Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation

Rasmus Nielsen; Joanna L. Mountain; John P. Huelsenbeck; Montgomery Slatkin

Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation

Rasmus Nielsen^*, Joanna L. Mountain, John P. Huelsenbeck, Montgomery Slatkin

^*Corresponding author for this work

42 Citations (Scopus)

Abstract

In this paper we present a method for estimating population divergence times by maximum likelihood in models without mutation. The maximum-likelihood estimator is compared to a commonly applied estimator based on Wright's F(ST) statistic. Simulations suggest that the maximum-likelihood estimator is less biased and has a lower variance than the F(ST)-based estimator. The maximum-likelihood estimator provides a statistical framework for the analysis of population history given genetic data. We demonstrate how maximum-likelihood estimates of the branching pattern of divergence of multiple populations may be obtained. We also describe how the method may be applied to test hypotheses such as whether populations have maintained equal population sizes. We illustrate the method by applying it to two previously published sets of human restriction fragment length polymorphism (RFLP) data.

Original language	English
Journal	Evolution
Volume	52
Issue number	3
Pages (from-to)	669-677
Number of pages	9
ISSN	0014-3820
Publication status	Published - 1 Jan 1998

Keywords

F(ST)
Maximum likelihood
Phylogeny
Population divergence
Population history
Population size
Population subdivision

Cite this

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title = "Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation",

abstract = "In this paper we present a method for estimating population divergence times by maximum likelihood in models without mutation. The maximum-likelihood estimator is compared to a commonly applied estimator based on Wright's F(ST) statistic. Simulations suggest that the maximum-likelihood estimator is less biased and has a lower variance than the F(ST)-based estimator. The maximum-likelihood estimator provides a statistical framework for the analysis of population history given genetic data. We demonstrate how maximum-likelihood estimates of the branching pattern of divergence of multiple populations may be obtained. We also describe how the method may be applied to test hypotheses such as whether populations have maintained equal population sizes. We illustrate the method by applying it to two previously published sets of human restriction fragment length polymorphism (RFLP) data.",

keywords = "F(ST), Maximum likelihood, Phylogeny, Population divergence, Population history, Population size, Population subdivision",

author = "Rasmus Nielsen and Mountain, {Joanna L.} and Huelsenbeck, {John P.} and Montgomery Slatkin",

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T1 - Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation

AU - Nielsen, Rasmus

AU - Mountain, Joanna L.

AU - Huelsenbeck, John P.

AU - Slatkin, Montgomery

PY - 1998/1/1

Y1 - 1998/1/1

N2 - In this paper we present a method for estimating population divergence times by maximum likelihood in models without mutation. The maximum-likelihood estimator is compared to a commonly applied estimator based on Wright's F(ST) statistic. Simulations suggest that the maximum-likelihood estimator is less biased and has a lower variance than the F(ST)-based estimator. The maximum-likelihood estimator provides a statistical framework for the analysis of population history given genetic data. We demonstrate how maximum-likelihood estimates of the branching pattern of divergence of multiple populations may be obtained. We also describe how the method may be applied to test hypotheses such as whether populations have maintained equal population sizes. We illustrate the method by applying it to two previously published sets of human restriction fragment length polymorphism (RFLP) data.

AB - In this paper we present a method for estimating population divergence times by maximum likelihood in models without mutation. The maximum-likelihood estimator is compared to a commonly applied estimator based on Wright's F(ST) statistic. Simulations suggest that the maximum-likelihood estimator is less biased and has a lower variance than the F(ST)-based estimator. The maximum-likelihood estimator provides a statistical framework for the analysis of population history given genetic data. We demonstrate how maximum-likelihood estimates of the branching pattern of divergence of multiple populations may be obtained. We also describe how the method may be applied to test hypotheses such as whether populations have maintained equal population sizes. We illustrate the method by applying it to two previously published sets of human restriction fragment length polymorphism (RFLP) data.

KW - F(ST)

KW - Maximum likelihood

KW - Phylogeny

KW - Population divergence

KW - Population history

KW - Population size

KW - Population subdivision

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M3 - Journal article

AN - SCOPUS:0031879154

SN - 0014-3820

VL - 52

SP - 669

EP - 677

JO - Evolution

JF - Evolution

IS - 3

ER -

Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation

Abstract

Keywords

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