scholarly journals SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates, and effective population sizes

2015 ◽  
Author(s):  
Matthias Steinrücken ◽  
Ethan M Jewett ◽  
Yun S Song
Keyword(s):  
Spectral Representation ◽  
Diffusion Processes ◽  
Transition Density ◽  
Effective Population ◽  
Piecewise Constant ◽  
Practical Applications ◽  
Transition Density Function ◽  
Transition Densities ◽  
Population Sizes ◽  
Selection Parameters

In the Wright-Fisher diffusion, the transition density function (TDF) describes the time-evolution of the population-wide frequency of an allele. This function has several practical applications in population genetics, and computing it for biologically realistic scenarios with selection and demography is an important problem. We develop an efficient method for finding a spectral representation of the TDF for a general model where the effective population size, selection coefficients, and mutation parameters vary over time in a piecewise constant manner. The method, called SpectralTDF, is available at https://sourceforge.net/projects/spectraltdf/.

scholarly journals Transition densities and sample frequency spectra of diffusion processes with selection and variable population size

2015 ◽  
Author(s):  
Daniel Zivkovic ◽  
Matthias Steinrücken ◽  
Yun S. Song ◽  
Wolfgang Stephan
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Diffusion Processes ◽  
Transition Density ◽  
Effective Population ◽  
Frequency Spectra ◽  
Transition Densities ◽  
Population Sizes ◽  
Sample Frequency ◽  
The Impact

Advances in empirical population genetics have made apparent the need for models that simultaneously account for selection and demography. To address this need, we here study the Wright-Fisher diffusion under selection and variable effective population size. In the case of genic selection and piecewise-constant effective population sizes, we obtain the transition density function by extending a recently developed method for computing an accurate spectral representation for a constant population size. Utilizing this extension, we show how to compute the sample frequency spectrum (SFS) in the presence of genic selection and an arbitrary number of instantaneous changes in the effective population size. We also develop an alternate, efficient algorithm for computing the SFS using a method of moments. We apply these methods to answer the following questions: If neutrality is incorrectly assumed when there is selection, what effects does it have on demographic parameter estimation? Can the impact of negative selection be observed in populations that undergo strong exponential growth?

scholarly journals ASYMPTOTIC EXPANSION FOR THE TRANSITION DENSITIES OF STOCHASTIC DIFFERENTIAL EQUATIONS DRIVEN BY THE GAMMA PROCESSES

2020 ◽  
pp. 1-32
Author(s):  
Fan Jiang ◽  
Xin Zang ◽  
Jingping Yang
Keyword(s):  
Asymptotic Expansion ◽  
Differential Equations ◽  
Stochastic Differential Equations ◽  
Closed Form ◽  
Diffusion Processes ◽  
Transition Density ◽  
Maximum Relative Error ◽  
Dirac Delta ◽  
Transition Densities ◽  
Gamma Processes

In this paper, enlightened by the asymptotic expansion methodology developed by Li [(2013). Maximum-likelihood estimation for diffusion processes via closed-form density expansions. Annals of Statistics 41: 1350–1380] and Li and Chen [(2016). Estimating jump-diffusions using closed-form likelihood expansions. Journal of Econometrics 195(1): 51–70], we propose a Taylor-type approximation for the transition densities of the stochastic differential equations (SDEs) driven by the gamma processes, a special type of Lévy processes. After representing the transition density as a conditional expectation of Dirac delta function acting on the solution of the related SDE, the key technical method for calculating the expectation of multiple stochastic integrals conditional on the gamma process is presented. To numerically test the efficiency of our method, we examine the pure jump Ornstein–Uhlenbeck model and its extensions to two jump-diffusion models. For each model, the maximum relative error between our approximated transition density and the benchmark density obtained by the inverse Fourier transform of the characteristic function is sufficiently small, which shows the efficiency of our approximated method.

scholarly journals EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON SHORT-TERM RESPONSE TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽  
1973 ◽  
Vol 73 (3) ◽  
pp. 513-530
Author(s):  
J P Hanrahan ◽  
E J Eisen ◽  
J E Legates
Keyword(s):  
Population Size ◽  
Selection Response ◽  
Selection Intensity ◽  
Realized Heritability ◽  
Family Selection ◽  
Effective Population ◽  
Population Sizes ◽  
Selection For ◽  
Selection Intensities ◽  
Term Response

ABSTRACT The effects of population size and selection intensity on the mean response was examined after 14 generations of within full-sib family selection for postweaning gain in mice. Population sizes of 1, 2, 4, 8 and 16 pair matings were each evaluated at selection intensities of 100% (control), 50% and 25% in a replicated experiment. Selection response per generation increased as selection intensity increased. Selection response and realized heritability tended to increase with increasing population size. Replicate variability in realized heritability was large at population sizes of 1, 2 and 4 pairs. Genetic drift was implicated as the primary factor causing the reduced response and lowered repeatability at the smaller population sizes. Lines with intended effective population sizes of 62 yielded larger selection responses per unit selection differential than lines with effective population sizes of 30 or less.

Collective influence maximization for multiple competing products with an awareness-to-influence model

2021 ◽  
Vol 14 (7) ◽  
pp. 1124-1136
Author(s):  
Dimitris Tsaras ◽  
George Trimponias ◽  
Lefteris Ntaflos ◽  
Dimitris Papadias
Keyword(s):  
Diffusion Processes ◽  
Influence Maximization ◽  
Second Phase ◽  
Social Graph ◽  
Practical Applications ◽  
Influence Model ◽  
Best Response ◽  
The Social ◽  
Game Theoretic ◽  
Collective Influence

Influence maximization (IM) is a fundamental task in social network analysis. Typically, IM aims at selecting a set of seeds for the network that influences the maximum number of individuals. Motivated by practical applications, in this paper we focus on an IM variant, where the owner of multiple competing products wishes to select seeds for each product so that the collective influence across all products is maximized. To capture the competing diffusion processes, we introduce an Awareness-to-Influence (AtI) model. In the first phase, awareness about each product propagates in the social graph unhindered by other competing products. In the second phase, a user adopts the most preferred product among those encountered in the awareness phase. To compute the seed sets, we propose GCW, a game-theoretic framework that views the various products as agents, which compete for influence in the social graph and selfishly select their individual strategy. We show that AtI exhibits monotonicity and submodularity; importantly, GCW is a monotone utility game. This allows us to develop an efficient best-response algorithm, with quality guarantees on the collective utility. Our experimental results suggest that our methods are effective, efficient, and scale well to large social networks.

scholarly journals The effect of life-history and mode of inheritance on neutral genetic variability

2001 ◽  
Vol 77 (2) ◽  
pp. 153-166 ◽  
Author(s):  
BRIAN CHARLESWORTH
Keyword(s):  
Sequence Variation ◽  
Adult Mortality ◽  
Structured Populations ◽  
Human Populations ◽  
Effective Population ◽  
Transmission Modes ◽  
Population Sizes ◽  
Age Structured ◽  
Infinite Sites Model ◽  
Site Diversity

Formulae for the effective population sizes of autosomal, X-linked, Y-linked and maternally transmitted loci in age-structured populations are developed. The approximations used here predict both asymptotic rates of increase in probabilities of identity, and equilibrium levels of neutral nucleotide site diversity under the infinite-sites model. The applications of the results to the interpretation of data on DNA sequence variation in Drosophila, plant, and human populations are discussed. It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X-linked loci relative to autosomal or Y-linked loci. These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes.

Contemporary and historical effective population sizes of Atlantic sturgeon Acipenser oxyrinchus oxyrinchus

2018 ◽  
Vol 20 (2) ◽  
pp. 167-184 ◽  
Author(s):  
John Waldman ◽  
S. Elizabeth Alter ◽  
Douglas Peterson ◽  
Lorraine Maceda ◽  
Nirmal Roy ◽  
...  
Keyword(s):  
Atlantic Sturgeon ◽  
Effective Population ◽  
Population Sizes ◽  
Acipenser Oxyrinchus
Sign in / Sign up

Export Citation Format

Share Document