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Power of neutrality tests for detecting natural selection

Detection of natural selection is one of the main interests in population genetics. Thus, many tests have been developed for detecting natural selection using genomic data. Although it is recognized that the utility of tests depends on several evolutionary factors, such as the timing of selection, s...

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Autores principales: Tanaka, Tomotaka, Hayakawa, Toshiyuki, Teshima, Kosuke M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10542275/
https://www.ncbi.nlm.nih.gov/pubmed/37481468
http://dx.doi.org/10.1093/g3journal/jkad161
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author Tanaka, Tomotaka
Hayakawa, Toshiyuki
Teshima, Kosuke M
author_facet Tanaka, Tomotaka
Hayakawa, Toshiyuki
Teshima, Kosuke M
author_sort Tanaka, Tomotaka
collection PubMed
description Detection of natural selection is one of the main interests in population genetics. Thus, many tests have been developed for detecting natural selection using genomic data. Although it is recognized that the utility of tests depends on several evolutionary factors, such as the timing of selection, strength of selection, frequency of selected alleles, demographic events, and initial frequency of selected allele when selection started acting (softness of selection), the relationships between such evolutionary factors and the power of tests are not yet entirely clear. In this study, we investigated the power of 4 tests: Tajiama's D, Fay and Wu's H, relative extended haplotype homozygosity (rEHH), and integrated haplotype score (iHS), under ranges of evolutionary parameters and demographic models to quantitatively expand the understanding of approaches for detecting selection. The results show that each test detects selection within a limited parameter range, and there are still wide ranges of parameters for which none of these tests work effectively. In addition, the parameter space in which each test shows the highest power overlaps the empirical results of previous research. These results indicate that our present perspective of adaptation is limited to only a part of actual adaptation.
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spelling pubmed-105422752023-10-03 Power of neutrality tests for detecting natural selection Tanaka, Tomotaka Hayakawa, Toshiyuki Teshima, Kosuke M G3 (Bethesda) Investigation Detection of natural selection is one of the main interests in population genetics. Thus, many tests have been developed for detecting natural selection using genomic data. Although it is recognized that the utility of tests depends on several evolutionary factors, such as the timing of selection, strength of selection, frequency of selected alleles, demographic events, and initial frequency of selected allele when selection started acting (softness of selection), the relationships between such evolutionary factors and the power of tests are not yet entirely clear. In this study, we investigated the power of 4 tests: Tajiama's D, Fay and Wu's H, relative extended haplotype homozygosity (rEHH), and integrated haplotype score (iHS), under ranges of evolutionary parameters and demographic models to quantitatively expand the understanding of approaches for detecting selection. The results show that each test detects selection within a limited parameter range, and there are still wide ranges of parameters for which none of these tests work effectively. In addition, the parameter space in which each test shows the highest power overlaps the empirical results of previous research. These results indicate that our present perspective of adaptation is limited to only a part of actual adaptation. Oxford University Press 2023-07-22 /pmc/articles/PMC10542275/ /pubmed/37481468 http://dx.doi.org/10.1093/g3journal/jkad161 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigation
Tanaka, Tomotaka
Hayakawa, Toshiyuki
Teshima, Kosuke M
Power of neutrality tests for detecting natural selection
title Power of neutrality tests for detecting natural selection
title_full Power of neutrality tests for detecting natural selection
title_fullStr Power of neutrality tests for detecting natural selection
title_full_unstemmed Power of neutrality tests for detecting natural selection
title_short Power of neutrality tests for detecting natural selection
title_sort power of neutrality tests for detecting natural selection
topic Investigation
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10542275/
https://www.ncbi.nlm.nih.gov/pubmed/37481468
http://dx.doi.org/10.1093/g3journal/jkad161
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