Correcting the site frequency spectrum for divergence-based ascertainment.
Comparative genomics based on sequenced referenced genomes is essential to hypothesis generation and testing within population genetics. However, selection of candidate regions for further study on the basis of elevated or depressed divergence between species leads to a divergence-based ascertainmen...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2009-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2666160?pdf=render |
| _version_ | 1818433405576019968 |
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| author | Andrew D Kern |
| author_facet | Andrew D Kern |
| author_sort | Andrew D Kern |
| collection | DOAJ |
| description | Comparative genomics based on sequenced referenced genomes is essential to hypothesis generation and testing within population genetics. However, selection of candidate regions for further study on the basis of elevated or depressed divergence between species leads to a divergence-based ascertainment bias in the site frequency spectrum within selected candidate loci. Here, a method to correct this problem is developed that obtains maximum-likelihood estimates of the unascertained allele frequency distribution using numerical optimization. I show how divergence-based ascertainment may mimic the effects of natural selection and offer correction formulae for performing proper estimation into the strength of selection in candidate regions in a maximum-likelihood setting. |
| first_indexed | 2024-12-14T16:20:34Z |
| format | Article |
| id | doaj.art-febb692fe5854cd49c8dff3b9ed2b12c |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T16:20:34Z |
| publishDate | 2009-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-febb692fe5854cd49c8dff3b9ed2b12c2022-12-21T22:54:48ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-01-0144e515210.1371/journal.pone.0005152Correcting the site frequency spectrum for divergence-based ascertainment.Andrew D KernComparative genomics based on sequenced referenced genomes is essential to hypothesis generation and testing within population genetics. However, selection of candidate regions for further study on the basis of elevated or depressed divergence between species leads to a divergence-based ascertainment bias in the site frequency spectrum within selected candidate loci. Here, a method to correct this problem is developed that obtains maximum-likelihood estimates of the unascertained allele frequency distribution using numerical optimization. I show how divergence-based ascertainment may mimic the effects of natural selection and offer correction formulae for performing proper estimation into the strength of selection in candidate regions in a maximum-likelihood setting.http://europepmc.org/articles/PMC2666160?pdf=render |
| spellingShingle | Andrew D Kern Correcting the site frequency spectrum for divergence-based ascertainment. PLoS ONE |
| title | Correcting the site frequency spectrum for divergence-based ascertainment. |
| title_full | Correcting the site frequency spectrum for divergence-based ascertainment. |
| title_fullStr | Correcting the site frequency spectrum for divergence-based ascertainment. |
| title_full_unstemmed | Correcting the site frequency spectrum for divergence-based ascertainment. |
| title_short | Correcting the site frequency spectrum for divergence-based ascertainment. |
| title_sort | correcting the site frequency spectrum for divergence based ascertainment |
| url | http://europepmc.org/articles/PMC2666160?pdf=render |
| work_keys_str_mv | AT andrewdkern correctingthesitefrequencyspectrumfordivergencebasedascertainment |