Fisher KJ, Buskirk SW, Vignogna RC, Marad DA, Lang GI. Adaptive genome duplication affects patterns of molecular evolution in Saccharomyces cerevisiae.
PLoS Genet 2018;
14:e1007396. [PMID:
29799840 PMCID:
PMC5991770 DOI:
10.1371/journal.pgen.1007396]
[Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/07/2018] [Accepted: 05/07/2018] [Indexed: 11/19/2022] Open
Abstract
Genome duplications are important evolutionary events that impact the rate and spectrum of beneficial mutations and thus the rate of adaptation. Laboratory evolution experiments initiated with haploid Saccharomyces cerevisiae cultures repeatedly experience whole-genome duplication (WGD). We report recurrent genome duplication in 46 haploid yeast populations evolved for 4,000 generations. We find that WGD confers a fitness advantage, and this immediate fitness gain is accompanied by a shift in genomic and phenotypic evolution. The presence of ploidy-enriched targets of selection and structural variants reveals that autodiploids utilize adaptive paths inaccessible to haploids. We find that autodiploids accumulate recessive deleterious mutations, indicating an increased susceptibility for nonadaptive evolution. Finally, we report that WGD results in a reduced adaptation rate, indicating a trade-off between immediate fitness gains and long-term adaptability.
Whole genome duplications—the simultaneous doubling of each chromosome—can have a profound influence on evolution. Evidence of ancient whole genome duplications can be seen in most modern genomes. Experimental evolution, the long-term propagation of organisms under well-controlled laboratory conditions, yields valuable insight into the processes of adaptation and genome evolution. One interesting, and common, outcome of laboratory evolution experiments that start with haploid yeast populations is the emergence of diploid lineages via whole genome duplication. We show that, under our laboratory conditions, whole genome duplication provides a direct fitness benefit, and we identify several consequences of whole genome duplication on adaptation. Following whole-genome duplication, the rate of adaptation slows, the biological targets of selection change, and aneuploidies, copy-number variants and recessive lethal mutations accumulate. By studying the effect of whole genome duplication on adaptation, we can better understand how selection acts on ploidy, a fundamental biological parameter that varies considerably across life.
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