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The Genomic Signal of Partial Sweeps in Mimulus guttatus

The molecular signature of selection depends strongly on whether new mutations are immediately favorable and sweep to fixation (hard sweeps) as opposed to when selection acts on segregating variation (soft sweeps). The prediction of reduced sequence variation around selected polymorphisms is much st...

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Autores principales: Kelly, John K., Koseva, Boryana, Mojica, Julius P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762192/
https://www.ncbi.nlm.nih.gov/pubmed/23828880
http://dx.doi.org/10.1093/gbe/evt100
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author Kelly, John K.
Koseva, Boryana
Mojica, Julius P.
author_facet Kelly, John K.
Koseva, Boryana
Mojica, Julius P.
author_sort Kelly, John K.
collection PubMed
description The molecular signature of selection depends strongly on whether new mutations are immediately favorable and sweep to fixation (hard sweeps) as opposed to when selection acts on segregating variation (soft sweeps). The prediction of reduced sequence variation around selected polymorphisms is much stronger for hard than soft sweeps, particularly when considering quantitative traits where sweeps are likely to be incomplete. Here, we directly investigate the genomic signal of soft sweeps within an artificial selection experiment on Mimulus guttatus. We first develop a statistical method based on Fisher’s angular transformation of allele frequencies to identify selected loci. Application of this method identifies about 400 significant windows, but no fixed differences between phenotypically divergent populations. With two notable exceptions, we find a modest average effect of partial sweeps on the amount of molecular variation. The first exception is a polymorphic inversion on chromosome 6. The increase of the derived haplotype has a broad genomic effect due to recombination suppression coupled with substantial initial haplotype structure within the population. Second, we found significant increases in nucleotide variation around selected loci in the population evolving larger flowers. This suggests that “high” alleles for flower size were initially less frequent than “low” alleles. This result is consistent with prior studies of M. guttatus and illustrates how molecular evolution can depend on the allele frequency spectrum at quantitative trait loci.
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spelling pubmed-37621922013-09-04 The Genomic Signal of Partial Sweeps in Mimulus guttatus Kelly, John K. Koseva, Boryana Mojica, Julius P. Genome Biol Evol Research Article The molecular signature of selection depends strongly on whether new mutations are immediately favorable and sweep to fixation (hard sweeps) as opposed to when selection acts on segregating variation (soft sweeps). The prediction of reduced sequence variation around selected polymorphisms is much stronger for hard than soft sweeps, particularly when considering quantitative traits where sweeps are likely to be incomplete. Here, we directly investigate the genomic signal of soft sweeps within an artificial selection experiment on Mimulus guttatus. We first develop a statistical method based on Fisher’s angular transformation of allele frequencies to identify selected loci. Application of this method identifies about 400 significant windows, but no fixed differences between phenotypically divergent populations. With two notable exceptions, we find a modest average effect of partial sweeps on the amount of molecular variation. The first exception is a polymorphic inversion on chromosome 6. The increase of the derived haplotype has a broad genomic effect due to recombination suppression coupled with substantial initial haplotype structure within the population. Second, we found significant increases in nucleotide variation around selected loci in the population evolving larger flowers. This suggests that “high” alleles for flower size were initially less frequent than “low” alleles. This result is consistent with prior studies of M. guttatus and illustrates how molecular evolution can depend on the allele frequency spectrum at quantitative trait loci. Oxford University Press 2013 2013-07-04 /pmc/articles/PMC3762192/ /pubmed/23828880 http://dx.doi.org/10.1093/gbe/evt100 Text en © The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Research Article
Kelly, John K.
Koseva, Boryana
Mojica, Julius P.
The Genomic Signal of Partial Sweeps in Mimulus guttatus
title The Genomic Signal of Partial Sweeps in Mimulus guttatus
title_full The Genomic Signal of Partial Sweeps in Mimulus guttatus
title_fullStr The Genomic Signal of Partial Sweeps in Mimulus guttatus
title_full_unstemmed The Genomic Signal of Partial Sweeps in Mimulus guttatus
title_short The Genomic Signal of Partial Sweeps in Mimulus guttatus
title_sort genomic signal of partial sweeps in mimulus guttatus
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762192/
https://www.ncbi.nlm.nih.gov/pubmed/23828880
http://dx.doi.org/10.1093/gbe/evt100
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