Dataset Information

Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species.

ABSTRACT: It is now clear that the exploration of the genetic and phenotypic diversity of nonmodel species greatly improves our knowledge in biology. In this context, we recently launched a population genomic analysis of the protoploid yeast Lachancea kluyveri (formerly Saccharomyces kluyveri), highlighting a broad genetic diversity (? = 17 × 10(-3)) compared to the yeast model organism, S. cerevisiae (? = 4 × 10(-3)). Here, we sought to generate a comprehensive view of the phenotypic diversity in this species. In total, 27 natural L. kluyveri isolates were subjected to trait profiling using the following independent approaches: (i) analyzing growth in 55 growth conditions and (ii) investigating 501 morphological changes at the cellular level. Despite higher genetic diversity, the fitness variance observed in L. kluyveri is lower than that in S. cerevisiae However, morphological features show an opposite trend. In addition, there is no correlation between the origins (ecological or geographical) of the isolate and the phenotypic patterns, demonstrating that trait variation follows neither population history nor source environment in L. kluyveri Finally, pairwise comparisons between growth rate correlation and genetic diversity show a clear decrease in phenotypic variability linked to genome variation increase, whereas no such a trend was identified for morphological changes. Overall, this study reveals for the first time the phenotypic diversity of a distantly related species to S. cerevisiae Given its genetic properties, L. kluyveri might be useful in further linkage mapping analyses of complex traits, and could ultimately provide a better insight into the evolution of the genotype-phenotype relationship across yeast species.

SUBMITTER: Jung PP

PROVIDER: S-EPMC4825641 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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Publications

Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species.

Jung Paul P PP Sigwalt Anastasie A Ohnuki Shinsuke S de Montigny Jacky J Ohya Yoshikazu Y Schacherer Joseph J

G3 (Bethesda, Md.) 20160407 4

It is now clear that the exploration of the genetic and phenotypic diversity of nonmodel species greatly improves our knowledge in biology. In this context, we recently launched a population genomic analysis of the protoploid yeast Lachancea kluyveri (formerly Saccharomyces kluyveri), highlighting a broad genetic diversity (π = 17 × 10(-3)) compared to the yeast model organism, S. cerevisiae (π = 4 × 10(-3)). Here, we sought to generate a comprehensive view of the phenotypic diversity in this sp ...[more]

PMID: 26888866

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Project description:Intraspecific trait variation (ITV) is common feature of natural communities and has gained increasing attention due to its significant ecological effects on community dynamics and ecosystem functioning. However, the estimation of ITV per se has yet to receive much attention, despite the need for accurate ITV estimation for trait-based ecological inferences. It remains unclear if, and to what extent, current estimations of ITV are biased. The most common method used to quantify ITV is the coefficient of variation (CV), which is dimensionless and can therefore be compared across traits, species, and studies. Here, we asked which CV estimator and data normalization method are optimal for quantifying ITV, and further identified the minimum sample size required for ±5% accuracy assuming a completely random sample scheme. To these ends, we compared the performance of four existing CV estimators, together with new simple composite estimators, across different data normalizations, and sample sizes using both a simulated and empirical trait datasets from local to regional scales. Our results consistently showed that the most commonly used ITV estimator (CV 1= σsample /μsample ), often underestimated ITV-in some cases by nearly 50%-and that underestimation varies largely among traits and species. The extent of this bias depends on the sample size, skewness and kurtosis of the trait value distribution. The bias in ITV can be substantially reduced by using log-transforming trait data and alternative CV estimators that take into consideration the above dependencies. We find that the CV4 estimator, also known as Bao's CV estimator, combined with log data normalization, exhibits the lowest bias and can reach ±5% accuracy with sample sizes greater than 20 for almost all examined traits and species. These results demonstrated that many previous ITV measurements may be substantially underestimated and, further, that these underestimations are not equal among species and traits even using the same sample size. These problems can be largely solved by log-transforming trait data first and then using the Bao's CV to quantify ITV. Together, our findings facilitate a more accurate understanding of ITV in community structures and dynamics, and may also benefit studies in other research areas that depend on accurate estimation of CV.

Dataset Information

Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species.

Publications

Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species.

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