A General Framework for Neutrality Tests Based on the Site Frequency Spectrum
Ramos Onsins, Sebastián Ernesto (Centre de Recerca en Agrigenòmica)
Marmorini, Giacomo (Aoyama Gakuin University. Department of Physics and Mathematics)
Achaz, Guillaume (Collége de France. Institut de Systématique, Evolution, Biodiversité)
Ferretti, Luca (University of Oxford. Nuffield Department of Medicine)

Date:	2023
Abstract:	One of the main necessities for population geneticists is the availability of sensitive statistical tools that enable to accept or reject the standard Wright-Fisher model of neutral evolution. A number of statistical tests have been developed to detect specific deviations from the null frequency spectrum in different directions (e. g. , Tajima's D, Fu and Li's F and D tests, Fay and Wu's H). A general framework exists to generate all neutrality tests that are linear functions of the frequency spectrum. In this framework, it is possible to develop a family of optimal tests with almost maximum power against a specific alternative evolutionary scenario. In this paper we provide a thorough discussion of the structure and properties of linear and nonlinear neutrality tests. First, we present the general framework for linear tests and emphasise the importance of the property of scalability with the sample size (that is, the interpretation of the tests should not depend on the sample size), which, if missing, can lead to errors in interpreting the data. After summarising the motivation and structure of linear optimal tests, we present a more general framework for the optimisation of linear tests, leading to a new family of tunable neutrality tests. In a further generalisation, we extend the framework to nonlinear neutrality tests and we derive nonlinear optimal tests for polynomials of any degree in the frequency spectrum.
Grants:	Ministerio de Ciencia e Innovación CGL2009-0934 Agencia Estatal de Investigación PID2020-119255GB-I00
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Coalescent theory ; Site frequency spectrum ; Neutrality test ; Statistical power ; Summary statistics
Published in:	Genes, Vol. 14, Issue 9 (August 2023) art. 1714, ISSN 2073-4425

DOI: 10.3390/genes14091714
PMID: 37761854

32 p, 568.6 KB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles