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Interpreting the pervasive observation of U-shaped Site Frequency Spectra.

ABSTRACT: The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45 genome-wide site frequency spectra from a diverse set of species, most of which display an excess of low and high frequency variants compared to the expectation of the standard neutral model, resulting in U-shaped spectra. We show that multiple merger coalescent models often provide a better fit to these observations than the standard Kingman coalescent. Hence, in many circumstances these under-utilized models may serve as the more appropriate reference for genomic analyses. We further discuss the underlying evolutionary processes that may result in the widespread U-shape of frequency spectra.

SUBMITTER: Freund F

PROVIDER: S-EPMC10072462 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Interpreting the pervasive observation of U-shaped Site Frequency Spectra.

Freund Fabian F Kerdoncuff Elise E Matuszewski Sebastian S Lapierre Marguerite M Hildebrandt Marcel M Jensen Jeffrey D JD Ferretti Luca L Lambert Amaury A Sackton Timothy B TB Achaz Guillaume G

PLoS genetics 20230323 3

The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45 genome-wide site frequency spectra from a diverse set of species, most of which display an excess of low and high frequency variants compared to the expectation of the standard neutral model, resulting in U-shaped spectra. We show that multiple merger coalescent models often provide a better fit to these observations than the standard Kingman coa ...[more]

PMID: 36952570

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