Testing the neutral hypothesis of phenotypic evolution

Abstract

It is generally accepted that a large fraction of genomic sequence variations within and between species are neutral or nearly so 1 . Whether the same is true for phenotypic variations is a central question in biology 2-7 . On the one hand, numerous phenotypic adaptations have been documented 2,8,9 and even Kimura, the champion of the neutral theory of molecular evolution, believed in widespread adaptive phenotypic evolution 1 . On the other hand, phenotypic studies are strongly biased toward traits that are likely to be adaptive 9 , contrasting genomic studies that are typically unbiased. It is thus desirable to test the neutral hypothesis of phenotypic evolution using traits irrespective of their potential involvement in adaptation. Here we present such a test for 210 morphological traits measured in multiple strains of the yeast Saccharomyces cerevisiae and two related species. Our test is based on the premise that, under neutrality, the rate of phenotypic evolution declines as the trait becomes more important to fitness, analogous to the neutral paradigm that functional genes evolve more slowly than functionless pseudogenes 10 .Neutrality is rejected in favor of adaptation if important traits evolve faster than less important ones, parallel to the demonstration of molecular adaptation when a functional gene evolves faster than pseudogenes. After controlling for the mutational size, we find faster evolution of more important morphological traits within and between species. By contrast, an analysis of 3466 yeast gene expression traits fails to reject neutrality. Thus, yeast morphological evolution is largely adaptive, but the same may not apply to other classes of phenotypes.Analogous to the neutral hypothesis of molecular evolution 1 , the neutral hypothesis of phenotypic evolution allows the presence of purifying selection; neutrality is rejected only when positive selection is invoked. Under the neutral hypothesis, compared with traits that are 3 relatively unimportant to fitness, relatively important traits should be subject to stronger purifying selection and evolve more slowly given the same speed of mutational input (Fig. 1a).However, if relatively important traits evolve faster than relatively unimportant traits, the neutral hypothesis would no longer hold and the only reasonable explanation would be stronger positive selection acting on relatively important traits than relatively unimportant ones ( Fig. 1b). This test of phenotypic neutrality differs from previous tests 3,4,[11][12][13][14][15] , which consider only one trait at a time and effectively require the intensity of positive selection to surpass that of purifying selection to reject neutrality. Because this requirement is sufficient but not necessary for demonstrating positive selection, it is replaced with the criterion of a positive correlation between trait importance and evolutionary rate to improve the power of the test (see Methods and Discussion).We first tested the neutral hypothesis of phenotypic evolution in a set of 210 morphologic...

Intra- and inter-specific variations of gene expression levels in yeast are largely neutral

“…Interestingly, both PD ww /PD wo and V w /V t are significantly skewed towards lower values when compared with the three controls ( Figs. 4C and D), consistent with the adaptive evolution hypothesis of morphological traits (19).…”

“…While this argument may be valid, the adaptive hypothesis cannot explain the significant topological similarity between the transcriptome tree and the genome tree, because the differences among the environments of the nine strains are certainly not represented by the genome tree. The similarity between the transcriptome and genome trees, in contrast to the dissimilarity between the morphology and genome trees, strongly supports the neutral explanation of the expression variations among the nine yeast strains, particularly in the light of the recent finding of adaptive variations of the morphological traits examined (19). 20 Fourth, we assumed that environmental adaptation means that there is a single optimal expression level or a continuous range of equally optimal expression levels for a given gene in an environment.…”

“…Four of the five wild strains studied here (except DBVPG1788) form a monophyly in the growth traits-based tree (17), suggesting 10 that phylogenetic clustering is able to detect at least some potential adaptations. As a further verification, we analyzed 219 morphological traits previously measured from fluorescent microscopic images of triple-stained yeast cells (18,19). Using this dataset and controlling for mutational size, we recently discovered that morphological traits that are more important to organismal fitness tend to differ more between strains, strongly suggesting that the intra-and inter-specific morphological variations in this dataset have been shaped by adaptive evolution to a large extent (19).…”

“…As a further verification, we analyzed 219 morphological traits previously measured from fluorescent microscopic images of triple-stained yeast cells (18,19). Using this dataset and controlling for mutational size, we recently discovered that morphological traits that are more important to organismal fitness tend to differ more between strains, strongly suggesting that the intra-and inter-specific morphological variations in this dataset have been shaped by adaptive evolution to a large extent (19). We thus subjected the yeast morphological data to the same phylogenetic analysis used for the transcriptome data.…”

“…The data of 219 morphological traits from nine strains were obtained from two studies (18,19). The original data contained 220 traits (19), but one of them (trait ID A103_C) was not used because the data from strain YJM145 were missing. The phylogenetic analysis using these traits was conducted in exactly the same way as the analysis using the gene expression data.…”