolution of signaler and that of receiver occur in an interdependent manner. Three classes of communication, mutualistic, altruistic, and exploiting, are distinguished depending on who gains a benefit or suffers a cost from successful communication. Communication is also dichotomized according to whether individuals are innately able to send and receive relevant signals or they have to acquire those signals culturally. We develop two-locus haploid models that represent the coevolutionary nature of the evolution of communication, and derive the conditions under which communicators can invade a population of non-communicators and those under which a population of communicators is... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4635860 Thu, 17 Mar 2011 00:00:00 +0100 4635860 http://www.medworm.com/index.php?rid=4572154&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21376069%26dopt%3DAbstract Authors: Lukić S, Hey J, Chen K A major challenge in the analysis of population genomics data consists of isolating signatures of natural selection from background noise caused by random drift and gene flow. Analyses of massive amounts of data from many related populations require high-performance algorithms to determine the likelihood of different demographic scenarios that could have shaped the observed neutral single nucleotide polymorphism (SNP) allele frequency spectrum. In many areas of applied mathematics, Fourier Transforms and Spectral Methods are firmly established tools to analyze spectra of signals and model their dynamics as solutions of certain Partial Differential Equations (PDEs). When spectral methods are applicable, they have excellent error properties and are the fa... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4572154 Tue, 01 Mar 2011 00:00:00 +0100 4572154 http://www.medworm.com/index.php?rid=4572155&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21354194%26dopt%3DAbstract In this study, I consider individual variation in two predator traits (prey density perception and handling time) as the sources of the variation in the threshold density, which can make empirical data appear deviated from the expectation. I examine how community models with partial preference and individual variation differ in their dynamics and show that the differences can be substantial. For example, the dynamics of a model based on individual variation can be more stable (e.g., stable in a wider parameter region) than that of a model based on partial preference. As the general statistical property (Jensen's inequality) is a main factor that causes the differences, the results of the study have general implications to the interpretation of models based on average per-capita rates. ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4572155 Thu, 24 Feb 2011 00:00:00 +0100 4572155 http://www.medworm.com/index.php?rid=4572156&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21354193%26dopt%3DAbstract Authors: Sharkey KJ The relationship between system-level and subsystem-level master equations is investigated and then utilised for a systematic and potentially automated derivation of the hierarchy of moment equations in a susceptible-infectious-removed (SIR) epidemic model. In the context of epidemics on contact networks we use this to show that the approximate nature of some deterministic models such as mean-field and pair-approximation models can be partly understood by the identification of implicit anomalous terms. These terms describe unbiological processes which can be systematically removed up to and including the nth order by nth order moment closure approximations. These terms lead to a detailed understanding of the correlations in network-based epidemic models and contribu... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4572156 Wed, 23 Feb 2011 00:00:00 +0100 4572156 http://www.medworm.com/index.php?rid=4517796&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21315753%26dopt%3DAbstract Authors: Aoki K, Lehmann L, Feldman MW Cultural variation in a population is affected by the rate of occurrence of cultural innovations, whether such innovations are preferred or eschewed, how they are transmitted between individuals in the population, and the size of the population. An innovation, such as a modification in an attribute of a handaxe, may be lost or may become a property of all handaxes, which we call "fixation of the innovation." Alternatively, several innovations may attain appreciable frequencies, in which case properties of the frequency distribution-for example, of handaxe measurements-is important. Here we apply the Moran model from the stochastic theory of population genetics to study the evolution of cultural innovations. We obtain the probability that an initia... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4517796 Tue, 15 Feb 2011 00:00:00 +0100 4517796 http://www.medworm.com/index.php?rid=4517797&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21296095%26dopt%3DAbstract We present and discuss new importance sampling schemes for the approximate computation of the sample probability of observed genetic types in the infinitely many sites model from population genetics. More specifically, we extend the 'classical framework', where genealogies are assumed to be governed by Kingman's coalescent, to the more general class of Lambda-coalescents and develop further Hobolth et al.'s (2008) idea of deriving importance sampling schemes based on 'compressed genetrees'. The resulting schemes extend earlier work by Griffiths and Tavaré (1994), Stephens and Donnelly (2000), Birkner and Blath (2008) and Hobolth et al. (2008). We conclude with a performance comparison of classical and new schemes for Beta- and Kingman coalescents. PMID: 21296095 [PubMed - as supplied... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4517797 Fri, 04 Feb 2011 00:00:00 +0100 4517797 http://www.medworm.com/index.php?rid=4517798&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21277883%26dopt%3DAbstract Authors: Buzbas EO, Joyce P, Rosenberg NA Existing inference methods for estimating the strength of balancing selection in multi-locus genotypes rely on the assumption that there are no epistatic interactions between loci. Complex systems in which balancing selection is prevalent, such as sets of human immune system genes, are known to contain components that interact epistatically. Therefore, current methods may not produce reliable inference on the strength of selection at these loci. In this paper, we address this problem by presenting statistical methods that can account for epistatic interactions in making inference about balancing selection. A theoretical result due to Fearnhead (2006) is used to build a multi-locus Wright-Fisher model of balancing selection, allowing for epistat... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4517798 Wed, 26 Jan 2011 00:00:00 +0100 4517798 http://www.medworm.com/index.php?rid=4517799&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21266180%26dopt%3DAbstract Authors: Malaspinas AS, Slatkin M, Song YS We generalize a recently introduced graphical framework to compute the probability that haplotypes or genotypes of two individuals drawn from a finite, subdivided population match. As in the previous work, we assume an infinite-alleles model. We focus on the case of a population divided into two subpopulations, but the underlying framework can be applied to a general model of population subdivision. We examine the effect of population subdivision on the match probabilities and the accuracy of the product rule which approximates multi-locus match probabilities as a product of one-locus match probabilities. We quantify the deviation from predictions of the product rule by R, the ratio of the multi-locus match probability to the product of the on... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4517799 Sun, 23 Jan 2011 00:00:00 +0100 4517799 http://www.medworm.com/index.php?rid=4393891&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21238471%26dopt%3DAbstract Authors: Delitala M, Lorenzi T This paper deals with the development of a mathematical model that describes cancer dynamics at the cellular scale. The selected case study concerns colon and rectum cancer, which originates in colorectal crypts. Cells inside the crypts are assumed to be organized according to a compartmental-like arrangement and to be homogeneously mixing. A mathematical model for cancer progression is proposed here. This model describes the generation of multiple clonal sub-populations of cells at different progression stages in a single crypt. Asymptotic analysis and simulations are developed with an exploratory aim. The obtained results offer some insights into the role played by mutation, proliferation and differentiation phenomena on cancer dynamics. In particular, ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4393891 Fri, 14 Jan 2011 00:00:00 +0100 4393891 http://www.medworm.com/index.php?rid=4314247&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21192962%26dopt%3DAbstract Authors: Rettelbach A, Hermisson J, Dieckmann U, Kopp M We consider a model of sympatric speciation due to frequency-dependent competition, in which it was previously assumed that the evolving traits have a very simple genetic architecture. In the present study, we numerically analyze the consequences of relaxing this assumption. First, previous models assumed that assortative mating evolves in infinitesimal steps. Here, we show that the range of parameters for which speciation is possible increases when mutational steps are large. Second, it was assumed that the trait under frequency-dependent selection is determined by a single locus with two alleles and additive effects. As a consequence, the resultant intermediate phenotype is always heterozygous and can never breed true. To relax ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4314247 Mon, 27 Dec 2010 00:00:00 +0100 4314247 http://www.medworm.com/index.php?rid=4314248&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21185323%26dopt%3DAbstract Authors: Novak S The Levene model is the simplest mathematical model to describe the evolution of gene frequencies in spatially subdivided populations. It provides insight into how locally varying selection promotes a population's genetic diversity. Despite its simplicity, interesting problems have remained unsolved even in the diallelic case. In this paper we answer an open problem by establishing that for two alleles at one locus and J demes, up to 2J-1 polymorphic equilibria may coexist. We first present a proof for the case of stable monomorphisms and then show that the result also holds for protected alleles. These findings allow us to prove that any odd number (up to 2J-1) of equilibria are possible, before we extend the proof to even numbers. We conclude with some numerical resu... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4314248 Wed, 22 Dec 2010 00:00:00 +0100 4314248 http://www.medworm.com/index.php?rid=4314249&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21167191%26dopt%3DAbstract Authors: Tyson RC, Wilson JB, Lane WD The distribution of foragers on the landscape has important consequences to, for example, the spread rate of an invasive species or the outcrossing levels between neighbouring crops. Since forager distribution can be difficult to measure directly, mathematical models are often used to predict the population density of dispersing foragers on the landscape. We model organism movement using a diffusion framework in which the foraging population is divided into two subpopulations engaged in intensive and extensive search modes respectively. Movement in the intensive search mode (ISM) is modeled by diffusion, and movement in the extensive search mode (ESM) is modeled by advection. We show that our model provides a superior fit to organism movement data ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4314249 Wed, 15 Dec 2010 00:00:00 +0100 4314249 http://www.medworm.com/index.php?rid=4214927&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21094655%26dopt%3DAbstract Authors: Leviyang S, Hamilton MB Weir and Cockerham introduced single locus and multiloci F(st) estimators for the parameter θ. These estimators are commonly used, but little beyond their bias and variance is known. In this work, we develop formulas that allow us to describe how the underlying value of θ and the genetic diversity of sampled loci affect the distributions of these estimators. We show that in certain settings, these estimator are close to normal, while in others they are far from normal. We use these results to analyze confidence interval construction for θ, showing that the percentile-t bootstrap works well while the BCa bootstrap works poorly. Our results are derived using a novel coalescent based method. PMID: 21094655 [PubMed - as supplied by publisher] (Source... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4214927 Fri, 19 Nov 2010 00:00:00 +0100 4214927 http://www.medworm.com/index.php?rid=4075259&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20937293%26dopt%3DAbstract Authors: Rendel MD In RNA fitness landscapes with interconnected networks of neutral mutations, neutral precursor mutations can play an important role in facilitating the accessibility of epistatic adaptive mutant combinations. I use an exhaustively surveyed fitness landscape model based on short sequence RNA genotypes (and their secondary structure phenotypes) to calculate the minimum rate at which mutants initially appearing as neutral are incorporated into an adaptive evolutionary walk. I show first, that incorporating neutral mutations significantly increases the number of point mutations in a given evolutionary walk when compared to estimates from previous adaptive walk models. Second, that incorporating neutral mutants into such a walk significantly increases the final fitness en... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4075259 Thu, 07 Oct 2010 23:00:00 +0100 4075259 http://www.medworm.com/index.php?rid=4040841&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20883708%26dopt%3DAbstract In this study, a metapopulation model for hepatitis A virus (HAV) transmission is proposed and analyzed. Analytical results on the asymptotic and transient behaviors of the system are carried out. Based on the available Italian movement data, a national spatial contact matrix at the regional level, which could be used for new studies on the transmission dynamics of other infectious diseases, is derived for modeling fluxes of individuals. Despite the small number of fitted parameters, model simulations are in good agreement with the observed average HAV incidence in all regions. Our results suggest that the mass vaccination program introduced in one Italian region only (Puglia, the one with the highest endemicity level) could have played a role in the decline of HAV incidence in the country... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4040841 Sun, 26 Sep 2010 23:00:00 +0100 4040841 http://www.medworm.com/index.php?rid=4025541&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20875440%26dopt%3DAbstract Authors: Kinezaki N, Kawasaki K, Shigesada N To address how spatial configuration of habitat fragmentation influences the persistence and the rate of spread of an invasive species, we consider three simple periodically fragmented environments, lattice-like corridor environment, island-like environment and striped environment. By numerically analyzing Fisher's equation with the spatially varying diffusion coefficient and the intrinsic growth rate, we find: (1) When the scale of fragmentation is sufficiently large, the minimum favorable area needed for successful invasion is smaller in the order of the lattice-like corridor, striped and island-like environments; (2) When the scale of fragmentation and the fraction of favorable area are sufficiently large, the spreading speeds along conti... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4025541 Thu, 23 Sep 2010 23:00:00 +0100 4025541 http://www.medworm.com/index.php?rid=4025540&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20875441%26dopt%3DAbstract Authors: Pueyo Y, Kefi S, Diaz-Sierra R, Alados CL, Rietkerk M The dynamics of semi-arid plant communities are determined by the interplay between competition and facilitation among plants. The sign and strength of these biotic interactions depend on plant traits. However, the relationships between plant traits and biotic interactions, and the consequences for plant communities are still poorly understood. Our objective here was to investigate, with a modelling approach, the role of plant reproductive traits on biotic interactions, and the consequences for processes such as plant succession and invasion. The dynamics of two plant types were modelled with a spatially-explicit integrodifferential model: (1) a plant with seed dispersal (colonizer of bare soil) and (2)a plant with local ve... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4025540 Thu, 23 Sep 2010 23:00:00 +0100 4025540 http://www.medworm.com/index.php?rid=4025542&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20869378%26dopt%3DAbstract Authors: Nagylaki T Partial panmixia can be regarded as the limiting case of long-distance migration. The effect of incorporating partial panmixia into neutral models of geographical variation is investigated. The monoecious, diploid population is subdivided into randomly mating colonies that exchange gametes independently of genotype. The gametes fuse wholly at random, including self-fertilization. Generations are discrete and nonoverlapping; the analysis is restricted to a single locus; every allele mutates to new alleles at the same rate. Introducing some panmixia intensifies sufficiently weak migration. A general formula is derived for the migration effective population number, N(e), and N(e) is evaluated explicitly in a number of models with nonconservative migration. Usually, N(e... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=4025542 Tue, 21 Sep 2010 23:00:00 +0100 4025542 http://www.medworm.com/index.php?rid=3981401&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20832414%26dopt%3DAbstract Authors: Provorov NA, Vorobyov NI We created the mathematical model for evolution of the Efficiency of Mutualistic Symbioses (EMS) which was estimated as the microsymbiont impacts on the host reproductive potential. Using the example of rhizobia-legume interaction, the relationships were studied between EMS and Functional Integrity of Symbiosis (FIS) which is represented as a measure for concordance of changes in the partners' genotypic frequencies under the environmental fluctuations represented by the minor deviations of the systemic model parameters. The FIS indices correlate positively with EMS values suggesting an enhancement of FIS via the natural selection operating in the partners' populations in favor of high EMS. Due to this selection, nodular habitats may be closed for colon... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3981401 Tue, 07 Sep 2010 23:00:00 +0100 3981401 http://www.medworm.com/index.php?rid=3954595&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20826173%26dopt%3DAbstract Authors: Vuilleumier S, Goudet J, Perrin N Although dispersal is recognized as a key issue in several fields of population biology (such as behavioral ecology, population genetics, metapopulation dynamics or evolutionary modeling), these disciplines focus on different aspects of the concept and often make different implicit assumptions regarding migration models. Using simulations, we investigate how such assumptions translate into effective gene flow and fixation probability of selected alleles. Assumptions regarding migration type (e.g. source-sink, resident pre-emption, or balanced dispersal) and patterns (e.g. stepping-stone versus island dispersal) have large impacts when demes differ in sizes or selective pressures. The effects of fragmentation, as well as the spatial localizatio... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3954595 Thu, 02 Sep 2010 23:00:00 +0100 3954595 http://www.medworm.com/index.php?rid=3954596&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20816882%26dopt%3DAbstract Authors: Bichsel M, Barbour AD, Wagner A Bacterial insertion sequences are the simplest form of autonomous mobile DNA. It is unknown whether they need to have beneficial effects to infect and persist in bacterial populations, or whether horizontal gene transfer suffices for their persistence. We address this question by using branching process models to investigate the critical, early phase of an insertion sequence infection. We find that the probability of a successful infection is low and depends linearly on the difference between the rate of horizontal gene transfer and the fitness cost of the insertion sequences. Our models show that the median time to extinction of an insertion sequence that dies out is very short, while the median time for a successful infection to reach a modest... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3954596 Wed, 01 Sep 2010 23:00:00 +0100 3954596 http://www.medworm.com/index.php?rid=3954597&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20736029%26dopt%3DAbstract Authors: Fishman MA, Hadany L We formulate and analyze a multi-generation population dynamics model for pollinators' mutualism with plants. The centerpiece of our model is an analytical expression for population-level plant-pollinator interactions extrapolated from a model of individual-level flowers and bees interactions. We also show that this analytical expression can be productively approximated by the Beddington-DeAngelis formula-a function used to model trophic interactions in mathematical ecology. PMID: 20736029 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3954597 Sat, 21 Aug 2010 23:00:00 +0100 3954597 http://www.medworm.com/index.php?rid=3899815&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20727367%26dopt%3DAbstract Authors: Nakahashi W Humans strongly depend on individual and social learning, both of which are highly effective and accurate. I study the effects of environmental change on the evolution of the effectiveness and accuracy of individual and social learning (individual and social learning levels) and the number of pieces of information learned individually and socially (individual and social learning capacities) by analyzing a mathematical model. I show that individual learning capacity decreases and social learning capacity increases when the environment becomes more stable; both decrease when the environment becomes milder. I also show that individual learning capacity increases when individual learning level increases or social learning level decreases, while social learning capacity... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3899815 Mon, 16 Aug 2010 23:00:00 +0100 3899815 http://www.medworm.com/index.php?rid=3853097&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20691199%26dopt%3DAbstract We present an age-structured model for two Pacific salmon species with environmental variability in survival rate and in individual growth rate, hence spawning age distribution. We use computed frequency response curves and analysis of the linearized dynamics to obtain two main results. First, the frequency response of the population is affected by the life history stage at which variability affects the population; varying growth rate tends to excite periodic resonance in age structure, while varying survival tends to excite low-frequency fluctuation with more effect on total population size. Second, decreasing adult survival strengthens the cohort resonance effect at all frequencies, a finding that addresses the question of how fishing and climate change will interact. PMID: 20691199 ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3853097 Mon, 02 Aug 2010 23:00:00 +0100 3853097 http://www.medworm.com/index.php?rid=3823524&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20674582%26dopt%3DAbstract Authors: Saito Y, Miki T Competition theory has developed separately for direct competition and for exploitative competition. However, the combined effects of the two types of competition on species coexistence remain unclear. To examine how intra- and interspecific direct competition contributes to the coexistence of species competing for a single resource, we constructed a chemostat-type resource competition model. With general functions for intra- and interspecific direct competition, we derived necessary and sufficient conditions (except for a critical case that rarely occurs in a biological sense) that determine the number of stably coexisting species. From these conditions, we found that the number of coexisting species is determined just by the invasibility of each species into ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3823524 Wed, 28 Jul 2010 23:00:00 +0100 3823524 http://www.medworm.com/index.php?rid=3823525&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20673775%26dopt%3DAbstract Authors: Brooks M, Iwasa Y Almost all models of sex change evolution assume that reproductive rate increases with body size. However, size-dependent sex changing plants often show size-independent reproductive success, presumably due to pollen limitation. Can the observed size-dependent sex change pattern be the ESS in this case? To answer this question, we analyze a game model of size-dependent sex expression in plants. We assume: (1) reproductive rate is perfectly independent of size; (2) mortality decreases with size in the same way for both sexes; (3) growth rates decrease at maturity, more for females than males. We show that the ESS is size-dependent sex expression: small individuals are vegetative, intermediate individuals are male, and large individuals are female. These result... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3823525 Mon, 26 Jul 2010 23:00:00 +0100 3823525 http://www.medworm.com/index.php?rid=3776837&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20633572%26dopt%3DAbstract We present a statistical model for incorporating the extra variability in allelic counts due to subpopulation structures. In forensic genetics, this effect is modelled by the identical-by-descent-parameter theta, which measures the relationship between pairs of alleles within a population relative to the relationship of alleles between populations (Weir, 2007). In our statistical approach, we demonstrate that theta may be defined as an overdispersion parameter capturing the subpopulation effects. This formulation allows derivation of maximum likelihood estimates of the allele probabilities and theta together with computation of profile log-likelihood, confidence intervals and hypothesis testing. In order to compare our method with existing methods, we reanalysed FBI-data from Budowle and M... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3776837 Sun, 11 Jul 2010 23:00:00 +0100 3776837 http://www.medworm.com/index.php?rid=3758902&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20619285%26dopt%3DAbstract Authors: Sagitov S, Jagers P, Vatutin V We establish convergence to the Kingman coalescent for the genealogy of a geographically - or otherwise - structured version of the Wright-Fisher population model with fast migration. The new feature is that migration probabilities may change in a random fashion. This brings a novel formula for the coalescent effective population size (EPS). We call it a quenched EPS to emphasize the key feature of our model - random environment. The quenched EPS is compared with an annealed (mean-field) EPS which describes the case of constant migration probabilities obtained by averaging the random migration probabilities over possible environments. PMID: 20619285 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3758902 Mon, 05 Jul 2010 23:00:00 +0100 3758902 http://www.medworm.com/index.php?rid=3741784&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20609370%26dopt%3DAbstract Authors: Vuilleumier S, Bolker BM, Lévêque O Ocean currents, prevailing winds, and the hierarchical structures of river networks are known to create asymmetries in re-colonization between habitat patches. The impacts of such asymmetries on metapopulation persistence are seldom considered, especially rarely in theoretical studies. Considering three classical models (the island, the stepping stone and the distance-dependent model), we explore how metapopulation persistence is affected by (i) asymmetry in dispersal strength, in which the colonization rate between two patches differs in direction, and (ii) asymmetry in connectivity in which the overall colonization pattern displays asymmetry (circulating or dendritic networks). Viability can be drastically reduced when directional bi... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3741784 Fri, 02 Jul 2010 23:00:00 +0100 3741784 http://www.medworm.com/index.php?rid=3733463&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20600206%26dopt%3DAbstract Authors: Schneider KA, Kim Y We analytically study a deterministic model for the spread of drug resistance among human malaria parasites. The model incorporates all major characteristics of the complex malaria-transmission cycle and accounts for the fact that only a fraction alpha of infected hosts receive drug treatment. Furthermore, the model incorporates that hosts can be co-infected. The number m of parasites co-infecting a host is either a constant or, more generally, follows a given frequency distribution. Although the model is formulated in a multilocus setup, for our results we assume that drug resistance is caused by a single locus with two alleles - a sensitive one and a resistant one. We assume that the resistant allele has a selective advantage only in treated hosts and pay... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3733463 Fri, 18 Jun 2010 23:00:00 +0100 3733463 http://www.medworm.com/index.php?rid=3733460&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20600209%26dopt%3DAbstract Authors: Cyran KA, Kimmel M Methods of calculating the distributions of the time to coalescence depend on the underlying model of population demography. In particular, the models assuming deterministic evolution of population size may not be applicable to populations evolving stochastically. Therefore the study of coalescence models involving stochastic demography is important for applications. One interesting approach which includes stochasticity is the O'Connell limit theory of genealogy in branching processes. Our paper explores how many generations are needed for the limiting distributions of O'Connell to become adequate approximations of exact distributions. We perform extensive simulations of slightly supercritical branching processes and compare the results to the O'Connell limi... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3733460 Fri, 18 Jun 2010 23:00:00 +0100 3733460 http://www.medworm.com/index.php?rid=3733464&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20598723%26dopt%3DAbstract Authors: Ediev DM The eigenvalues of a population projection matrix-except for the Lotka coefficient-are uniquely determined by the reproductive values and the survival. This relation (proposed earlier, but not really well known in western literature) follows from another useful relation between fertility, reproductive values, survival, and Lotka's coefficient. These results are applied to provide demographic interpretations to the intrinsically dynamic and metastable population models by Schoen and co-workers. PMID: 20598723 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3733464 Thu, 17 Jun 2010 23:00:00 +0100 3733464 http://www.medworm.com/index.php?rid=3733462&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20600207%26dopt%3DAbstract Authors: Zu Dohna H, Pineda-Krch M Populations that are structured into small local patches are a common feature of ecological and epidemiological systems. Models describing this structure are often referred to as metapopulation models in ecology or household models in epidemiology. Small local populations are subject to demographic stochasticity. Theoretical studies of household disease models without resistant stages (SIS models) have shown that local stochasticity can be ignored for between patch disease transmission if the number of connected patches is large. In that case the distribution of the number of infected individuals per household reaches a stationary distribution described by a birth-death process with a constant immigration term. Here we show how this result, in conjunc... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3733462 Wed, 16 Jun 2010 23:00:00 +0100 3733462 http://www.medworm.com/index.php?rid=3733461&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20600208%26dopt%3DAbstract Authors: Chesson P, Kuang JJ Frequency-dependent seed predation (FDP) has been shown to be a powerful coexistence mechanism in models of annual plant communities. However, FDP undermines the competition-based coexistence mechanism called the storage effect (SEc), which relies on temporal environmental fluctuations that drive fluctuations in competition. Although environmental fluctuations also drive fluctuations in predation, a storage effect due to predation (SEp) may not arise due to a time lag between a change in the environment and the resulting change in the predation rate. Here we show how SEp can arise with multispecies FDP, and in a two-species setting with density-dependent frequency-dependence, partially compensating for the reduction in SEc, in the presence of predation. The... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3733461 Wed, 16 Jun 2010 23:00:00 +0100 3733461 http://www.medworm.com/index.php?rid=3691212&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20561538%26dopt%3DAbstract Authors: Bürger R Evolution and the maintenance of polymorphism under the multilocus Levene model with soft selection is studied. The number of loci and alleles, the number of demes, the linkage map, and the degree of dominance are arbitrary, but epistasis is absent or weak. We prove that, without epistasis and under mild, generic conditions, every trajectory converges to a stationary point in linkage equilibrium. Consequently, the equilibrium and stability structure can be determined by investigating the much simpler gene-frequency dynamics on the linkage-equilibrium manifold. For a haploid species an analogous result is shown. For weak epistasis, global convergence to quasi-linkage equilibrium is established. As an application, the maintenance of multilocus polymorphism is explore... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3691212 Mon, 14 Jun 2010 23:00:00 +0100 3691212 http://www.medworm.com/index.php?rid=3691211&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20566407%26dopt%3DAbstract We present a Bayesian method for the reconstruction of pedigrees in clonal populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). The accuracy of the algorithm is demonstrated for simulated data. We show that the joint estimation of parameters of interest such as the rate of self-fertilization is possible with high accuracy even with marker panels of moderate power. Classical methods can only assign a very limited number of statistically significant parentages in this case and would therefore fail. Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The method is implemented in a fast and easy to use open source software that scales to large datasets with many thousand individuals. PMID: 20566407 [P... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3691211 Sat, 22 May 2010 23:00:00 +0100 3691211 http://www.medworm.com/index.php?rid=3589992&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20488197%26dopt%3DAbstract Authors: Durrett R, Foo J, Leder K, Mayberry J, Michor F Most human tumors result from the accumulation of multiple genetic and epigenetic alterations in a single cell. Mutations that confer a fitness advantage to the cell are known as driver mutations and are causally related to tumorigenesis. Other mutations, however, do not change the phenotype of the cell or even decrease cellular fitness. While much experimental effort is being devoted to the identification of the functional effects of individual mutations, mathematical modeling of tumor progression generally considers constant fitness increments as mutations are accumulated. In this paper we study a mathematical model of tumor progression with random fitness increments. We analyze a multi-type branching process in which cells acc... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3589992 Sun, 16 May 2010 23:00:00 +0100 3589992 http://www.medworm.com/index.php?rid=3555046&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20452368%26dopt%3DAbstract Authors: Rorres C, Pelletier ST, Keeling M, Smith G Three different estimators are presented for the types of parameters present in mathematical models of animal epidemics. The estimators make use of data collected during an epidemic, which may be limited, incomplete, or under collection on an ongoing basis. When data are being collected on an ongoing basis, the estimated parameters can be used to evaluate putative control strategies. These estimators were tested using simulated epidemics based on a spatial, discrete-time, gravity-type, stochastic mathematical model containing two parameters. Target epidemics were simulated with the model and the three estimators were implemented using various combinations of collected data to independently determine the two parameters. PMID: 20452... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3555046 Wed, 05 May 2010 23:00:00 +0100 3555046 http://www.medworm.com/index.php?rid=3480324&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20394765%26dopt%3DAbstract Authors: Kang Y, Chesson P We modify the commonly used invasibility concept for coexistence of species to the stronger concept of uniform invasbility. For two-species discrete-time competition and predator-prey models, we use this concept to find broad easily checked sufficient conditions for the rigorous concept of permanent coexistence. With these results, permanent coexistence becomes a tractable concept for many discrete-time population models. To understand how these conditions apply to nonpoint attractors, we generalize the concept of relative nonlinearity, and use it to show how population fluctuations affect the long-term low-density growth rate ("the invasion rate") of a species when it is invading the system consisting of the other species ("the resident") at a single-species... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3480324 Sun, 11 Apr 2010 23:00:00 +0100 3480324 http://www.medworm.com/index.php?rid=3464505&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20380844%26dopt%3DAbstract Authors: Xu D, Reeve JD, Wang X, Xiao M Insect host-parasitoid systems are often modeled using delay-differential equations, with a fixed development time for the juvenile host and parasitoid stages. We explore here the effects of distributed development on the stability of these systems, for a random parasitism model incorporating an invulnerable host stage, and negative binomial model that displays generation cycles. A shifted gamma distribution was used to model the distribution of development time for both host and parasitoid stages, using the range of parameter values suggested by a literature survey. For the random parasitism model, the addition of biologically plausible levels of developmental variability could potentially double the area of stable parameter space beyond that ge... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3464505 Mon, 05 Apr 2010 23:00:00 +0100 3464505 http://www.medworm.com/index.php?rid=3449480&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20363239%26dopt%3DAbstract We present a thorough numerical analysis of a two-deme three-allele model, which allows us to identify dominance and selection patterns that harbor the potential for stable triallelic equilibria. The information gained by this approach is then used to construct an example in which existence and asymptotic stability of a fully polymorphic equilibrium can be proved analytically. Noteworthy, in this example the parameter range in which three alleles can coexist is maximized for intermediate migration rates. Our results can be interpreted in a specialist-generalist context and (among others) show when two specialists can coexist with a generalist in two demes if the degree of dominance is deme independent and intermediate. The dominance relation between the generalist allele and the specialist... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3449480 Wed, 31 Mar 2010 23:00:00 +0100 3449480 http://www.medworm.com/index.php?rid=3416772&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20346368%26dopt%3DAbstract Authors: Snyder RE Although perturbations from a stable equilibrium must ultimately vanish, they can grow initially, and the maximum initial growth rate is called reactivity. Reactivity thus identifies systems that may undergo transient population surges or drops in response to perturbations; however, we lack biological and mathematical intuition about what makes a system reactive. This paper presents upper and lower bounds on reactivity for an arbitrary linearized model, explores their strictness, and discusses their biological implications. I find that less stable systems (i.e. systems with long transients) have a smaller possible range of reactivities for which no perturbations grow. Systems with more species have a higher capacity to be reactive, assuming species interactions do no... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3416772 Tue, 23 Mar 2010 00:00:00 +0100 3416772 http://www.medworm.com/index.php?rid=3399490&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20304000%26dopt%3DAbstract Authors: Arenas AJ, González-Parra G, Villanueva Micó RJ In this paper we present an epidemiological model to study the transmission dynamics of toxoplasmosis in a cat population under a continuous vaccination schedule. We explore the dynamics of toxoplasmosis at the population level using a mathematical model that includes the effect of oocyst, since the probability of acquisition of T. Gondii infection depends on the environmental load of the parasite. This model considers indirectly the infection of prey through the oocyst shedding by cats. We prove that the basic reproduction number R(0) is a threshold value that completely determines the global dynamics and the outcome of the disease. Numerical computer simulations are presented to investigate different scenarios. These ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3399490 Thu, 18 Mar 2010 00:00:00 +0100 3399490 http://www.medworm.com/index.php?rid=3379658&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20226804%26dopt%3DAbstract Authors: Chasnov JR A fast algorithm for computing recombination is developed for model organisms with selection on haploids. Haplotype frequencies are transformed to marginal frequencies; random mating and recombination are computed; marginal frequencies are transformed back to haplotype frequencies. With L diallelic loci, this algorithm is theoretically a factor of (3/8)(L) faster than standard computations with selection on diploids, and up to 16 recombining loci have been computed. This algorithm is then applied to model the opposing evolutionary forces of multilocus epistatic selection and recombination. Selection is assumed to favor haplotypes with specific alleles either all present or all absent. When the number of linked loci exceeds a critical value, a jump bifurcation occurs... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3379658 Wed, 10 Mar 2010 00:00:00 +0100 3379658 http://www.medworm.com/index.php?rid=3379659&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20226204%26dopt%3DAbstract Authors: Kurokawa S, Wakano JY, Ihara Y The evolution of cooperation has been a major challenge in evolutionary biology. Unconditional cooperators who help others at a cost to themselves are exploited by defectors who enjoy the benefits without any help in return. It has been argued that cooperation can be established in repeated dyadic interactions if cooperators punish defectors by withholding future cooperation. In social interactions involving more than two individuals, however, withholding future cooperation may result in penalizing not only defectors but also other cooperators. Hence, in such social interactions, it is unclear whether cooperation is most likely to evolve when cooperators are intolerant of any defectors. Here we show, by analyzing a stochastic model of n-player Pr... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3379659 Tue, 09 Mar 2010 00:00:00 +0100 3379659 http://www.medworm.com/index.php?rid=3354625&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20214914%26dopt%3DAbstract We present a simple model in which competition between the exploitation of resources and stochastic fluctuations leads to victory by either the faster or slower of two species depending on the environmental parameters. A simplified limiting case of the model, analyzed by closing the moment and correlation hierarchy, quantitatively predicts which species will win in the complete model under given parameters of spatial variation and average carrying capacity. PMID: 20214914 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3354625 Sat, 06 Mar 2010 00:00:00 +0100 3354625 http://www.medworm.com/index.php?rid=3354624&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20214915%26dopt%3DAbstract Authors: Altenberg L Feldman and Karlin conjectured that the number of isolated fixed points for deterministic models of viability selection and recombination among n possible haplotypes has an upper bound of 2(n)-1. Here a proof is provided. The upper bound of 3(n-1) obtained by Lyubich et al. (2001) using Bézout's Theorem (1779) is reduced here to 2(n) through a change of representation that reduces the third-order polynomials to second order. A further reduction to 2(n)-1 is obtained using the homogeneous representation of the system, which yields always one solution 'at infinity'. While the original conjecture was made for systems of selection and recombination, the results here generalize to viability selection with any arbitrary system of bi-parental transmission, which incl... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3354624 Sat, 06 Mar 2010 00:00:00 +0100 3354624 http://www.medworm.com/index.php?rid=3327997&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20188120%26dopt%3DAbstract Authors: Brøns M, Kaasen R We consider a three-variable forest pest model, proposed by Rinaldi & Muratori (1992) [Rinaldi, S., Muratori, S., 1992. Limit Cycles in Slow-Fast Forest-Pest Models. Theor. Popul. Biol. 41, 26-43]. The model allows relaxation oscillations where long pest-free periods are interspersed with outbreaks of high pest concentration. For small values of the time scale of the young trees, the model can be reduced to a two-dimensional model. By a geometrical analysis we identify a canard explosion in the reduced model, that is, a change over a narrow parameter interval from outbreak dynamics to small oscillations around an endemic state. For larger values of the time scale of the young trees the two-dimensional approximation breaks down, and a broader paramete... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3327997 Tue, 23 Feb 2010 00:00:00 +0100 3327997 http://www.medworm.com/index.php?rid=3302818&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20171975%26dopt%3DAbstract Authors: Roques L, Hamel F, Fayard J, Fady B, Klein EK Diffusion is one of the most frequently used assumptions to explain dispersal. Diffusion models and in particular reaction-diffusion equations usually lead to solutions moving at constant speeds, too slow compared to observations. As early as 1899, Reid had found that the rate of spread of tree species migrating to northern environments at the beginning of the Holocene was too fast to be explained by diffusive dispersal. Rapid spreading is generally explained using long distance dispersal events, modelled through integro-differential equations (IDEs) with exponentially unbounded (EU) kernels, i.e. decaying slower than any exponential. We show here that classical reaction-diffusion models of the Fisher-Kolmogorov-Petrovsky-Piskunov ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3302818 Thu, 18 Feb 2010 00:00:00 +0100 3302818 http://www.medworm.com/index.php?rid=3267958&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20149814%26dopt%3DAbstract Authors: Rouzine IM, Coffin JM The adverse effect of co-inheritance linkage of a large number of sites on adaptation has been studied extensively for asexual populations. However, it is insufficiently understood for multi-site populations in the presence of recombination. In the present work motivated by our studies of HIV evolution in infected patients, we consider a model of haploid populations with infrequent recombination. We assume that small quantities of beneficial alleles preexist at a large number of sites and neglect new mutation. Using a generalized form of the traveling wave method, we show that the effectiveness of recombination is impeded and the adaptation rate is decreased by inter-sequence correlations, arising due to the fact that some pairs of homologous sites have c... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3267958 Mon, 08 Feb 2010 00:00:00 +0100 3267958 http://www.medworm.com/index.php?rid=3236617&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20117125%26dopt%3DAbstract Authors: Ghirlanda S, Enquist M, Perc M We consider models of the interactions between human population dynamics and cultural evolution, asking whether they predict sustainable or unsustainable patterns of growth. Phenomenological models predict either unsustainable population growth or stabilization in the near future. The latter prediction, however, is based on extrapolation of current demographic trends and does not take into account causal processes of demographic and cultural dynamics. Most existing causal models assume (or derive from simplified models of the economy) a positive feedback between cultural evolution and demographic growth, and predict unlimited growth in both culture and population. We augment these models taking into account that: (1) cultural transmission is not ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3236617 Thu, 28 Jan 2010 00:00:00 +0100 3236617 http://www.medworm.com/index.php?rid=3223879&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20109479%26dopt%3DAbstract Authors: Ghosh A, Haccou P Introgression is the permanent incorporation of genes from one population into another through hybridization and backcrossing. It can have large environmental consequences, such as the spread of insecticide or herbicide resistance genes, the escape of transgenes from genetically modified crops, and the invasion of exotic genes into new habitats. Introgression usually involves strong random components, such as rare hybridization and backcrossing events, and demographic variation in reproduction and survival. Most introgression studies ignore these random effects, and consequently fail to accurately assess the risk of introgression. This paper presents a methodology for quantifying stochastic introgression processes, based on multitype branching process models.... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3223879 Mon, 25 Jan 2010 00:00:00 +0100 3223879 http://www.medworm.com/index.php?rid=3212726&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20096297%26dopt%3DAbstract Authors: Wrzaczek S, Kuhn M, Prskawetz A, Feichtinger G We show that in a large class of distributed optimal control models (DOCM), where population is described by a McKendrick type equation with an endogenous number of newborns, the reproductive value of Fisher shows up as part of the shadow price of the population. Depending on the objective function, the reproductive value may be negative. Moreover, we show results of the reproductive value for changing vital rates. To motivate and demonstrate the general framework, we provide examples in health economics, epidemiology, and population biology. PMID: 20096297 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3212726 Fri, 22 Jan 2010 00:00:00 +0100 3212726 http://www.medworm.com/index.php?rid=3194523&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20085779%26dopt%3DAbstract Authors: Chevalet C, Nikolic N We investigate the effects of past changes of the effective population size on the present allelic diversity at a microsatellite marker locus. We first derive the analytical expression of the generating function of the joint probabilities of the time to the Most Recent Common Ancestor for a pair of alleles and of their distance (the difference in allele size). We give analytical solutions in the case of constant population size and geometrical mutation model. Otherwise numerical inversion allows the distributions to be calculated in general cases. The effects of population expansion or decrease and the possibility to detect an ancient bottleneck are discussed. The method is extended to samples of three and four alleles, which allows investigating the cova... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3194523 Sat, 16 Jan 2010 00:00:00 +0100 3194523 http://www.medworm.com/index.php?rid=3172249&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20064540%26dopt%3DAbstract Authors: Rosenberg NA, Degnan JH Given a gene tree and a species tree, a coalescent history is a list of the branches of the species tree on which coalescences in the gene tree take place. Each pair consisting of a gene tree topology and a species tree topology has some number of possible coalescent histories. Here we show that for each n>/=7, there exist a species tree topology S and a gene tree topology G not equalS, both with n leaves, for which the number of coalescent histories exceeds the corresponding number of coalescent histories when the species tree topology is S and the gene tree topology is also S. This result has the interpretation that the gene tree topology G discordant with the species tree topology S can be produced by the evolutionary process in more ways than can... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3172249 Fri, 08 Jan 2010 00:00:00 +0100 3172249 http://www.medworm.com/index.php?rid=3129940&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20036681%26dopt%3DAbstract Authors: Le Rouzic A, Skaug HJ, Hansen TF Artificial-selection experiments on plants and animals generate large datasets reporting phenotypic changes in the course of time. The dynamics of the changes reflect the underlying genetic architecture, but only simple statistical tools have so far been made available to analyze such time series. This manuscript describes a general statistical framework based on random-effect models aiming at estimating key parameters of genetic architectures from artificial-selection responses. We derive explicit Mendelian models (in which the genetic architecture relies on one or two large-effect loci), and compare them with classical polygenic models. With simulations, we show that the models are accurate and powerful enough to provide useful estimates from... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3129940 Thu, 24 Dec 2009 00:00:00 +0100 3129940 http://www.medworm.com/index.php?rid=3105417&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20005884%26dopt%3DAbstract In this study we incorporate positive resource-mediated interactions in classic resource competition theory and investigate the main consequences for plant population dynamics and species coexistence. We focus on plant communities for which water infiltration rates exhibit positive dependency on plant biomass and where plant responses can be improved by shading, particularly under water limiting conditions. We show that the effects of these two resource-mediated positive interactions are similar and additive. We predict that positive interactions shift the transition points between different species compositions along environmental gradients and that realized niche widths will expand or shrink. Furthermore, continuous transitions between different community compositions can become disconti... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3105417 Thu, 10 Dec 2009 00:00:00 +0100 3105417 http://www.medworm.com/index.php?rid=3105418&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20005241%26dopt%3DAbstract Authors: Hu XS Selection on nuclear (or organelle) sites inevitably affects the spatial distribution of a neutral organelle (or nuclear) allele via transient cytonuclear disequilibrium. Here I examine this effect in terms of F(st) for a neutral allele by bringing together cytonuclear genomes with contrasting modes of inheritance. The relationships between cytonuclear disequilibrium and increment in F(st) are explored and confirmed through Monte Carlo simulations. Results show that the transient increment in F(st) for a neutral allele is not only related to the vectors of seed and pollen dispersal but also to the mode of its inheritance. Such increments can be substantial in certain conditions. Seed dispersal is more effective than pollen dispersal in changing the transient increment. T... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3105418 Wed, 09 Dec 2009 00:00:00 +0100 3105418 http://www.medworm.com/index.php?rid=3048961&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19948179%26dopt%3DAbstract In this study, simulation is used to estimate the impact of social network structure on the probability of an SIR epidemic occurring and, if it does, the final size. Increases in assortativity and clustering coefficient are associated with smaller epidemics and the impact is cumulative. Derived values of R(0) over networks with the highest property values are more than 20% lower than those derived from simulations with zero values of these network properties. PMID: 19948179 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3048961 Fri, 27 Nov 2009 00:00:00 +0100 3048961 http://www.medworm.com/index.php?rid=3048962&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19945475%26dopt%3DAbstract Authors: Kuang JJ, Chesson P We study frequency-dependent seed predation (FDP) in a model of competing annual plant species in a variable environment. The combination of a variable environment and competition leads to the storage-effect coexistence mechanism (SE), which is a leading hypothesis for coexistence of desert annual plants. However, seed predation in such systems demands attention to coexistence mechanisms associated with predation. FDP is one such mechanism, which promotes coexistence by shifting predation to more abundant plant species, facilitating the recovery of species perturbed to low density. When present together, FDP and SE interact, undermining each other's effects. Predation weakens competition, and therefore weakens mechanisms associated with competition: here SE... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3048962 Thu, 26 Nov 2009 00:00:00 +0100 3048962 http://www.medworm.com/index.php?rid=3008979&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19917301%26dopt%3DAbstract In conclusion, the formation of a search image causes the predator to control the prey densities such that the ratio of available prey is kept constant by the predator. PMID: 19917301 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=3008979 Fri, 13 Nov 2009 00:00:00 +0100 3008979 http://www.medworm.com/index.php?rid=2977840&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19896491%26dopt%3DAbstract Authors: Durrett R, Moseley S Inspired by previous work of Iwasa, Nowak, and Michor (2006), and Haeno, Iwasa, and Michor (2007), we consider an exponentially growing population of cancerous cells that will evolve resistance to treatment after one mutation or display a disease phenotype after two or more mutations. We prove results about the distribution of the first time when k mutations have accumulated in some cell, and about the growth of the number of type k cells. We show that our results can be used to derive the previous results about the tumor grown to a fixed size. PMID: 19896491 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2977840 Wed, 04 Nov 2009 00:00:00 +0100 2977840 http://www.medworm.com/index.php?rid=2977841&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19895825%26dopt%3DAbstract We present a single, comprehensible analytical result which summarizes most effects of environmental fluctuations on evolutionary branching driven by resource competition. Corroborating earlier findings, we show that branching may be delayed or impeded if the underlying resources have uncorrelated or negatively correlated responses to environmental fluctuations. There is also a strong impeding effect of positive environmental autocorrelation, which can be related to results from recent experiments on adaptive radiation in bacterial microcosms. In addition, we find that environmental fluctuations can lead to cycles of repeated branching and extinction. PMID: 19895825 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2977841 Tue, 03 Nov 2009 00:00:00 +0100 2977841 http://www.medworm.com/index.php?rid=2923963&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850057%26dopt%3DAbstract Authors: Shimatani IK Spatially explicit models relating to plant populations have developed little since Felsenstein (1975) pointed out that if limited seed dispersal causes clustering of individuals, such models cannot reach an equilibrium. This paper aims to resolve this issue by modifying the Neyman-Scott cluster point process. The new point processes are dynamic models with random immigration, and the continuous increase in the clustering of individuals stops at some level. Hence, an equilibrium state is achieved, and new individual-based spatially explicit neutral coalescent models are established. By fitting the spatial structure at equilibrium to individual spatial distribution data, we can indirectly estimate seed dispersal and effective population density. These estimates are... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2923963 Mon, 19 Oct 2009 00:00:00 +0100 2923963 http://www.medworm.com/index.php?rid=2917027&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19843476%26dopt%3DAbstract Authors: Jain K We study the evolutionary dynamics of a haploid population of infinite size recombining with a probability r in a two locus model. Starting from a low fitness locus, the population is evolved under mutation, selection and recombination until a finite fraction of the population reaches the fittest locus. An analytical method is developed to calculate the fixation time T to the fittest locus for various choices of epistasis. We find that (1) for negative epistasis, T decreases slowly for small r but decays fast at larger r (2) for positive epistasis, T increases linearly for small r and mildly for large r (3) for compensatory mutation, T diverges as a power law with logarithmic corrections as the recombination fraction approaches a critical value. Our calculations are see... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2917027 Fri, 16 Oct 2009 23:00:00 +0100 2917027 http://www.medworm.com/index.php?rid=2917026&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19843477%26dopt%3DAbstract Authors: Boettiger C, Dushoff J, Weitz JS We derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this expression gives rise to the notion of fluctuation domains-parts of the fitness landscape where the rate of evolution is very predictable (due to fluctuation dissipation) and parts where it is highly variable (due to fluctuation enhancement). These fluctuation domains are determined by the curvature of the fitness landscape. Regions of the fitness landscape with positive curvature, such as adaptive valleys or branching points, experience enhancement. Regions with negative curvature, such as adaptive peaks, experien... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2917026 Fri, 16 Oct 2009 23:00:00 +0100 2917026 http://www.medworm.com/index.php?rid=2909690&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19836408%26dopt%3DAbstract In this study, we use the Price equation to derive many such well-known results for the dynamics and equilibria of variances in a straightforward way and to develop them further. PMID: 19836408 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2909690 Tue, 13 Oct 2009 23:00:00 +0100 2909690 http://www.medworm.com/index.php?rid=2887250&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19819249%26dopt%3DAbstract Authors: Trotter MV, Spencer HG We examine the characteristics of non-equilibrium dynamics produced by a simple well-known model of frequency-dependent selection at a single diploid locus. An examination of the parameter space of this "pairwise-interaction model" (PIM) revealed non-equilibrium dynamics for polymorphisms of 3, 4 and 5 alleles; both allele-frequency cycling and aperiodic trajectories were detected. We measured the number, cycle length and domains of attraction of the various attractors produced by the model. Domains of attraction tended to be smaller, and cycles longer, for systems with larger number of alleles. Fitnesses that parametrized negative frequency-dependent selection were more likely to allow cycling, and these cycles also had larger domains of attraction. Ape... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2887250 Wed, 07 Oct 2009 23:00:00 +0100 2887250 http://www.medworm.com/index.php?rid=2887252&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19818799%26dopt%3DAbstract Authors: Ricotta C, Szeidl L Many applications of diversity indices are only valid if they are first transformed into their equivalent number of species. These equivalent numbers of species can be multiplicatively partitioned into independent alpha, beta and gamma components, and can be formed into mathematically consistent similarity measures. The utility of beta diversity and similarity measures that incorporate information about the degree of ecological dissimilarity between species is becoming increasingly recognized. The concept of equivalent number of species is here extended to Rao's quadratic entropy, opening the way to methods of diversity partitioning that take into account taxonomic or ecological differences between species. PMID: 19818799 [PubMed - as supplied by publis... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2887252 Tue, 06 Oct 2009 23:00:00 +0100 2887252 http://www.medworm.com/index.php?rid=2887251&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19818800%26dopt%3DAbstract Authors: Gertz J, Gerke JP, Cohen BA With technological advances in genetic mapping studies more of the genes and polymorphisms that underlie Quantitative Trait Loci (QTL) are now being identified. As the identities of these genes become known there is a growing need for an analysis framework that incorporates the molecular interactions affected by natural polymorphisms. As a step towards such a framework we present a molecular model of genetic variation in sporulation efficiency between natural isolates of the yeast, Saccharomyces cerevisiae. The model is based on the structure of the regulatory pathway that controls sporulation. The model captures the phenotypic variation between strains carrying different combinations of alleles at known QTL. Compared to a standard linear model the ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2887251 Tue, 06 Oct 2009 23:00:00 +0100 2887251 http://www.medworm.com/index.php?rid=2847077&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19781561%26dopt%3DAbstract Authors: Cowell RG A simple and efficient algorithm is presented for finding a maximum likelihood pedigree using microsatellite (STR) genotype information on a complete sample of related individuals. The computational complexity of the algorithm is at worst (O(n(3)2(n))), where n is the number of individuals. Thus it is possible to exhaustively search the space of all pedigrees of up to thirty individuals for one that maximizes the likelihood. A priori age and sex information can be used if available, but is not essential. The algorithm is applied in a simulation study, and to some real data on humans. PMID: 19781561 [PubMed - as supplied by publisher] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2847077 Mon, 21 Sep 2009 23:00:00 +0100 2847077 http://www.medworm.com/index.php?rid=2821493&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19765601%26dopt%3DAbstract Authors: Chalub FA, Souza MO We study the large population limit of the Moran process, under the assumption of weak-selection, and for different scalings. Depending on the particular choice of scalings, we obtain a continuous model that may highlight the genetic-drift (neutral evolution) or natural selection; for one precise scaling, both effects are present. For the scalings that take the genetic-drift into account, the continuous model is given by a singular diffusion equation, together with two conservation laws that are already present at the discrete level. For scalings that take into account only natural selection, we obtain a hyperbolic singular equation that embeds the Replicator Dynamics and satisfies only one conservation law. The derivation is made in two steps: a formal one... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2821493 Mon, 14 Sep 2009 23:00:00 +0100 2821493 http://www.medworm.com/index.php?rid=2810153&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19761783%26dopt%3DAbstract Authors: Kelly CK, Bowler MG The impact on plants of herbivores and other pests varies greatly from year to year. Here we develop an analytical model of a temporal niche dynamic as a tool to examine how natural fluctuations in pest (enemy) levels may determine coexistence in competing annual plant species when one but not the other is affected by the pest. We show that the probability and speed with which the resistant drives out the sensitive species, coexists with it, or is driven out by its sensitive competitor depends on the cost of pest-resistance to the unaffected species, the frequency of high pest levels in the habitat and the competitive advantage of the sensitive species when the pest is not actively present. The interaction is regulated primarily by pest impact on relative s... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2810153 Sun, 13 Sep 2009 23:00:00 +0100 2810153 http://www.medworm.com/index.php?rid=2804766&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19751753%26dopt%3DAbstract Authors: Cressman R, Garay J A refuge model is developed for a single predator species and either one or two prey species where no predators are present in the prey refuge. An individual's fitness depends on its strategy choice or ecotype (predators decide which prey species to pursue and prey decide what proportion of their time to spend in the refuge) as well as on the population sizes of all three species. It is shown that, when there is a single prey species with a refuge or the two prey species with no refuge compete only indirectly (i.e. there is only apparent competition between prey species), that stable resident systems where all individuals in each species have the same ecotype cannot be destabilized by the introduction of mutant ecotypes that are initially selectively neutra... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2804766 Thu, 10 Sep 2009 23:00:00 +0100 2804766 http://www.medworm.com/index.php?rid=2782381&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19737575%26dopt%3DAbstract Authors: Zavala Sansón L, Provenzale A Plankton population dynamics in the upper layer of the ocean depends on upwelling processes that bring nutrients from deeper waters. In turn, these depend on the structure of the vertical velocity field. In coastal areas and in oceanic regions characterized by the presence of strong submarine topographic features, the variable bottom topography induces significant effects on vertical velocities and upwelling/downwelling patterns. As a consequence, large plankton and fish abundances are frequently observed above seamounts, canyons and steep continental shelves. In this work, the dynamics of an NPZ (nutrient-phytoplankton-zooplankton) system is numerically studied by coupling the ecosystem model with a quasi two-dimensional (2D) fluid model wit... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2782381 Fri, 04 Sep 2009 23:00:00 +0100 2782381 http://www.medworm.com/index.php?rid=2782382&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19735670%26dopt%3DAbstract Authors: Wagner BG, Earn DJ Viruses contained in live-attenuated virus vaccines (LAVV) can be transmitted between individuals, resulting in secondary or contact vaccinations. This fact has been exploited successfully in the use of the Oral Polio Vaccine (OPV) to better control wild-type polio viruses. In this work we analyze general LAVV vaccination models for infections that confer lifelong immunity. We consider both standard (continuous) vaccination strategies and pulse vaccination programs (where mass vaccination is carried out at regular intervals). For continuous vaccination, we provide a complete global analysis of a very general compartmental ordinary differential equation LAVV model. We find that the threshold vaccination level required for eradication of wild-type virus depend... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2782382 Thu, 03 Sep 2009 23:00:00 +0100 2782382 http://www.medworm.com/index.php?rid=2734977&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19703483%26dopt%3DAbstract Authors: Varughese MM The traditional Kolmogorov equations treat the size of a population as a discrete random variable. A model is introduced that extends these equations to incorporate environmental variability. Difficulties with this discrete model motivate approximating the population size as a continuous random variable through the use of diffusion processes. The set of cumulants for both the population size and the environmental factors affecting the population size characterize the population-environmental system. The evolution of this set, as predicted by the diffusion approximation, closely matches the corresponding predictions for the discrete model. It is also noted that the simulation estimates of the cumulants against which the predictions of the diffusion model are checke... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2734977 Thu, 20 Aug 2009 23:00:00 +0100 2734977 http://www.medworm.com/index.php?rid=2712828&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19682475%26dopt%3DAbstract Authors: Mari L, Gatto M, Casagrandi R We investigate how central-place seed foragers with a nest in the proximity of one or more seed sources determine the formation of different vegetation patterns. In particular, we discuss the ecological conditions that lead to the formation of hump-shaped (Janzen-Connell) patterns in a two-dimensional landscape. Our analysis shows that central-place predation can generate Janzen-Connell patterns even if predators' movement strategies are exclusively based on resource abundance, both in the single-plant/single-nest case and in a forest with several seed sources. We also show that social foraging may either promote or work against the formation of Janzen-Connell patterns, depending upon the way foragers take advantage of social interactions. PMI... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2712828 Tue, 11 Aug 2009 23:00:00 +0100 2712828 http://www.medworm.com/index.php?rid=2702995&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19679143%26dopt%3DAbstract Authors: Nagylaki T Evolution under the multilocus Levene model is investigated. The linkage map is arbitrary, but epistasis is absent. The geometric-mean fitness, w(rho), depends only on the vector of gene frequencies, rho; it is nondecreasing, and the single-generation change is zero only on the set, Lambda, of gametic frequencies at gene-frequency equilibrium. The internal gene-frequency equilibria are the stationary points of w(rho). If the equilibrium points rho^ of rho(t) (where t denotes time in generations) are isolated, as is generic, then rho(t) converges as t-->infinity to some rho^. Generically, rho(t) converges to a local maximum of w(rho). Write the vector of gametic frequencies, p, as (rho,d)(T), where d represents the vector of linkage disequilibria. If rho^ is a loc... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2702995 Sun, 09 Aug 2009 23:00:00 +0100 2702995 http://www.medworm.com/index.php?rid=2696658&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19664647%26dopt%3DAbstract Authors: Bürger R For the Levene model with soft selection in two demes, the maintenance of polymorphism at two diallelic loci is studied. Selection is nonepistatic and dominance is intermediate. Thus, there is directional selection in every deme and at every locus. We assume that selection is in opposite directions in the two demes because otherwise no polymorphism is possible. If at one locus there is no dominance, then a complete analysis of the dynamical and equilibrium properties is performed. In particular, a simple necessary and sufficient condition for the existence of an internal equilibrium and sufficient conditions for global asymptotic stability are obtained. These results are extended to deme-independent degree of dominance at one locus. A perturbation analysis establ... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2696658 Mon, 03 Aug 2009 23:00:00 +0100 2696658 http://www.medworm.com/index.php?rid=2547181&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19371755%26dopt%3DAbstract Authors: Bell AV, Rader RB, Peck SL, Sih A Spatial overlap between predators and prey is key to predicting their interaction strength and population dynamics. We constructed a spatially-explicit simulation model to explore how predator and prey behavioral traits and patterns of resource distribution influence spatial overlap between predators, prey, and prey resources. Predator and prey spatial association primarily followed the ideal free distribution. Departures from this model were intriguing, especially from the interactions of predator and prey behavior. When prey weakly avoided conspecifics, they associated more highly with resources when predators were present. Predators increased the rate of prey movement between patches, which increased their ability to sample their environmen... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547181 Sun, 28 Jun 2009 04:08:42 +0100 2547181 http://www.medworm.com/index.php?rid=2547178&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19393256%26dopt%3DAbstract Authors: Kandler A, Laland KN In this paper we apply reaction-diffusion models to explore the relationship between the rate of behavioural innovation and the level of cultural diversity. We investigate how both independent invention and the modification and refinement of established innovations impact on cultural dynamics and diversity. Further, we analyse these relationships in the presence of biases in cultural learning and find that the introduction of new variants typically increases cultural diversity substantially in the short term, but may decrease long-term diversity. Independent invention generally supports higher levels of cultural diversity than refinement. Repeated patterns of innovation through refinement generate characteristic oscillating trends in diversity, with increa... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547178 Sun, 28 Jun 2009 04:08:36 +0100 2547178 http://www.medworm.com/index.php?rid=2547177&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19426748%26dopt%3DAbstract Authors: Hou W, Liu T, Li Y, Li Q, Li J, Das K, Berg A, Wu R The structure and organization of natural plant populations can be understood by estimating the genetic parameters related to mating behavior, recombination frequency, and gene associations with DNA-based markers typed throughout the genome. We developed a statistical and computational model for estimating and testing these parameters from multilocus data collected in a natural population. This model, constructed by a maximum likelihood approach and implemented within the EM algorithm, is shown to be robust for simultaneously estimating the outcrossing rate, recombination frequencies and linkage disequilibria. The algorithm built with three or more markers allows the characterization of crossover interference in meiosis and h... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547177 Sun, 28 Jun 2009 04:08:34 +0100 2547177 http://www.medworm.com/index.php?rid=2547172&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19486781%26dopt%3DAbstract Authors: Lehmann L, Rousset F Natural populations are of finite size and organisms carry multilocus genotypes. There are, nevertheless, few results on multilocus models when both random genetic drift and natural selection affect the evolutionary dynamics. In this paper we describe a formalism to calculate systematic perturbation expansions of moments of allelic states around neutrality in populations of constant size. This allows us to evaluate multilocus fixation probabilities (long-term limits of the moments) under arbitrary strength of selection and gene action. We show that such fixation probabilities can be expressed in terms of selection coefficients weighted by mean first passages times of ancestral gene lineages within a single ancestor. These passage times extend the coalescen... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547172 Sun, 28 Jun 2009 04:08:24 +0100 2547172 http://www.medworm.com/index.php?rid=2547163&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19540865%26dopt%3DAbstract Authors: Lee CT, Puleston CO, Tuljapurkar S The population dynamics of preindustrial societies depend intimately on their surroundings, and food is a primary means through which environment influences population size and individual well-being. Food production requires labor; thus, dependence of survival and fertility on food involves dependence of a population's future on its current state. We use a perturbation approach to analyze the effects of random environmental variation on this nonlinear, age-structured system. We show that in expanding populations, direct environmental effects dominate induced population fluctuations, so environmental variability has little effect on mean hunger levels although it does decrease population growth. Growth rate determines the time until population... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547163 Wed, 17 Jun 2009 23:00:00 +0100 2547163 http://www.medworm.com/index.php?rid=2547164&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19523479%26dopt%3DAbstract Authors: Guill C The population dynamics of a consumer population with an internal structure is investigated. The population is divided into juvenile and adult individuals that consume different resources and do not interfere with each other. Over a broad range of external conditions (varying mortality and different resource levels), alternative stable states exist. These population states correspond to domination of juveniles and domination of adults, respectively. When mortality is varied, hysteresis between the alternative states only occurs if juveniles have more resources than adults. In the opposite case the juvenile-dominated state is stable for all values of mortality, but the adult-dominated state is not. When the population is modelled with more than one juvenile stage, the a... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547164 Tue, 09 Jun 2009 23:00:00 +0100 2547164 http://www.medworm.com/index.php?rid=2547167&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19501606%26dopt%3DAbstract Authors: Adams B, Sasaki A In models of pathogen interaction and evolution discrete genotypes in the form of bit strings may be mapped to points in a discrete phenotype space based on similarity in antigenic structure. Cross-immunity between strains, that is the reduction in susceptibility to strain A conferred to a host by infection with strain B, can then be defined for pairs of points in the antigenic space by a specified function. Analysis of an SIR type model shows that, if two strains are at equilibrium, the shape of the cross-immunity function has a strong influence on the invasion and coexistence of a third strain and, consequently, the expected evolutionary pathway. A function that is constant except for discontinuities at the end points is expected to result in the accumulati... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547167 Fri, 05 Jun 2009 23:00:00 +0100 2547167 http://www.medworm.com/index.php?rid=2547166&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19501607%26dopt%3DAbstract Authors: Lion S, van Baalen M We study the evolution of a spatially structured population with two age classes using spatial moment equations. In the model, adults can either help juveniles by increasing their survival, or adopt a cannibalistic behaviour and consume juveniles. While cannibalism is the sole evolutionary outcome when the population is well-mixed, both cannibalism and parental care can be evolutionarily stable if the population is viscous. Our analysis allows us to make two main technical points. First, we present a method to define invasion fitness in class-structured viscous populations, which allows us to apply adaptive dynamics methodology. Second, we show that ordinary pair approximation introduces an important quantitative bias in the evolutionary model, even on ran... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547166 Fri, 05 Jun 2009 23:00:00 +0100 2547166 http://www.medworm.com/index.php?rid=2547165&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19505487%26dopt%3DAbstract Authors: Higgins K Metapopulation extinction risk is the probability that all local populations are simultaneously extinct during a fixed time frame. Dispersal may reduce a metapopulation's extinction risk by raising its average per-capita growth rate. By contrast, dispersal may raise a metapopulation's extinction risk by reducing its average population density. Which effect prevails is controlled by habitat fragmentation. Dispersal in mildly fragmented habitat reduces a metapopulation's extinction risk by raising its average per-capita growth rate without causing any appreciable drop in its average population density. By contrast, dispersal in severely fragmented habitat raises a metapopulation's extinction risk because the rise in its average per-capita growth rate is more than offse... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547165 Fri, 05 Jun 2009 23:00:00 +0100 2547165 http://www.medworm.com/index.php?rid=2547168&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19500610%26dopt%3DAbstract Authors: Li T, Anderson JJ A four-parameter model describing mortality as the first passage of an abstract measure of survival capacity, vitality, is developed and used to explore four classic problems in demography: (1) medfly demographic paradox, (2) effect of diet restriction on longevity, (3) cross-life stage effects on survival curves and (4) mortality plateaus. The model quantifies the sources of mortality in these classical problems into vitality-dependent and independent parts, and characterizes the vitality-dependent part in terms of initial and evolving heterogeneities. Three temporal scales express the balance of these factors: a time scale of death from senescence, a time scale of accidental mortality and a crossover time between evolving vs. initial heterogeneity. The exam... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547168 Tue, 02 Jun 2009 23:00:00 +0100 2547168 http://www.medworm.com/index.php?rid=2547183&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19362099%26dopt%3DAbstract We describe a new approximate likelihood for population genetic data under a model in which a single ancestral population has split into two daughter populations. The approximate likelihood is based on the 'Product of Approximate Conditionals' likelihood and 'copying model' of Li and Stephens [Li, N., Stephens, M., 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165 (4), 2213-2233]. The approach developed here may be used for efficient approximate likelihood-based analyses of unlinked data. However our copying model also considers the effects of recombination. Hence, a more important application is to loosely-linked haplotype data, for which efficient statistical models explicitly featuring non-equilibrium pop... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547183 Sun, 31 May 2009 23:00:00 +0100 2547183 http://www.medworm.com/index.php?rid=2547182&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19371754%26dopt%3DAbstract We present the results of computer simulations to support our heuristic mathematical results. We also present a more rigorous demonstration that the neutral conditional ancestral process converges to the Kingman coalescent in the limit as the mutation rate tends to infinity. PMID: 19371754 [PubMed - in process] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547182 Sun, 31 May 2009 23:00:00 +0100 2547182 http://www.medworm.com/index.php?rid=2547180&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19371756%26dopt%3DAbstract Authors: Ganapathy G, Uyenoyama MK Genomic survey data now permit an unprecedented level of sensitivity in the detection of departures from canonical evolutionary models, including expansions in population size and selective sweeps. Here, we examine the effects of seemingly subtle differences among sampling distributions on goodness of fit analyses of site frequency spectra constructed from single nucleotide polymorphisms. Conditioning on the observation of exactly two alleles in a random sample results in a site frequency spectrum that is independent of the scaled rate of neutral substitution (theta). Other sampling distributions, including conditioning on a single mutational event in the sample genealogy or randomly selecting a single mutation from a genealogy with multiple mutations... Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547180 Sun, 31 May 2009 23:00:00 +0100 2547180 http://www.medworm.com/index.php?rid=2547179&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19383508%26dopt%3DAbstract Authors: PMID: 19383508 [PubMed - in process] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547179 Sun, 31 May 2009 23:00:00 +0100 2547179 http://www.medworm.com/index.php?rid=2547171&cid=s_36104_62_f&fid=36104&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19496242%26dopt%3DAbstract Authors: Bodmer W In the 1960s Karlin and Bodmer established an active programme in mathematical population genetics with NIH support that, in turn, supported the work of Ewens and Feldman with Karlin. Subsequently Karlin established a similar programme in Israel. The overall contributions of Karlin to population genetics and molecular biology are briefly reviewed from a personal perspective. PMID: 19496242 [PubMed - in process] (Source: Theoretical Population Biology) Theoretical Population Biology journals http://www.medworm.com/rss/comments.php?id=2547171 Sun, 31 May 2009 23:00:00 +0100 2547171