uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
McSwan: A joint site frequency spectrum method to detect and date selective sweeps across multiple population genomes
Univ Montpellier, IRD, UMR DIADE, BP 64501, Montpellier 5, France.
Univ Montpellier, IRD, UMR DIADE, BP 64501, Montpellier 5, France.
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Dept Anthropol & Dev Studies, Ctr Anthropol Res, Auckland Pk, South Africa.ORCID iD: 0000-0001-7840-7853
Univ Montpellier, IRD, UMR DIADE, BP 64501, Montpellier 5, France.
Show others and affiliations
2019 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 19, no 1, p. 283-295Article in journal (Refereed) Published
Abstract [en]

Inferring the mode and tempo of natural selection helps further our understanding of adaptation to past environmental changes. Here, we introduce McSwan, a method to detect and date past and recent natural selection events in the case of a hard sweep. The method is based on the comparison of site frequency spectra obtained under various demographic models that include selection. McSwan demonstrated high power (high sensitivity and specificity) in capturing hard selective sweep events without requiring haplotype phasing. It performed slightly better than SweeD when the recent effective population size was low and the genomic region was small. We then applied our method to a European (CEU) and an African (LWK) human re-sequencing data set. Most hard sweeps were detected in the CEU population (96%). Moreover, hard sweeps in the African population were estimated to have occurred further back in time (mode: 43,625 years BP) compared to those of Europeans (mode: 24,850 years BP). Most of the estimated ages of hard sweeps in Europeans were associated with the Last Glacial Maximum and were enriched in immunity-associated genes.

Place, publisher, year, edition, pages
2019. Vol. 19, no 1, p. 283-295
Keywords [en]
age of selection, coalescent process, high-performance computing, human, selective sweep, site frequency spectrum
National Category
Ecology
Identifiers
URN: urn:nbn:se:uu:diva-377712DOI: 10.1111/1755-0998.12957ISI: 000457579800022PubMedID: 30358170OAI: oai:DiVA.org:uu-377712DiVA, id: diva2:1294673
Funder
Knut and Alice Wallenberg FoundationForte, Swedish Research Council for Health, Working Life and WelfareAvailable from: 2019-03-08 Created: 2019-03-08 Last updated: 2019-03-08Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textPubMed

Authority records BETA

Jakobsson, Mattias

Search in DiVA

By author/editor
Jakobsson, Mattias
By organisation
Science for Life Laboratory, SciLifeLabHuman Evolution
In the same journal
Molecular Ecology Resources
Ecology

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 108 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf