Using genetic data to estimate diffusion rates in heterogeneous landscapes

DOI10.1007/S00285-015-0954-4zbMATH Open1388.35103arXiv1503.05440OpenAlexW1628324013WikidataQ31034115 ScholiaQ31034115MaRDI QIDQ304044FDOQ304044

Authors: Lionel Roques, E. Walker, P. Franck, S. Soubeyrand, E. K. Klein 

Publication date: 23 August 2016

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Abstract: Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to increase the survival of endangered species. In this paper, we propose a mechanistic-statistical method to estimate space-dependent diffusion parameters of spatially-explicit models based on stochastic differential equations, using genetic data. Dividing the total population into subpopulations corresponding to different habitat patches with known allele frequencies, the expected proportions of individuals from each subpopulation at each position is computed by solving a system of reaction-diffusion equations. Modelling the capture and genotyping of the individuals with a statistical approach, we derive a numerically tractable formula for the likelihood function associated with the diffusion parameters. In a simulated environment made of three types of regions, each associated with a different diffusion coefficient, we successfully estimate the diffusion parameters with a maximum-likelihood approach. Although higher genetic differentiation among subpopulations leads to more accurate estimations, once a certain level of differentiation has been reached, the finite size of the genotyped population becomes the limiting factor for accurate estimation.

Full work available at URL: https://arxiv.org/abs/1503.05440

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zbMATH Keywords

stochastic differential equationinferencereaction-diffusionallele frequenciesgenotype measurementsmechanistic-statistical model

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Ecology (92D40) Initial value problems for second-order parabolic systems (35K45) Reaction-diffusion equations (35K57) PDEs in connection with biology, chemistry and other natural sciences (35Q92) Numerical solutions to stochastic differential and integral equations (65C30)

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Cited In (6)

• Forecasting pathogen dynamics with Bayesian model-averaging: application to \textit{Xylella fastidiosa}
• Equilibrium and sensitivity analysis of a spatio-temporal host-vector epidemic model
• Simultaneous determination of the drift and diffusion coefficients in stochastic differential equations
• A Bayesian estimation approach for the mortality in a stage-structured demographic model
• Dispersal and good habitat quality promote neutral genetic diversity in metapopulations
• Dating and localizing an invasion from post-introduction data and a coupled reaction-diffusion-absorption model

Uses Software

• FreeFem++
• STRUCTURE

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