Parallel Genome-Wide Fixation of Ancestral Alleles in Partially Outcrossing Experimental Populations of Caenorhabditis elegans

Experimental evolution studies, coupled with new advances in DNA sequencing technology, have become a powerful tool for exploring how populations respond to selection at the genomic level. Recent experiments in microbes typically have found evidence for multiple novel mutations, which are usually fi...

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Autor principal: Chandler, Christopher H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169157/
https://www.ncbi.nlm.nih.gov/pubmed/24989146
http://dx.doi.org/10.1534/g3.114.012914
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author Chandler, Christopher H.
author_facet Chandler, Christopher H.
author_sort Chandler, Christopher H.
collection PubMed
description Experimental evolution studies, coupled with new advances in DNA sequencing technology, have become a powerful tool for exploring how populations respond to selection at the genomic level. Recent experiments in microbes typically have found evidence for multiple novel mutations, which are usually fixed. In contrast, in animal model systems, evolutionary responses seem to involve more modest changes in the frequencies of pre-existing alleles, probably because these populations outcross and are usually initialized with greater levels of standing variation. In this experiment, I used whole-genome resequencing to estimate allele frequencies and look for novel substitutions in experimentally evolved populations of Caenorhabditis elegans. These populations were founded with a fixed pair of deleterious mutations introgressed into multiple wild genetic backgrounds and allowed to evolve for 50 generations with a mixed mating system. There is evidence for some recombination between ancestral haplotypes, but selective sweeps seem to have resulted in the fixation of large chromosomal segments throughout most of the genome. In addition, a few new mutations were detected. Simulations suggest that strong selection and low outcrossing rates are likely explanations for the observed outcomes, consistent with earlier work showing large fitness increases in these populations over 50 generations. These results also show clear parallels to population genetic patterns in C. elegans in nature: recent selective sweeps, high linkage disequilibrium, and low effective recombination rates. Thus, the genomic consequences of selection depend heavily on the biology of the organism in question, including its mating system and levels of genetic variation.
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spelling pubmed-41691572014-09-24 Parallel Genome-Wide Fixation of Ancestral Alleles in Partially Outcrossing Experimental Populations of Caenorhabditis elegans Chandler, Christopher H. G3 (Bethesda) Investigations Experimental evolution studies, coupled with new advances in DNA sequencing technology, have become a powerful tool for exploring how populations respond to selection at the genomic level. Recent experiments in microbes typically have found evidence for multiple novel mutations, which are usually fixed. In contrast, in animal model systems, evolutionary responses seem to involve more modest changes in the frequencies of pre-existing alleles, probably because these populations outcross and are usually initialized with greater levels of standing variation. In this experiment, I used whole-genome resequencing to estimate allele frequencies and look for novel substitutions in experimentally evolved populations of Caenorhabditis elegans. These populations were founded with a fixed pair of deleterious mutations introgressed into multiple wild genetic backgrounds and allowed to evolve for 50 generations with a mixed mating system. There is evidence for some recombination between ancestral haplotypes, but selective sweeps seem to have resulted in the fixation of large chromosomal segments throughout most of the genome. In addition, a few new mutations were detected. Simulations suggest that strong selection and low outcrossing rates are likely explanations for the observed outcomes, consistent with earlier work showing large fitness increases in these populations over 50 generations. These results also show clear parallels to population genetic patterns in C. elegans in nature: recent selective sweeps, high linkage disequilibrium, and low effective recombination rates. Thus, the genomic consequences of selection depend heavily on the biology of the organism in question, including its mating system and levels of genetic variation. Genetics Society of America 2014-07-01 /pmc/articles/PMC4169157/ /pubmed/24989146 http://dx.doi.org/10.1534/g3.114.012914 Text en Copyright © 2014 Chandler http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigations
Chandler, Christopher H.
Parallel Genome-Wide Fixation of Ancestral Alleles in Partially Outcrossing Experimental Populations of Caenorhabditis elegans
title Parallel Genome-Wide Fixation of Ancestral Alleles in Partially Outcrossing Experimental Populations of Caenorhabditis elegans
title_full Parallel Genome-Wide Fixation of Ancestral Alleles in Partially Outcrossing Experimental Populations of Caenorhabditis elegans
title_fullStr Parallel Genome-Wide Fixation of Ancestral Alleles in Partially Outcrossing Experimental Populations of Caenorhabditis elegans
title_full_unstemmed Parallel Genome-Wide Fixation of Ancestral Alleles in Partially Outcrossing Experimental Populations of Caenorhabditis elegans
title_short Parallel Genome-Wide Fixation of Ancestral Alleles in Partially Outcrossing Experimental Populations of Caenorhabditis elegans
title_sort parallel genome-wide fixation of ancestral alleles in partially outcrossing experimental populations of caenorhabditis elegans
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169157/
https://www.ncbi.nlm.nih.gov/pubmed/24989146
http://dx.doi.org/10.1534/g3.114.012914
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