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PubMed Journal Database | Theoretical population biology RSS

06:51 EDT 24th May 2019 | BioPortfolio

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Showing PubMed Articles 1–25 of 78 from Theoretical population biology

Cyclic outbreaks of forest insects: A two-dimensional individual-based model.

An individual-based model is presented which shows that cyclic insects outbreaks in the forest (here presented as a certain type of the dynamics of total numbers of insects in the forest) can be a result of the joint action of four factors: (1) spatial structure of the system - resources, green tree biomass, used by larval insects are distributed in a two-dimensional space, (2) properties of trees - their limited resistance to feeding by insects, and regeneration ability after some time of relaxation, when ...

Fitting Markovian binary trees using global and individual demographic data.

We consider a class of continuous-time branching processes called Markovian binary trees (MBTs), in which the individuals lifetime and reproduction epochs are modeled using a transient Markovian arrival process (TMAP). We develop methods for estimating the parameters of the TMAP by using either age-specific averages of reproduction and mortality rates, or age-specific individual demographic data. Depending on the degree of detail of the available information, we follow a weighted non-linear regression or a ...

Life history and temporal variability of escape events interactively determine the fitness consequences of aquaculture escapees on wild populations.

Domesticated individuals are likely to be maladaptive in the wild due to adaptation to captivity. Escaped aquaculture fish can cause unintended fitness and demographic consequences for their wild conspecifics through interbreeding and competition. Escape events from different sources exhibit great heterogeneity in their frequencies and magnitudes, ranging from rare but large spillover during a storm, to continuous low-level leakage caused by operational errors. The timescale of escape events determines the ...

Cultural bistability and connectedness in a subdivided population.

We propose a stochastic model of cultural evolution in a hunter-gatherer population that is subdivided into demes (subpopulations) of variable size and distributed over a finite or infinite number of sites. We assume a skill acquirable by either social or individual learning, such as the knowhow for positive niche construction, which raises the carrying capacity of a site. We further assume a positive feedback between the number of individuals in a deme with the skill and the size of that deme, which entail...

Ecological dynamics and large scale phenotypic differentiation in density-dependent populations.

Spatial differentiation of phenotypes is assumed to be determined by a combination of fluctuating selection producing adaptations to the local environment and a homogenizing effect of migration. We present a model with density regulation and a density-dependent fitness function affected by spatio-temporal variability in population size driven by spatially correlated fluctuations in the environment causing fluctuating r- and K-selection on a set of traits. We derive the variance in local mean phenotypes and ...

A spatial Markovian framework for estimating regional and local dynamics of annual plants with dormancy.

Many species have a dormant stage in their life cycle, including seeds for plants. The dormancy stage influences the species dynamics but is often undetectable. One way to include dormancy is to model it as a hidden dynamical state within a Markovian framework. Models within this framework have already been proposed but with different limitations: only presence/absence observations are modelled, the dormancy stage is limited to one year, or colonisation from neighbouring patches is not taken into account. W...

A stochastic epidemic model for the dynamics of two pathogens in a single tick population.

Understanding tick-transmitted pathogens in tick infested areas is crucial for the development of preventive and control measures in response to the increasing cases of tick-borne diseases. A stochastic model for the dynamics of two pathogens, Rickettsia parkeri and Rickettsia amblyommii, in a single tick, Amblyomma americanum, is developed and analysed. The model, a continuous-time Markov chain, is based on a deterministic tick-borne disease model. The extinction threshold for the stochastic model is compu...

Pinned, locked, pushed, and pulled traveling waves in structured environments.

Traveling fronts describe the transition between two alternative states in a great number of physical and biological systems. Examples include the spread of beneficial mutations, chemical reactions, and the invasions by foreign species. In homogeneous environments, the alternative states are separated by a smooth front moving at a constant velocity. This simple picture can break down in structured environments such as tissues, patchy landscapes, and microfluidic devices. Habitat fragmentation can pin the fr...

An empirical approach to demographic inference with genomic data.

Inference with population genetic data usually treats the population pedigree as a nuisance parameter, the unobserved product of a past history of random mating. However, the history of genetic relationships in a given population is a fixed, unobserved object, and so an alternative approach is to treat this network of relationships as a complex object we wish to learn about, by observing how genomes have been noisily passed down through it. This paper explores this point of view, showing how to translate qu...

Replicated point processes with application to population dynamics models.

In this paper we study spatially clustered distribution of individuals using point process theory. In particular we discuss the spatially explicit neutral model of population dynamics of Shimatani (2010) which extends previous works on Malécot theory of isolation by distance. We reformulate Shimatani model of replicated Neyman-Scott process to allow for a general dispersal kernel function and we show that the random migration hypothesis can be substituted by the long dispersal distance property of the kern...

Modelling and simulating Lenski's long-term evolution experiment.

We revisit the model by Wiser et al. (2013), which describes how the mean fitness increases over time due to beneficial mutations in Lenski's long-term evolution experiment. We develop the model further both conceptually and mathematically. Conceptually, we describe the experiment with the help of a Cannings model with mutation and selection, where the latter includes diminishing returns epistasis. The analysis sheds light on the growth dynamics within every single day and reveals a runtime effect, that is,...

Analysis of author gender in TPB, 1991-2018.

The opportunity cost of walking away in the spatial iterated prisoner's dilemma.

Previous work with the spatial iterated prisoner's dilemma has shown that the ability to respond to a partner's defection by simply "walking away" allows so-called walk away cooperators to outcompete defectors as well as cooperators that do not respond to defection. These findings are important because they suggest a relatively simple route by which cooperation can evolve. But it remains to be seen just how robust the walk away strategy is to ecologically important variables such as population density, stra...

Modelling high pathogenic avian influenza outbreaks in the commercial poultry industry.

Highly pathogenic avian influenza (HPAI) outbreaks are devastating to poultry industries and pose a risk to human health. There is concern that demand for free-range poultry products could increase the number of HPAI outbreaks by increasing the potential for low pathogenic avian influenza (LPAI) introduction to commercial flocks. We formulate stochastic mathematical models to understand how poultry-housing (barn, free-range and caged) within the meat and layer sectors interacts with a continuous low-level r...

Phase-type distributions in population genetics.

Probability modelling for DNA sequence evolution is well established and provides a rich framework for understanding genetic variation between samples of individuals from one or more populations. We show that both classical and more recent models for coalescence (with or without recombination) can be described in terms of the so-called phase-type theory, where complicated and tedious calculations are circumvented by the use of matrix manipulations. The application of phase-type theory in population genetics...

Adult sex ratio as an index for male strategy in primates.

The adult sex ratio (ASR) is defined as the number of fertile males divided by the number of fertile females in a population. We build an ODE model with minimal age structure, in which males compete for paternities using either a multiple-mating or searching-then-guarding strategy, to investigate the value of ASR as an index for predicting which strategy males will adopt, with a focus in our investigation on the differences of strategy choice between chimpanzees (Pan troglodytes) and human hunter-gatherer...

The evolutionary advantage of cultural memory on heterogeneous contact networks.

Cultural processes, as well as the selection pressures experienced by individuals in a population over time and space, are fundamentally stochastic. Phenotypic variability, together with imperfect phenotypic transmission between parents and offspring, has been previously shown to play an important role in evolutionary rescue and (epi)genetic adaptation of populations to fluctuating temporal environmental pressures. This type of evolutionary bet-hedging does not confer a direct benefit to a single individual...

Density-dependent selection and the limits of relative fitness.

Selection is commonly described by assigning constant relative fitness values to genotypes. Yet population density is often regulated by crowding. Relative fitness may then depend on density, and selection can change density when it acts on a density-regulating trait. When strong density-dependent selection acts on a density-regulating trait, selection is no longer describable by density-independent relative fitnesses, even in demographically stable populations. These conditions are met in most previous mod...

PRDM9 and the evolution of recombination hotspots.

Recombination in mammals is not uniformly distributed along the chromosome but concentrated in small regions known as recombination hotspots. Recombination starts with the double-strand break of a chromosomal sequence and results in the transmission of the sequence that does not break (preventing recombination) more often than the sequence that breaks (allowing recombination). Thus recombination itself renders individual recombination hotspots inactive and over time should drive them to extinction in the ge...

Multi-task learning improves ancestral state reconstruction.

We consider the ancestral state reconstruction problem where we need to infer phenotypes of ancestors using observations from present-day species. For this problem, we propose a multi-task learning method that uses regularized maximum likelihood to estimate the ancestral states of various traits simultaneously. We then show both theoretically and by simulation that this method improves the estimates of the ancestral states compared to the maximum likelihood method. The result also indicates that for the pro...

Inductive determination of allele frequency spectrum probabilities in structured populations.

We present a method for inductively determining exact allele frequency spectrum (AFS) probabilities for samples derived from a population comprising two demes under the infinite-allele model of mutation. This method builds on a labeled coalescent argument to extend the Ewens sampling formula (ESF) to structured populations. A key departure from the panmictic case is that the AFS conditioned on the number of alleles in the sample is no longer independent of the scaled mutation rate (θ). In particular, biall...

Some topics in theoretical population genetics: Editorial commentaries on a selection of Marc Feldman's TPB papers.

This article consists of commentaries on a selected group of papers of Marc Feldman published in Theoretical Population Biology from 1970 to the present. The papers describe a diverse set of population-genetic models, covering topics such as cultural evolution, social evolution, and the evolution of recombination. The commentaries highlight Marc Feldman's role in providing mathematically rigorous formulations to explore qualitative hypotheses, in many cases generating surprising conclusions.

Spatial evolutionary dynamics produce a negative cooperation-population size relationship.

Natural selection can favour cooperation, but it is unclear when cooperative populations should be larger than less cooperative ones. While experiments have shown that cooperation can increase population size, cooperation and population size can become negatively correlated if spatial processes affect both variables in opposite directions. We use a simple mathematical model of spatial common-pool resource production to investigate how space affects the cooperation-population size relationship. We find that ...

Exact limits of inference in coalescent models.

Recovery of population size history from molecular sequence data is an important problem in population genetics. Inference commonly relies on a coalescent model linking the population size history to genealogies. The high computational cost of estimating parameters from these models usually compels researchers to select a subset of the available data or to rely on insufficient summary statistics for statistical inference. We consider the problem of recovering the true population size history from two possib...

General theory for stochastic admixture graphs and F-statistics.

We provide a general mathematical framework based on the theory of graphical models to study admixture graphs. Admixture graphs are used to describe the ancestral relationships between past and present populations, allowing for population merges and migration events, by means of gene flow. We give various mathematical properties of admixture graphs with particular focus on properties of the so-called F-statistics. Also the Wright-Fisher model is studied and a general expression for the loss of heterozygosit...


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