A Fast and Reliable Computational Method for Estimating Population Genetic Parameters by ProQuest

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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-squares estimators may show significantly less estimation bias for growth rate and genetic diversity than a corresponding maximum-likelihood estimator for the same coalescent process. The least-squares statistics also scale up to genome-sized data sets with many nucleotides and loci. These results demonstrate that least-squares statistics will likely prove useful for nonlinear parameter estimation when the underlying population genomic processes have complex evolutionary dynamics involving interactions between mutation, selection, demography, and recombination. [PUBLICATION ABSTRACT]

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									Copyright Ó 2008 by the Genetics Society of America
DOI: 10.1534/genetics.108.087049



     A Fast and Reliable Computational Method for Estimating Population
                            Genetic Parameters

                                                               Daniel A. Vasco1
                                      Odum School of Ecology, University of Georgia, Athens, Georgia 30602
                                                       Manuscript received January 14, 2008
                                                      Accepted for publication March 31, 2008


                                                               ABSTRACT
                The estimation of ancestral and current effective population sizes in expanding populations is a
             fundamental problem in population genetics. Recently
								
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