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https://doi.org/10.1101/078618...
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Genetics
Article . 2017 . Peer-reviewed
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Genetics
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Genetics
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Accuracy of demographic inferences from site frequency spectrum: the case of the yoruba population

Authors: Lapierre, Marguerite; Lambert, Amaury; Achaz, Guillaume;

Accuracy of demographic inferences from site frequency spectrum: the case of the yoruba population

Abstract

Abstract Some methods for demographic inference based on the observed genetic diversity of current populations rely on the use of summary statistics such as the Site Frequency Spectrum (SFS). Demographic models can be either model-constrained with numerous parameters such as growth rates, timing of demographic events and migration rates, or model-flexible, with an unbounded collection of piecewise constant sizes. It is still debated whether demographic histories can be accurately inferred based on the SFS. Here we illustrate this theoretical issue on an example of demographic inference for an African population. The SFS of the Yoruba population (data from the 1000 Genomes Project) is fit to a simple model of population growth described with a single parameter ( e.g. , founding time). We infer a time to the most recent common ancestor of 1.7 million years for this population. However, we show that the Yoruba SFS is not informative enough to discriminate between several different models of growth. We also show that for such simple demographies, the fit of one-parameter models outperforms the model-flexible method recently developed by Liu and Fu. The use of this method on simulated data suggests that it is biased by the noise intrinsically present in the data.

Country
France
Keywords

site frequency spectrum, [MATH.MATH-PR] Mathematics [math]/Probability [math.PR], [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], model identifiability, Models, Genetic, Black People, Genetic Variation, Models, Theoretical, Polymorphism, Single Nucleotide, human demography, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV] Life Sciences [q-bio], Genetics, Population, [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Humans, coalescent theory, Demography

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    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
81
Top 1%
Top 10%
Top 10%
Green
hybrid