Interpreting the pervasive observation of U-shaped Site Frequency Spectra

Fabian Freund, Elise Kerdoncuff, Sebastian Matuszewski, Marguerite Lapierre, Marcel Hildebrandt, Jeffrey D. Jensen, Luca Ferretti, Amaury Lambert, Timothy B. Sackton, Guillaume Achaz

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

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.

Original languageEnglish (US)
Article numbere1010677
JournalPLoS genetics
Volume19
Issue number3
DOIs
StatePublished - Mar 23 2023
Externally publishedYes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

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