An Evolutionary Advantage of Haploidy in Large Yeast Populations

Zeyl, Clifford; Vanderford, Thomas H.; Carter, Michele

doi:10.1126/science.1078417

Cited by 136 publications

(130 citation statements)

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“…Accordingly, we might expect to observe faster-X evolution, provided that new beneficial mutations are, on average, at least partially recessive. There is little relevant information on the levels of dominance of beneficial mutations, although indirect evidence from the genetics of species differences in highly selfing taxa of plants (Charlesworth, 1992), and from comparisons of rates of adaptive evolution of haploid and diploid laboratory populations of yeast (Zeyl et al, 2003 ;Anderson et al, 2004), is consistent with a predominance of at least partial recessivity of new, selectively favourable mutations.…”

Section: Introductionmentioning

confidence: 99%

A multispecies approach for comparing sequence evolution of X-linked and autosomal sites inDrosophila

Vicoso

Haddrill²,

Charlesworth

2008

Genet. Res.

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This version is available at https://strathprints.strath.ac.uk/47568/ Strathprints is designed to allow users to access the research output of the University of Strathclyde. Unless otherwise explicitly stated on the manuscript, Copyright © and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. Please check the manuscript for details of any other licences that may have been applied. You may not engage in further distribution of the material for any profitmaking activities or any commercial gain. You may freely distribute both the url (https://strathprints.strath.ac.uk/) and the content of this paper for research or private study, educational, or not-for-profit purposes without prior permission or charge.Any correspondence concerning this service should be sent to the SummaryPopulation genetics models show that, under certain conditions, the X chromosome is expected to be under more efficient selection than the autosomes. This could lead to 'faster-X evolution ', if a large proportion of mutations are fixed by positive selection, as suggested by recent studies in Drosophila. We used a multispecies approach to test this : Muller's element D, an autosomal arm, is fused to the ancestral X chromosome in Drosophila pseudoobscura and its sister species, Drosophila affinis. We tested whether the same set of genes had higher rates of non-synonymous evolution when they were X-linked (in the D. pseudoobscura/D. affinis comparison) than when they were autosomal (in Drosophila melanogaster/Drosophila yakuba). Although not significant, our results suggest this may be the case, but only for genes under particularly strong positive selection/weak purifying selection. They also suggest that genes that have become X-linked have higher levels of codon bias and slower synonymous site evolution, consistent with more effective selection on codon usage at X-linked sites.

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Section: Introductionmentioning

confidence: 99%

A multispecies approach for comparing sequence evolution of X-linked and autosomal sites inDrosophila

Vicoso

Haddrill²,

Charlesworth

2008

Genet. Res.

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“…Depending on the question being asked, batch culture with serial dilution can be a simple and scalable solution (e.g., Zeyl et al 2003;Lang et al 2011). However, such cultures are only rarely propagated in a relatively constant environment and growth rate regime because doing so can require a heroic sampling regimen where back dilution is performed multiple times per day (e.g., Torres et al 2010).…”

Section: Batch Culturementioning

confidence: 99%

Chemostat Culture for Yeast Physiology and Experimental Evolution

Dunham

Kerr

Miller

et al. 2017

Cold Spring Harb Protoc

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Continuous culture provides many benefits over the classical batch style of growing yeast cells. Steadystate cultures allow for precise control of growth rate and environment. Cultures can be propagated for weeks or months in these controlled environments, which is important for the study of experimental evolution. Despite these advantages, chemostats have not become a highly used system, in large part because of their historical impracticalities, including low throughput, large footprint, systematic complexity, commercial unavailability, high cost, and insufficient protocol availability. However, we have developed methods for building a relatively simple, low-cost, small footprint array of chemostats that can be run in multiples of 32. This "ministat array" can be applied to problems in yeast physiology and experimental evolution. BATCH CULTUREThe most common method of growing yeast cell cultures is the standard "batch" culture. In this regime, a small number of cells are inoculated into nutrient-rich medium and allowed to divide at maximal growth rate through nutrient exhaustion and into saturation. Sampling of the culture for the experiment of choice is most typically done from the saturated culture or from cells growing in midlog phase before the diauxic shift. Batch culture provides a number of obvious benefits-it is easy, uses glassware commonly available in any laboratory, and is consistent with a vast literature. However, batch cultures can be problematic for certain applications. When comparing cells of different genotypes, for example, differences in the maximal growth rate are a common phenotype. Many other phenotypes co-vary with growth rate, leading to a nonspecific suite of cell biological, gene expression, and other physiological changes that may not be directly related to the mutation of interest (Regenberg et al. 2006;Castrillo et al. 2007;Brauer et al. 2008).Batch culture has also been a standard for long-term evolution experiments. Depending on the question being asked, batch culture with serial dilution can be a simple and scalable solution (e.g., Zeyl et al. 2003;Lang et al. 2011). However, such cultures are only rarely propagated in a relatively constant environment and growth rate regime because doing so can require a heroic sampling regimen where back dilution is performed multiple times per day (e.g., Torres et al. 2010). More typically, cultures are allowed to exhaust nutrients before transfer to new medium, leading to a variation in growth rate and nutrient access over the evolutionary time course. These discontinuities in selective pressure can lead to complex subpopulation structures in which different genotypes specialize for the various stages of the growth cycle (e.g., dividing a few extra times or failing to die after saturation, shortening lag phase,

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“…In yeast, the question was addressed concerning whether haploidy or diploidy confers an evolutionary advantage (Zeyl, Vanderford et al 2003;Zeyl 2004). Conventional wisdom suggested that having an extra gene copy would prevent harmful mutations from accumulating in the genome whereas in haploid species, harmful mutations would be detrimental to the organism.…”

Section: Sexuality In Fungimentioning

confidence: 99%