Genetics, Vol 138, 1375-1386, Copyright © 1994

INVESTIGATIONS

Estimating Effective Population Size or Mutation Rate Using the Frequencies of Mutations of Various Classes in a Sample of DNA Sequences

Y. X. Fu
Center for Demographic and Population Genetics, University of Texas, Houston, Texas 77225

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 can be inferred from the sample. A framework for estimating the essential parameter {theta} = 4Nu utilizing the frequencies of mutations of various sizes and types is developed in this paper, where N is the effective size of a population and {mu} is mutation rate per sequence per generation. The framework is a combination of coalescent theory, general linear model and Monte-Carlo integration, which leads to two new estimators {theta}({xi}) and {theta}({eta}) as well as a general Watterson's estimator {theta}(K) and a general Tajima's estimator {theta}({pi}). The greatest strength of the framework is that it can be used under a variety of population models. The properties of the framework and the four estimators {theta}(K), {theta}({pi}), {theta}({xi}) and {theta}({eta}) are investigated under three important population models: the neutral Wright-Fisher model, the neutral model with recombination and the neutral Wright's finite-islands model. Under all these models, it is shown that {theta}({xi}) is the best estimator among the four even when recombination rate or migration rate has to be estimated. Under the neutral Wright-Fisher model, it is shown that the new estimator {theta}({xi}) has a variance close to a lower bound of variances of all unbiased estimators of {theta} which suggests that {theta}({xi}) is a very efficient estimator.

This article has been cited by other articles:

				C. L. Sole, A. D. S. Bastos, and C. H. Scholtz Intraspecific Patterns of Mitochondrial Variation in Natural Population Fragments of a Localized Desert Dung Beetle Species, Pachysoma gariepinum (Coleoptera: Scarabaeidae) J. Hered., June 9, 2008; (2008) esn046v1. [Abstract] [Full Text] [PDF]

				D. A. Vasco A Fast and Reliable Computational Method for Estimating Population Genetic Parameters Genetics, June 1, 2008; 179(2): 951 - 963. [Abstract] [Full Text] [PDF]

				E. B. Rosenblum and J. Novembre Ascertainment Bias in Spatially Structured Populations: A Case Study in the Eastern Fence Lizard J. Hered., July 4, 2007; (2007) esm031v1. [Abstract] [Full Text] [PDF]

				M. G. B. Blum and N. A. Rosenberg Estimating the Number of Ancestral Lineages Using a Maximum-Likelihood Method Based on Rejection Sampling Genetics, July 1, 2007; 176(3): 1741 - 1757. [Abstract] [Full Text] [PDF]

				H. E. Walsh, I. L. Jones, and V. L. Friesen A Test of Founder Effect Speciation Using Multiple Loci in the Auklets (Aethia spp.) Genetics, December 1, 2005; 171(4): 1885 - 1894. [Abstract] [Full Text] [PDF]

				H.-Y. Wang, H. Tang, C.-K. J. Shen, and C.-I Wu Rapidly Evolving Genes in Human. I. The Glycophorins and Their Possible Role in Evading Malaria Parasites Mol. Biol. Evol., November 1, 2003; 20(11): 1795 - 1804. [Abstract] [Full Text] [PDF]

				B. Rannala and Z. Yang Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci Genetics, August 1, 2003; 164(4): 1645 - 1656. [Abstract] [Full Text] [PDF]

				H. Li, Y. Zhang, Y.-P. Zhang, and Y.-X. Fu Neutrality Tests Using DNA Polymorphism From Multiple Samples Genetics, March 1, 2003; 163(3): 1147 - 1151. [Abstract] [Full Text] [PDF]

				N. Yu, Y.-X. Fu, and W.-H. Li DNA Polymorphism in a Worldwide Sample of Human X Chromosomes Mol. Biol. Evol., December 1, 2002; 19(12): 2131 - 2141. [Abstract] [Full Text] [PDF]

				Y.-X. Fu and R. Chakraborty Simultaneous Estimation of All the Parameters of a Stepwise Mutation Model Genetics, September 1, 1998; 150(1): 487 - 497. [Abstract] [Full Text]