Grys et al. review computer vision and machine-learning methods that have been applied to phenotypic profiling of image-based data. Descriptions are provided for segmentation, feature extraction, selection, and dimensionality reduction, as well as clustering, outlier detection, and classification of data.

Beneficial mutations are required for adaptation to novel environments, yet the range of mutational pathways that are available to a population has been poorly characterized, particularly in eukaryotes. We assessed the genetic changes of the first mutations acquired during adaptation to a novel environment (exposure to the fungicide, nystatin) in 35 haploid lines of Saccharomyces cerevisiae. Through whole-genome resequencing we found that the genomic scope for adaptation was narrow; all adapted lines acquired a mutation in one of four late-acting genes in the ergosterol biosynthesis pathway, with very few other mutations found. Lines that acquired different ergosterol mutations in the same gene exhibited very similar tolerance to nystatin. All lines were found to have a cost relative to wild type in an unstressful environment; the level of this cost was also strongly correlated with the ergosterol gene bearing the mutation. Interestingly, we uncovered both positive and negative effects on tolerance to other harsh environments for mutations in the different ergosterol genes, indicating that these beneficial mutations have effects that differ in sign among environmental challenges. These results demonstrate that although the genomic target was narrow, different adaptive mutations can lead populations down different evolutionary pathways, with respect to their ability to tolerate (or succumb to) other environmental challenges.

Copper is a micronutrient essential for growth due to its role as a cofactor in enzymes involved in respiration, defense against oxidative damage, and iron uptake. Yet too much of a good thing can be lethal, and yeast cells typically do not have tolerance to copper levels much beyond the concentration in their ancestral environment. Here, we report a short-term evolutionary study of Saccharomyces cerevisiae exposed to levels of copper sulfate that are inhibitory to the initial strain. We isolated and identified adaptive mutations soon after they arose, reducing the number of neutral mutations, to determine the first genetic steps that yeast take when adapting to copper. We analyzed 34 such strains through whole-genome sequencing and by assaying fitness within different environments; we also isolated a subset of mutations through tetrad analysis of four lines. We identified a multilayered evolutionary response. In total, 57 single base-pair mutations were identified across the 34 lines. In addition, gene amplification of the copper metallothionein protein, CUP1-1, was rampant, as was chromosomal aneuploidy. Four other genes received multiple, independent mutations in different lines (the vacuolar transporter genes VTC1 and VTC4; the plasma membrane H+-ATPase PMA1; and MAM3, a protein required for normal mitochondrial morphology). Analyses indicated that mutations in all four genes, as well as CUP1-1 copy number, contributed significantly to explaining variation in copper tolerance. Our study thus finds that evolution takes both common and less trodden pathways toward evolving tolerance to an essential, but highly toxic, micronutrient.KEYWORDS Saccharomyces cerevisiae; genetic basis of adaptation; copper tolerance; aneuploidy; CUP1; fitness; parallel adaptation I N his book, Wonderful Life (Gould 1989, p. 51), Stephen J. Gould famously opined that evolution is a historical and contingent process, so much so that "any replay of the tape would lead evolution down a pathway radically different from the road actually taken." While this is undoubtedly true when one considers the full complexity of an organism, refrains are often observed in evolution at the trait level. Repeated evolution, defined as "the independent appearance of similar phenotypic traits in distinct evolutionary lineages" (Gompel and Prud'homme 2009) has been documented in both ecological and clinical environments at all taxonomic levels, e.g., repeated loss of stickleback lateral plates in freshwater (Schluter et al. 2004), ecomorphs of Anolis lizards (Losos 1992), the acquisition of "cystic fibrosis lung" phenotypes in Pseudomonas aeruginosa in patients with cystic fibrosis (Huse et al. 2010), to name but a few. The development of sequencing technologies has recently allowed biologists to ask whether parallel genetic changes underlie observations of parallel phenotypic change. In some cases, parallel phenotypic evolution has been attributed to parallel genotypic evolution, for example, repeated changes to cis-regulatory regions of the same...

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