Assessing population differentiation and isolation from single-nucleotide polymorphism data

We introduce a new, hierarchical, model for single-nucleotide polymorphism allele frequencies in a structured population, which is naturally fitted via Markov chain Monte Carlo methods. There is one parameter for each population, closely analogous to a population-specific version of Wright's FS...

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Bibliographic Details
Published in:Journal of the Royal Statistical Society. Series B, Statistical methodology Vol. 64; no. 4; pp. 695 - 715
Main Authors: Nicholson, George, Smith, Albert V., Jónsson, Frosti, Gústafsson, Ómar, Stefánsson, Kári, Donnelly, Peter
Format: Journal Article
Language:English
Published: Oxford, UK Blackwell Publishers 01.10.2002
Blackwell
Royal Statistical Society
Series:Journal of the Royal Statistical Society Series B
Subjects:
Bayes estimators
Biological and medical sciences
Bottleneck
Chromosomes
Coalescent
Datasets
Demography
Estimation
Estimators
Exact sciences and technology
Fixation indices
Forensic genetics
France
Fundamental and applied biological sciences. Psychology
Gene frequency
General aspects
Genetic loci
Human genetics
Iceland
Inference from stochastic processes; time series analysis
Markov chain Monte Carlo methods
Markov processes
Markovian processes
Mathematics
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Monte Carlo simulation
Population
Population genetics
Population histories
Population parameters
Probability and statistics
Probability theory and stochastic processes
Sciences and techniques of general use
Statistical methods
Statistical models
Statistics
Sufficiency and information
U.S.A
Utah
United States
Europe
America
France
North America
Atlantic Ocean Islands
Iceland
Utah
Human
Bottleneck
Stochastic model
Monte Carlo method
Parameter estimation
Demography
Index
History
Population genetics
Markov chain
Statistical method
Fixation
Wright Fisher diffusion
Genetics
Hierarchical model
Population dynamics
Diffusion
Differentiation
Fixation index
Population history
ISSN:1369-7412, 1467-9868
Online Access:Get full text
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Description
Summary:We introduce a new, hierarchical, model for single-nucleotide polymorphism allele frequencies in a structured population, which is naturally fitted via Markov chain Monte Carlo methods. There is one parameter for each population, closely analogous to a population-specific version of Wright's FST, which can be interpreted as measuring how isolated the relevant population has been. Our model includes the effects of single-nucleotide polymorphism ascertainment and is motivated by population genetics considerations, explicitly in the transient setting after divergence of populations, rather than as the equilibrium of a stochastic model, as is traditionally the case. For the sizes of data set that we consider the method provides good parameter estimates and considerably outperforms estimation methods analogous to those currently used in practice. We apply the method to one new and one existing human data set, each with rather different characteristics-the first consisting of three rather close European populations; the second of four populations taken from across the globe. A novelty of our framework is that the fit of the underlying model can be assessed easily, and these results are encouraging for both data sets analysed. Our analysis suggests that Iceland is more differentiated than the other two European populations (France and Utah), a finding which is consistent with the historical record, but not obvious from comparisons of simple summary statistics.
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ArticleID:RSSB357
ObjectType-Article-2
SourceType-Scholarly Journals-1
ObjectType-Feature-1
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ISSN:1369-7412
1467-9868
DOI:10.1111/1467-9868.00357