Dataset Information

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

ABSTRACT:

Motivation

In the Wright-Fisher diffusion, the transition density function 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.

Results

We develop an efficient method for finding a spectral representation of the transition density function for a general model where the effective population size, selection coefficients and mutation parameters vary over time in a piecewise constant manner.

Availability and implementation

The method, called SpectralTDF, is available at https://sourceforge.net/projects/spectraltdf/

Contact

yss@berkeley.edu

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Steinrucken M

PROVIDER: S-EPMC4907395 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Steinrücken Matthias M Jewett Ethan M EM Song Yun S YS

Bioinformatics (Oxford, England) 20151109 5

<h4>Motivation</h4>In the Wright-Fisher diffusion, the transition density function 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.<h4>Results</h4>We develop an efficient method for finding a spectral representation of the transition density function for a general model where the effective p ...[more]

PMID: 26556388

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Project description:BackgroundThe influence of environmental and climatic factors on malaria vector bionomics and transmission is an important topic in the context of climatic change particularly at macro-geographical level. Sahelian areas could be particularly affected due to heterogeneous features including high inter-annual variability in rainfall and others associated parameters. Therefore, baseline information on the impact of environmental and climatic factors on malaria transmission at micro-geographical level is required for vector risk management and implementation of control strategies.MethodsMalaria vectors were collected indoors by pyrethrum spray catches in 14 villages belonging to 4 different landscape classes (wooded savanna, shrubby savanna, bare soils and steppe) in the sylvo-pastoral area of Senegal. Plasmodium falciparum infection rates were determined using an indirect enzyme-linked immunosorbent assay (ELISA).ResultsAn. arabiensis was the predominant species in all landscape classes and was the only species collected at the end of the rainy season excepted in villages located in bare soils where it cohabited with An. coluzzii. Mean temperature and relative humidity showed similar variations in all the landscape classes covered whereas rainfall was more heterogeneous in terms of pattern, frequency and amount. The mean densities of An. arabiensis displayed high seasonal differences with peaks observed in August or September. A positive non-significant correlation was observed between An. arabiensis densities for rainfall and humidity whereas a negative non-significant correlation was reported for temperature. Plasmodium falciparum-infected mosquitoes were detected only in wooded savanna and bare soils villages.ConclusionsThese observations suggest key roles played by landscape classes and rainfall in malaria vector densities, infection rates and malaria transmission that could be more pronounced in villages situated in wooded savanna and bare soils. Due to the close relationship between environmental and meteorological parameters in this Sahelian region, additional studies on the impact of these parameters are required to further ascertain their association with entomological parameters involved in malaria transmission. From the public health point of view, such information could be useful for human population settlements as well as for monitoring and modelling purposes giving early warning system for implementation of interventions in these unstable transmission zones.

Dataset Information

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

Motivation

Results

Availability and implementation

Contact

Supplementary information

Publications

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

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