Quantifying how constraints limit the diversity of viable routes to adaptation

Abstract

Convergent adaptation can occur at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel metric to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This metric is explicitly based on the probability of observing a given amount of repeatability by chance under an arbitrary null hypothesis, and is readily compared among different species and types of trait. We also formulate a metric to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these metrics can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to antibiotics in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution.

Genomic basis of parallel adaptation varies with divergence inArabidopsisand its relatives

“…A wealth of literature describes the probability of 'genetic' parallelism, showing why certain genes are involved in parallel adaptation more often than others 13 . There is theoretical and empirical evidence for the effect of pleiotropic constraints, availability of beneficial mutations or position in the regulatory network all having an impact on the degree of parallelism at the level of a single locus 4,[13][14][15][16][17][18] . In contrast, we know little about 'genomic' parallelism, i.e., what fraction of the genome evolves in parallel and why.…”

Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces

“…The answer to these questions may depend, to a certain extent, on the trait itself. For example, the genetic architecture of a phenotype is a primary determinant of whether trait convergence results from parallel selection on orthologous loci [9]. Such convergence is more likely for simple traits where only a few loci contribute or when loci are subject to antagonistic pleiotropy and less likely for highly polygenic traits such as biomass or height [7,9,10].…”

Quantifying local malignant adaptation in tissue‐specific evolutionary trajectories by harnessing cancer’s repeatability at the genetic level

“…To accurately reflect the genetic background of the clones that ultimately adapted to each environment, we only focused on clonal driver alterations (i.e., those present in all cells of a tumour). We investigated the repeatability of cancer evolution in each tumour type using a Jaccard Index based at the gene level, considering all sample‐specific sets of clonal alterations as the genotypes of similarly adapted phenotypes (Bailey, Rodrigue, & Kassen, ; Yeaman, Gerstein, Hodgins, & Whitlock, ). Results were compared to randomised distributions of mutations that followed the same mutational load per patient (see Methods).…”