Soft sweeps III: the signature of positive selection from recurrent mutation.
Polymorphism data can be used to identify loci at which a beneficial allele has recently gone to fixation, given that an accurate description of the signature of selection is available. In the classical model that is used, a favored allele derives from a single mutational origin. This ignores the fa...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2006-12-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC1698945?pdf=render |
| _version_ | 1828380080836968448 |
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| author | Pleuni S Pennings Joachim Hermisson |
| author_facet | Pleuni S Pennings Joachim Hermisson |
| author_sort | Pleuni S Pennings |
| collection | DOAJ |
| description | Polymorphism data can be used to identify loci at which a beneficial allele has recently gone to fixation, given that an accurate description of the signature of selection is available. In the classical model that is used, a favored allele derives from a single mutational origin. This ignores the fact that beneficial alleles can enter a population recurrently by mutation during the selective phase. In this study, we present a combination of analytical and simulation results to demonstrate the effect of adaptation from recurrent mutation on summary statistics for polymorphism data from a linked neutral locus. We also analyze the power of standard neutrality tests based on the frequency spectrum or on linkage disequilibrium (LD) under this scenario. For recurrent beneficial mutation at biologically realistic rates, we find substantial deviations from the classical pattern of a selective sweep from a single new mutation. Deviations from neutrality in the level of polymorphism and in the frequency spectrum are much less pronounced than in the classical sweep pattern. In contrast, for levels of LD, the signature is even stronger if recurrent beneficial mutation plays a role. We suggest a variant of existing LD tests that increases their power to detect this signature. |
| first_indexed | 2024-12-10T03:51:00Z |
| format | Article |
| id | doaj.art-1c462351ef2642b5b52aaa8a05ce72ac |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-10T03:51:00Z |
| publishDate | 2006-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-1c462351ef2642b5b52aaa8a05ce72ac2022-12-22T02:03:14ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042006-12-01212e18610.1371/journal.pgen.0020186Soft sweeps III: the signature of positive selection from recurrent mutation.Pleuni S PenningsJoachim HermissonPolymorphism data can be used to identify loci at which a beneficial allele has recently gone to fixation, given that an accurate description of the signature of selection is available. In the classical model that is used, a favored allele derives from a single mutational origin. This ignores the fact that beneficial alleles can enter a population recurrently by mutation during the selective phase. In this study, we present a combination of analytical and simulation results to demonstrate the effect of adaptation from recurrent mutation on summary statistics for polymorphism data from a linked neutral locus. We also analyze the power of standard neutrality tests based on the frequency spectrum or on linkage disequilibrium (LD) under this scenario. For recurrent beneficial mutation at biologically realistic rates, we find substantial deviations from the classical pattern of a selective sweep from a single new mutation. Deviations from neutrality in the level of polymorphism and in the frequency spectrum are much less pronounced than in the classical sweep pattern. In contrast, for levels of LD, the signature is even stronger if recurrent beneficial mutation plays a role. We suggest a variant of existing LD tests that increases their power to detect this signature.http://europepmc.org/articles/PMC1698945?pdf=render |
| spellingShingle | Pleuni S Pennings Joachim Hermisson Soft sweeps III: the signature of positive selection from recurrent mutation. PLoS Genetics |
| title | Soft sweeps III: the signature of positive selection from recurrent mutation. |
| title_full | Soft sweeps III: the signature of positive selection from recurrent mutation. |
| title_fullStr | Soft sweeps III: the signature of positive selection from recurrent mutation. |
| title_full_unstemmed | Soft sweeps III: the signature of positive selection from recurrent mutation. |
| title_short | Soft sweeps III: the signature of positive selection from recurrent mutation. |
| title_sort | soft sweeps iii the signature of positive selection from recurrent mutation |
| url | http://europepmc.org/articles/PMC1698945?pdf=render |
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