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Theoretical Population Biology

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https://www.readbyqxmd.com/read/30208298/haploids-polymorphisms-and-fluctuating-selection
#1
Antony M Dean
I analyze the joint impact of directional and fluctuating selection with reversible mutation in finite bi-allelic haploid populations using diffusion approximations of the Moran and chemostat models. Results differ dramatically from those of the classic Wright-Fisher diffusion. There, a strong dispersive effect attributable to fluctuating selection dissipates nascent polymorphisms promoted by a relatively weak emergent frequency dependent selective effect. The dispersive effect in the Moran diffusion with fluctuations every birth-death event is trivial...
September 9, 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/30165060/modelling-the-outbreak-of-infectious-disease-following-mutation-from-a-non-transmissible-strain
#2
C Y Chen, J P Ward, W B Xie
In-host mutation of a cross-species infectious disease to a form that is transmissible between humans has resulted with devastating global pandemics in the past. We use simple mathematical models to describe this process with the aim to better understand the emergence of an epidemic resulting from such a mutation and the extent of measures that are needed to control it. The feared outbreak of a human-human transmissible form of avian influenza leading to a global epidemic is the paradigm for this study. We extend the SIR approach to derive a deterministic and a stochastic formulation to describe the evolution of two classes of susceptible and infected states and a removed state, leading to a system of ordinary differential equations and a stochastic equivalent based on a Markov process...
August 27, 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/30121328/responses-of-generalist-and-specialist-species-to-fragmented-landscapes
#3
Tanjona Ramiadantsoa, Ilkka Hanski, Otso Ovaskainen
Empirical studies have shown that, unlike species with specialized resource requirements, generalist species may benefit from habitat destruction. We use a family of models to probe the causes of the contrasting responses of these two types of species to habitat destruction. Our approach allows a number of mechanisms to be switched on and off, thereby making it possible to study their marginal and joint effects. Unlike many previous models, we do not assume any intrinsic competitive asymmetry between the species, and we assume pre-emptive rather than displacement competition...
August 16, 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/30048667/full-likelihood-inference-from-the-site-frequency-spectrum-based-on-the-optimal-tree-resolution
#4
Raazesh Sainudiin, Amandine Véber
We develop a novel importance sampler to compute the full likelihood function of a demographic or structural scenario given the site frequency spectrum (SFS) at a locus free of intra-locus recombination. This sampler, instead of representing the hidden genealogy of a sample of individuals by a labelled binary tree, uses the minimal level of information about such a tree that is needed for the likelihood of the SFS and thus takes advantage of the huge reduction in the size of the state space that needs to be integrated...
July 23, 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29964061/the-neutral-frequency-spectrum-of-linked-sites
#5
Luca Ferretti, Alexander Klassmann, Emanuele Raineri, Sebastián E Ramos-Onsins, Thomas Wiehe, Guillaume Achaz
We introduce the conditional Site Frequency Spectrum (SFS) for a genomic region linked to a focal mutation of known frequency. An exact expression for its expected value is provided for the neutral model without recombination. Its relation with the expected SFS for two sites, 2-SFS, is discussed. These spectra derive from the coalescent approach of Fu (1995) for finite samples, which is reviewed. Remarkably simple expressions are obtained for the linked SFS of a large population, which are also solutions of the multi-allelic Kolmogorov equations...
June 28, 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29959946/effects-of-population-and-seed-bank-size-fluctuations-on-neutral-evolution-and-efficacy-of-natural-selection
#6
Lukas Heinrich, Johannes Müller, Aurélien Tellier, Daniel Živković
Population genetics models typically consider a fixed population size and a unique selection coefficient. However, population dynamics inherently generate fluctuations in numbers of individuals and selection acts on various components of the individuals' fitness. In plant species with seed banks, the size of both the above- and below-ground compartments induce fluctuations depending on seed production and the state of the seed bank. We investigate if this fluctuation has consequences on (1) the rate of genetic drift, and (2) the efficacy of selection...
June 28, 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/30025565/introduction-to-the-paul-joyce-special-issue
#7
EDITORIAL
Simon Tavaré, Erkan Ozge Buzbas
No abstract text is available yet for this article.
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29704515/ancestral-inference-from-haplotypes-and-mutations
#8
Robert C Griffiths, Simon Tavaré
We consider inference about the history of a sample of DNA sequences, conditional upon the haplotype counts and the number of segregating sites observed at the present time. After deriving some theoretical results in the coalescent setting, we implement rejection sampling and importance sampling schemes to perform the inference. The importance sampling scheme addresses an extension of the Ewens Sampling Formula for a configuration of haplotypes and the number of segregating sites in the sample. The implementations include both constant and variable population size models...
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29704514/the-coalescent-of-a-sample-from-a-binary-branching-process
#9
Amaury Lambert
At time 0, start a time-continuous binary branching process, where particles give birth to a single particle independently (at a possibly time-dependent rate) and die independently (at a possibly time-dependent and age-dependent rate). A particular case is the classical birth-death process. Stop this process at time T>0. It is known that the tree spanned by the N tips alive at time T of the tree thus obtained (called a reduced tree or coalescent tree) is a coalescent point process (CPP), which basically means that the depths of interior nodes are independent and identically distributed (iid)...
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29604302/inference-on-admixture-fractions-in-a-mechanistic-model-of-recurrent-admixture
#10
Erkan Ozge Buzbas, Paul Verdu
Signatures of recent historical admixture are ubiquitous in human populations. We present a mechanistic model of admixture with two source populations, encompassing recurrent admixture periods and study the distribution of admixture fractions for finite but arbitrary genome size. We provide simulation-based methods to estimate the introgression parameters and discuss the implications of reaching stationarity on estimability of parameters when there are recurrent admixture events with different rates.
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29574050/inference-from-the-stationary-distribution-of-allele-frequencies-in-a-family-of-wright-fisher-models-with-two-levels-of-genetic-variability
#11
Jake M Ferguson, Erkan Ozge Buzbas
The distribution of allele frequencies obtained from diffusion approximations to Wright-Fisher models is useful in developing intuition about the population level effects of evolutionary processes. The statistical properties of the stationary distributions of K-allele models have been extensively studied under neutrality or under selection. Here, we introduce a new family of Wright-Fisher models in which there are two hierarchical levels of genetic variability. The genotypes composed of alleles differing from each other at the selected level have fitness differences with respect to each other and evolve under selection...
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29452133/some-properties-of-the-conditioned-reconstructed-process-with-bernoulli-sampling
#12
Carsten Wiuf
In many areas of genetics it is of relevance to consider a population of individuals that is founded by a single individual in the past. One model for such a scenario is the conditioned reconstructed process with Bernoulli sampling that describes the evolution of a population of individuals that originates from a single individual. Several aspects of this reconstructed process are studied, in particular the Markov structure of the process. It is shown that at any given time in the past, the conditioned reconstructed process behaves as the original conditioned reconstructed process after a suitable time-dependent change of the sampling probability...
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29432792/simulating-the-component-counts-of-combinatorial-structures
#13
Richard Arratia, A D Barbour, W J Ewens, Simon Tavaré
This article describes and compares methods for simulating the component counts of random logarithmic combinatorial structures such as permutations and mappings. We exploit the Feller coupling for simulating permutations to provide a very fast method for simulating logarithmic assemblies more generally. For logarithmic multisets and selections, this approach is replaced by an acceptance/rejection method based on a particular conditioning relationship that represents the distribution of the combinatorial structure as that of independent random variables conditioned on a weighted sum...
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29289520/joint-coevolutionary-epidemiological-models-dampen-red-queen-cycles-and-alter-conditions-for-epidemics
#14
Ailene MacPherson, Sarah P Otto
Host-parasite interactions in the form of infectious diseases are a topic of interest in both evolutionary biology and public health. Both fields have relied on mathematical models to predict and understand the dynamics and consequences of these interactions. Yet few models explicitly incorporate both epidemiological and coevolutionary dynamics, allowing for genetic variation in both hosts and parasites. By comparing a matching-alleles model of coevolution, a susceptible-infected-recovered-susceptible compartmental model from epidemiology, and a combined coevolutionary-epidemiology model we assess the effect of the coevolutionary feedback on the epidemiological dynamics and vice versa...
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29246460/establishment-in-a-new-habitat-by-polygenic-adaptation
#15
N H Barton, A M Etheridge
Maladapted individuals can only colonise a new habitat if they can evolve a positive growth rate fast enough to avoid extinction, a process known as evolutionary rescue. We treat log fitness at low density in the new habitat as a single polygenic trait and use the infinitesimal model to follow the evolution of the growth rate; this assumes that the trait values of offspring of a sexual union are normally distributed around the mean of the parents' trait values, with variance that depends only on the parents' relatedness...
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29198859/selecting-among-three-basic-fitness-landscape-models-additive-multiplicative-and-stickbreaking
#16
Craig R Miller, James T Van Leuven, Holly A Wichman, Paul Joyce
Fitness landscapes map genotypes to organismal fitness. Their topographies depend on how mutational effects interact - epistasis - andare important for understanding evolutionary processes such as speciation, the rate of adaptation, the advantage of recombination, and the predictability versus stochasticity of evolution. The growing amount of data has made it possible to better test landscape models empirically. We argue that this endeavor will benefit from the development and use of meaningful basic models against which to compare more complex models...
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29174634/a-parametric-interpretation-of-bayesian-nonparametric-inference-from-gene-genealogies-linking-ecological-population-genetics-and-evolutionary-processes
#17
José Miguel Ponciano
Using a nonparametric Bayesian approach Palacios and Minin (2013) dramatically improved the accuracy, precision of Bayesian inference of population size trajectories from gene genealogies. These authors proposed an extension of a Gaussian Process (GP) nonparametric inferential method for the intensity function of non-homogeneous Poisson processes. They found that not only the statistical properties of the estimators were improved with their method, but also, that key aspects of the demographic histories were recovered...
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29132923/on-the-joint-distribution-of-tree-height-and-tree-length-under-the-coalescent
#18
Ilana M Arbisser, Ethan M Jewett, Noah A Rosenberg
Many statistics that examine genetic variation depend on the underlying shapes of genealogical trees. Under the coalescent model, we investigate the joint distribution of two quantities that describe genealogical tree shape: tree height and tree length. We derive a recursive formula for their exact joint distribution under a demographic model of a constant-sized population. We obtain approximations for the mean and variance of the ratio of tree height to tree length, using them to show that this ratio converges in probability to 0 as the sample size increases...
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/29042150/paul-joyce-and-the-infinite-alleles-model
#19
Stephen M Krone
Paul Joyce's work touched on a variety of topics in population genetics-from mathematical models of idealized systems to working closely with biologists on experimental evolution and landscape genetics. I will focus on his earlier mathematical/statistical work that centered on the infinite alleles model.
July 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/28993198/wright-fisher-diffusion-bridges
#20
Robert C Griffiths, Paul A Jenkins, Dario Spanò
The trajectory of the frequency of an allele which begins at x at time 0 and is known to have frequency z at time T can be modelled by the bridge process of the Wright-Fisher diffusion. Bridges when x=z=0 are particularly interesting because they model the trajectory of the frequency of an allele which appears at a time, then is lost by random drift or mutation after a time T. The coalescent genealogy back in time of a population in a neutral Wright-Fisher diffusion process is well understood. In this paper we obtain a new interpretation of the coalescent genealogy of the population in a bridge from a time t∈(0,T)...
July 2018: Theoretical Population Biology
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