A General Framework for Neutrality Tests Based on the Site Frequency Spectrum

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 spe...

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Autores: Ramos Onsins, Sebastián Ernesto|||0000-0002-1776-140X, Marmorini, Giacomo|||0000-0003-3492-276X, Achaz, Guillaume|||0000-0003-4514-5935, Ferretti, Luca
Tipo de recurso: artículo
Fecha de publicación:2023
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:296870
Acceso en línea:https://ddd.uab.cat/record/296870
https://dx.doi.org/urn:doi:10.3390/genes14091714
Access Level:acceso abierto
Palabra clave:Coalescent theory
Site frequency spectrum
Neutrality test
Statistical power
Summary statistics
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spelling A General Framework for Neutrality Tests Based on the Site Frequency SpectrumRamos Onsins, Sebastián Ernesto|||0000-0002-1776-140XMarmorini, Giacomo|||0000-0003-3492-276XAchaz, Guillaume|||0000-0003-4514-5935Ferretti, LucaCoalescent theorySite frequency spectrumNeutrality testStatistical powerSummary statisticsOne 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. 22023-01-0120232023-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/296870https://dx.doi.org/urn:doi:10.3390/genes14091714reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengMinisterio de Ciencia e Innovación https://doi.org/10.13039/501100004837 CGL2009-0934Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 PID2020-119255GB-I00open accesshttp://purl.org/coar/access_right/c_abf2Aquest 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.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2968702026-06-06T12:50:31Z
dc.title.none.fl_str_mv A General Framework for Neutrality Tests Based on the Site Frequency Spectrum
title A General Framework for Neutrality Tests Based on the Site Frequency Spectrum
spellingShingle A General Framework for Neutrality Tests Based on the Site Frequency Spectrum
Ramos Onsins, Sebastián Ernesto|||0000-0002-1776-140X
Coalescent theory
Site frequency spectrum
Neutrality test
Statistical power
Summary statistics
title_short A General Framework for Neutrality Tests Based on the Site Frequency Spectrum
title_full A General Framework for Neutrality Tests Based on the Site Frequency Spectrum
title_fullStr A General Framework for Neutrality Tests Based on the Site Frequency Spectrum
title_full_unstemmed A General Framework for Neutrality Tests Based on the Site Frequency Spectrum
title_sort A General Framework for Neutrality Tests Based on the Site Frequency Spectrum
dc.creator.none.fl_str_mv Ramos Onsins, Sebastián Ernesto|||0000-0002-1776-140X
Marmorini, Giacomo|||0000-0003-3492-276X
Achaz, Guillaume|||0000-0003-4514-5935
Ferretti, Luca
author Ramos Onsins, Sebastián Ernesto|||0000-0002-1776-140X
author_facet Ramos Onsins, Sebastián Ernesto|||0000-0002-1776-140X
Marmorini, Giacomo|||0000-0003-3492-276X
Achaz, Guillaume|||0000-0003-4514-5935
Ferretti, Luca
author_role author
author2 Marmorini, Giacomo|||0000-0003-3492-276X
Achaz, Guillaume|||0000-0003-4514-5935
Ferretti, Luca
author2_role author
author
author
dc.subject.none.fl_str_mv Coalescent theory
Site frequency spectrum
Neutrality test
Statistical power
Summary statistics
topic Coalescent theory
Site frequency spectrum
Neutrality test
Statistical power
Summary statistics
description 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.
publishDate 2023
dc.date.none.fl_str_mv 2
2023-01-01
2023
2023-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/296870
https://dx.doi.org/urn:doi:10.3390/genes14091714
url https://ddd.uab.cat/record/296870
https://dx.doi.org/urn:doi:10.3390/genes14091714
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Ministerio de Ciencia e Innovación https://doi.org/10.13039/501100004837 CGL2009-0934
Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 PID2020-119255GB-I00
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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