Academic Journal
A Genomic Map of the Effects of Linked Selection in Drosophila
| Τίτλος: | A Genomic Map of the Effects of Linked Selection in Drosophila |
|---|---|
| Συγγραφείς: | Elyashiv, Eyal, Sattath, Shmuel, Hu, Tina T., Strutsovsky, Alon, McVicker, Graham, Andolfatto, Peter, Coop, Graham, Sella, Guy |
| Έτος έκδοσης: | 2016 |
| Συλλογή: | Columbia University: Academic Commons |
| Θεματικοί όροι: | Evolutionary genetics, Biodiversity, Natural selection--Mathematical models, Genetics, Biology |
| Περιγραφή: | Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of “linked selection” on levels of genetic diversity is key to making reliable inference about demography, building a null model in scans for targets of adaptation, and learning about the dynamics of natural selection. Here, we introduce the first method that jointly infers parameters of distinct modes of linked selection, notably background selection and selective sweeps, from genome-wide diversity data, functional annotations and genetic maps. The central idea is to calculate the probability that a neutral site is polymorphic given local annotations, substitution patterns, and recombination rates. Information is then combined across sites and samples using composite likelihood in order to estimate genome-wide parameters of distinct modes of selection. In addition to parameter estimation, this approach yields a map of the expected neutral diversity levels along the genome. To illustrate the utility of our approach, we apply it to genome-wide resequencing data from 125 lines in Drosophila melanogaster and reliably predict diversity levels at the 1Mb scale. Our results corroborate estimates of a high fraction of beneficial substitutions in proteins and untranslated regions (UTR). They allow us to distinguish between the contribution of sweeps and other modes of selection around amino acid substitutions and to uncover evidence for pervasive sweeps in untranslated regions (UTRs). Our inference further suggests a substantial effect of other modes of linked selection and of adaptation in particular. More generally, we demonstrate that linked selection has had a larger effect in reducing diversity levels and increasing their variance in D. melanogaster than previously appreciated. |
| Τύπος εγγράφου: | article in journal/newspaper |
| Γλώσσα: | English |
| Relation: | https://doi.org/10.7916/D8M32W1M |
| DOI: | 10.7916/D8M32W1M |
| Διαθεσιμότητα: | https://doi.org/10.7916/D8M32W1M |
| Αριθμός Καταχώρησης: | edsbas.C10A9FFF |
| Βάση Δεδομένων: | BASE |
| FullText | Text: Availability: 0 CustomLinks: – Url: https://doi.org/10.7916/D8M32W1M# Name: EDS - BASE (ns324271) Category: fullText Text: View record from BASE |
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| Items | – Name: Title Label: Title Group: Ti Data: A Genomic Map of the Effects of Linked Selection in Drosophila – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Elyashiv%2C+Eyal%22">Elyashiv, Eyal</searchLink><br /><searchLink fieldCode="AR" term="%22Sattath%2C+Shmuel%22">Sattath, Shmuel</searchLink><br /><searchLink fieldCode="AR" term="%22Hu%2C+Tina+T%2E%22">Hu, Tina T.</searchLink><br /><searchLink fieldCode="AR" term="%22Strutsovsky%2C+Alon%22">Strutsovsky, Alon</searchLink><br /><searchLink fieldCode="AR" term="%22McVicker%2C+Graham%22">McVicker, Graham</searchLink><br /><searchLink fieldCode="AR" term="%22Andolfatto%2C+Peter%22">Andolfatto, Peter</searchLink><br /><searchLink fieldCode="AR" term="%22Coop%2C+Graham%22">Coop, Graham</searchLink><br /><searchLink fieldCode="AR" term="%22Sella%2C+Guy%22">Sella, Guy</searchLink> – Name: DatePubCY Label: Publication Year Group: Date Data: 2016 – Name: Subset Label: Collection Group: HoldingsInfo Data: Columbia University: Academic Commons – Name: Subject Label: Subject Terms Group: Su Data: <searchLink fieldCode="DE" term="%22Evolutionary+genetics%22">Evolutionary genetics</searchLink><br /><searchLink fieldCode="DE" term="%22Biodiversity%22">Biodiversity</searchLink><br /><searchLink fieldCode="DE" term="%22Natural+selection--Mathematical+models%22">Natural selection--Mathematical models</searchLink><br /><searchLink fieldCode="DE" term="%22Genetics%22">Genetics</searchLink><br /><searchLink fieldCode="DE" term="%22Biology%22">Biology</searchLink> – Name: Abstract Label: Description Group: Ab Data: Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of “linked selection” on levels of genetic diversity is key to making reliable inference about demography, building a null model in scans for targets of adaptation, and learning about the dynamics of natural selection. Here, we introduce the first method that jointly infers parameters of distinct modes of linked selection, notably background selection and selective sweeps, from genome-wide diversity data, functional annotations and genetic maps. The central idea is to calculate the probability that a neutral site is polymorphic given local annotations, substitution patterns, and recombination rates. Information is then combined across sites and samples using composite likelihood in order to estimate genome-wide parameters of distinct modes of selection. In addition to parameter estimation, this approach yields a map of the expected neutral diversity levels along the genome. To illustrate the utility of our approach, we apply it to genome-wide resequencing data from 125 lines in Drosophila melanogaster and reliably predict diversity levels at the 1Mb scale. Our results corroborate estimates of a high fraction of beneficial substitutions in proteins and untranslated regions (UTR). They allow us to distinguish between the contribution of sweeps and other modes of selection around amino acid substitutions and to uncover evidence for pervasive sweeps in untranslated regions (UTRs). Our inference further suggests a substantial effect of other modes of linked selection and of adaptation in particular. More generally, we demonstrate that linked selection has had a larger effect in reducing diversity levels and increasing their variance in D. melanogaster than previously appreciated. – Name: TypeDocument Label: Document Type Group: TypDoc Data: article in journal/newspaper – Name: Language Label: Language Group: Lang Data: English – Name: NoteTitleSource Label: Relation Group: SrcInfo Data: https://doi.org/10.7916/D8M32W1M – Name: DOI Label: DOI Group: ID Data: 10.7916/D8M32W1M – Name: URL Label: Availability Group: URL Data: https://doi.org/10.7916/D8M32W1M – Name: AN Label: Accession Number Group: ID Data: edsbas.C10A9FFF |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.7916/D8M32W1M Languages: – Text: English Subjects: – SubjectFull: Evolutionary genetics Type: general – SubjectFull: Biodiversity Type: general – SubjectFull: Natural selection--Mathematical models Type: general – SubjectFull: Genetics Type: general – SubjectFull: Biology Type: general Titles: – TitleFull: A Genomic Map of the Effects of Linked Selection in Drosophila Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Elyashiv, Eyal – PersonEntity: Name: NameFull: Sattath, Shmuel – PersonEntity: Name: NameFull: Hu, Tina T. – PersonEntity: Name: NameFull: Strutsovsky, Alon – PersonEntity: Name: NameFull: McVicker, Graham – PersonEntity: Name: NameFull: Andolfatto, Peter – PersonEntity: Name: NameFull: Coop, Graham – PersonEntity: Name: NameFull: Sella, Guy IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Type: published Y: 2016 Identifiers: – Type: issn-locals Value: edsbas – Type: issn-locals Value: edsbas.oa |
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