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
Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill-Robertson Interference, in an Avian System
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
2016 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 1, 216-227 p.Article in journal (Refereed) Published
Abstract [en]

The ratio of nonsynonymous to synonymous substitution rates (ω) is often used to measure the strength of natural selection. However, ω may be influenced by linkage among different targets of selection, that is, Hill-Robertson interference (HRI), which reduces the efficacy of selection. Recombination modulates the extent of HRI but may also affect ω by means of GC-biased gene conversion (gBGC), a process leading to a preferential fixation of G:C ("strong," S) over A:T ("weak," W) alleles. As HRI and gBGC can have opposing effects on ω, it is essential to understand their relative impact to make proper inferences of ω. We used a model that separately estimated S-to-S, S-to-W, W-to-S, and W-to-W substitution rates in 8,423 avian genes in the Ficedula flycatcher lineage. We found that the W-to-S substitution rate was positively, and the S-to-W rate negatively, correlated with recombination rate, in accordance with gBGC but not predicted by HRI. The W-to-S rate further showed the strongest impact on both dN and dS. However, since the effects were stronger at 4-fold than at 0-fold degenerated sites, likely because the GC content of these sites is farther away from its equilibrium, ω slightly decreases with increasing recombination rate, which could falsely be interpreted as a consequence of HRI. We corroborated this hypothesis analytically and demonstrate that under particular conditions, ω can decrease with increasing recombination rate. Analyses of the site-frequency spectrum showed that W-to-S mutations were skewed toward high, and S-to-W mutations toward low, frequencies, consistent with a prevalent gBGC-driven fixation bias.

Place, publisher, year, edition, pages
2016. Vol. 33, no 1, 216-227 p.
Keyword [en]
gBGC; Hill-Robertson interference; d(N)/d(S); divergence; diversity; rate of molecular evolution
National Category
Evolutionary Biology Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-280275DOI: 10.1093/molbev/msv214ISI: 000369992600017PubMedID: 26446902OAI: oai:DiVA.org:uu-280275DiVA: diva2:910416
Funder
Swedish Research Council, 2010-5650Swedish Research Council, 2013-8271EU, European Research Council, AdG 249976Knut and Alice Wallenberg Foundation
Available from: 2016-03-09 Created: 2016-03-09 Last updated: 2017-11-30Bibliographically approved

Open Access in DiVA

fulltext(389 kB)56 downloads
File information
File name FULLTEXT01.pdfFile size 389 kBChecksum SHA-512
4109dd54f50080bd38e58413a666fb965ab7e355d1d140914384582d4bd46311dc021291b9b5a1d349461861af5eef606c3ccd0d35c911715e69448bc45723ce
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Authority records BETA

Bolívar, PaulinaMugal, Carina FEllegren, Hans

Search in DiVA

By author/editor
Bolívar, PaulinaMugal, Carina FEllegren, Hans
By organisation
Evolutionary Biology
In the same journal
Molecular biology and evolution
Evolutionary BiologyBiochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 56 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 309 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