Estimating Recombination Rates From Population Genetic Data

Paul Fearnhead; Peter Donnelly

doi:10.1093/genetics/159.3.1299

Abstract

Abstract We introduce a new method for estimating recombination rates from population genetic data. The method uses a computationally intensive statistical procedure (importance sampling) to calculate the likelihood under a coalescent-based model. Detailed comparisons of the new algorithm with two existing methods (the importance sampling method of Griffiths and Marjoram and the MCMC method of Kuhner and colleagues) show it to be substantially more efficient. (The improvement over the existing importance sampling scheme is typically by four orders of magnitude.) The existing approaches not infrequently led to misleading results on the problems we investigated. We also performed a simulation study to look at the properties of the maximum-likelihood estimator of the recombination rate and its robustness to misspecification of the demographic model.

Keywords

Coalescent theoryEstimatorSampling (signal processing)StatisticsRobustness (evolution)Maximum likelihoodRecombinationPopulationBiologyMarkov chain Monte CarloComputer scienceMutation rateEconometricsMathematicsMonte Carlo methodGeneticsDemography

Affiliated Institutions

University of Oxford GB

Related Publications

LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters

Mary K. Kuhner

Abstract Summary: We present a Markov chain Monte Carlo coalescent genealogy sampler, LAMARC 2.0, which estimates population genetic parameters from genetic data. LAMARC can co-...

2006 Bioinformatics 646 citations

Inference in Molecular Population Genetics

Matthew Stephens , Peter Donnelly

Summary Full likelihood-based inference for modern population genetics data presents methodological and computational challenges. The problem is of considerable practical import...

2000 Journal of the Royal Statistical Soci... 313 citations

Sampling theory for neutral alleles in a varying environment

Robert Griffiths , Simon Tavaré

We develop a sampling theory for genes sampled from a population evolving with deterministically varying size. We use a coalescent approach to provide recursions for the probabi...

1994 Philosophical Transactions of the Roy... 647 citations

Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences.

Yun Fu

Abstract Mutations resulting in segregating sites of a sample of DNA sequences can be classified by size and type and the frequencies of mutations of different sizes and types c...

1994 Genetics 118 citations

Maximum-Likelihood Estimation of Migration Rates and Effective Population Numbers in Two Populations Using a Coalescent Approach

Peter Beerli , Joseph Felsenstein

Abstract A new method for the estimation of migration rates and effective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The ...

1999 Genetics 1023 citations

Publication Info

Year: 2001
Type: article
Volume: 159
Issue: 3
Pages: 1299-1318
Citations: 326
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

Estimating Recombination Rates From Population Genetic Data

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

326

OpenAlex

Cite This

APA Style

                            
                                    Paul Fearnhead, 
                                
                                    Peter Donnelly
                                
                            (2001). 
                            Estimating Recombination Rates From Population Genetic Data. 
                            Genetics
                            , 159
                            (3)
                            , 1299-1318.
                            https://doi.org/10.1093/genetics/159.3.1299

Identifiers

DOI: 10.1093/genetics/159.3.1299