(A) Comparative genomics refers to the comparison of gene content and genomic sequences across species differing in a given trait of interest (e.g. virulence towards a given host). By identifying genomic changes that correlate with the trait, hypotheses can be made on their possible relationships. This example shows a gene family with extra copies in some species, which may underlie virulence or drug resistance. (B) Population genomics is the comparative study of genomic variation within and across populations of a given species. This technique has been used to correlate genomic and phenotypic variation across strains of fungal pathogen species. This example shows a gene with several variants (in red) that underlie the emergence of virulence or drug resistance in some strains. Note that, since there is some divergence between strains, it is not trivial to distinguish causal (red) from passenger (black) variants. (C) Directed evolution experiments consist in using selective regimes (either in vivo (left) or in vitro (right)) to ‘force’ the appearance of the phenotypes under study. The selected strains are sequenced to identify variants underlying the phenotypes. This approach simplifies the detection of causal mutations as compared with population genomics studies because the evolutionary conditions are more controlled. This example represents a gene that acquired a single causal variant (in red) driving virulence or drug resistance during artificial evolution. Note that identifying causal variants here is easier (as compared with population genomics techniques (B)), because the evolutionary period is shorter and more controlled.