Optimal neutrality tests based on the frequency spectrum

Genetics
Luca FerrettiSebastian Ramos-Onsins

Abstract

The ascertainment of the demographic and selective history of populations has been a major research goal in genetics for decades. To that end, numerous statistical tests have been developed to detect deviations between expected and observed frequency spectra, e.g., Tajima's D, Fu and Li's F and D tests, and Fay and Wu's H. Recently, Achaz developed a general framework to generate tests that detect deviations in the frequency spectrum. In a further development, we argue that the results of these tests should be as independent on the sample size as possible and propose a scale-free form for them. Furthermore, using the same framework as that of Achaz, we develop a new family of neutrality tests based on the frequency spectrum that are optimal against a chosen alternative evolutionary scenario. These tests maximize the power to reject the standard neutral model and are scalable with the sample size. Optimal tests are derived for several alternative evolutionary scenarios, including demographic processes (population bottleneck, expansion, contraction) and selective sweeps. Within the same framework, we also derive an optimal general test given a generic evolutionary scenario as a null model. All formulas are relatively simple and c...Continue Reading

References

Apr 1, 1975·Theoretical Population Biology·G A Watterson
Oct 1, 1995·Theoretical Population Biology·Y X Fu
Nov 26, 2002·Molecular Biology and Evolution·Sebastian Ramos-Onsins, Julio Rozas
Mar 11, 2004·Journal of Molecular Evolution·Frantz DepaulisMichel Veuille
Nov 16, 2005·Annual Review of Genetics·Rasmus Nielsen
Jun 17, 2006·Science·P C SabetiE S Lander
Sep 15, 2007·Proceedings of the National Academy of Sciences of the United States of America·Greger LarsonAlan Cooper
Jan 23, 2008·Genetical Research·Sebastian Ramos-OnsinsWolfgang Stephan
Jun 20, 2008·Genetics·Guillaume Achaz
Aug 22, 2008·Genetics·Daniel Zivkovic, Thomas Wiehe
Apr 7, 2009·Bioinformatics·P Librado, Julio Rozas
May 27, 2010·Heredity·A OjedaMiguel Pérez-Enciso

Citations

May 23, 2013·PLoS Computational Biology·Haipeng Li, Thomas Wiehe
Jun 5, 2012·Genetics·Luca FerrettiSebastian Ramos-Onsins
Jun 10, 2014·Theoretical Population Biology·M RafajlovićB Mehlig
Jan 18, 2015·Theoretical Population Biology·Luca Ferretti, Sebastian Ramos-Onsins
Nov 9, 2018·Frontiers in Genetics·Luca FerrettiSebastian Ramos-Onsins
Sep 19, 2019·Nature Communications·Carla Giner-DelgadoMario Cáceres
Nov 8, 2015·G3 : Genes - Genomes - Genetics·Nicolas AlcalaSéverine Vuilleumier
Nov 12, 2017·Genetics·Sebastian MatuszewskiJeffrey D Jensen
Oct 8, 2020·Journal of Fungi·Daniel Wagner C L SantosConceição de Maria Pedrozo E Silva de Azevedo

Related Concepts

Genetics, Population
Selection, Genetic
Genomics
Evolution, Neutral
Cell Growth
Fluorouracil
Laboratory Procedures
Lithium
Neutralization Tests
Research

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