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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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Genetics Society of America
2014
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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. |
format | Online Article Text |
id | pubmed-4169157 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
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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