May 29, 2008

A fast and reliable computational method for estimating population genetic parameters

Genetics
Daniel A Vasco

Abstract

The estimation of ancestral and current effective population sizes in expanding populations is a fundamental problem in population genetics. Recently it has become possible to scan entire genomes of several individuals within a population. These genomic data sets can be used to estimate basic population parameters such as the effective population size and population growth rate. Full-data-likelihood methods potentially offer a powerful statistical framework for inferring population genetic parameters. However, for large data sets, computationally intensive methods based upon full-likelihood estimates may encounter difficulties. First, the computational method may be prohibitively slow or difficult to implement for large data. Second, estimation bias may markedly affect the accuracy and reliability of parameter estimates, as suggested from past work on coalescent methods. To address these problems, a fast and computationally efficient least-squares method for estimating population parameters from genomic data is presented here. Instead of modeling genomic data using a full likelihood, this new approach uses an analogous function, in which the full data are replaced with a vector of summary statistics. Furthermore, these least-sq...Continue Reading

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Mentioned in this Paper

Stochastic Processes
Genome
Likelihood Functions
Genetics, Population
Recombination, Genetic
Computer Programs and Programming
Rietveld Refinement
Genomics
Underpopulation
Chaos Theory

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