Population genomics perspectives on convergent adaptation

Abstract

Convergent adaptation is the independent evolution of similar traits conferring a fitness advantage in two or more lineages. Cases of convergent adaptation inform our ideas about the ecological and molecular basis of adaptation. In judging the degree to which putative cases of convergent adaptation provide independent replication of the process of adaptation, it is necessary to establish the degree to which the evolutionary change is unexpected under null models and to show that selection has repeatedly, independently driven these changes. Here, we discuss the issues that arise from these questions particularly for closely-related populations, where gene flow and standing variation add additional layers of complexity. We outline a conceptual framework to guide intuition as to the extent to which evolutionary change represents the independent gain of information due to selection and show that this is a measure of how surprised we should be by convergence. Additionally, we summarize the ways population and quantitative genetics and genomics may help us address questions related to convergent adaptation, as well as open new questions and avenues of research.

What can be learned by scanning the genome for molecular convergence in wild populations?

“…in Ref. ). Briefly, coancestry coefficients are generally high, particularly around the selected allele, under GF modes; generally low across the haplotype, but peaked around the selected allele under SGV; and consistently low across DNM haplotypes.…”

“…Recently, Lee and Coop developed a framework that distinguishes among modes of convergent evolution. This framework is based on examining the coancestry patterns of selected haplotypes, with each mode of convergence exhibiting a unique haplotype phylogeny and subsequent signature of coancestry (fig.…”

“…). DNM convergence is often regarded as the traditional interpretation of molecular convergence because mutations are independent, but in all three modes, populations are independently adapting to similar environments . To avoid added confusion, we will adopt the framework of Arendt and Reznick and refer to all mechanisms as convergent evolution and refer to specific modes of convergence when necessary.…”

“…To avoid added confusion, we will adopt the framework of Arendt and Reznick and refer to all mechanisms as convergent evolution and refer to specific modes of convergence when necessary. It is worth distinguishing among these modes because each one is predicted to require different strengths of selection and reflect different limitations of evolution (e.g., selection on a DNM with low starting frequency will need to be stronger than selection on SGV with higher starting frequency to reach fixation) …”

Gene expression links genotype and phenotype during rapid adaptation

“…Next, they investigated the extent that gene expression shifts were shared across drought events and across populations. Determining the extent of adaptive convergence at the genetic and phenotypic level has important implications for understanding the process of adaptation (Lee & Coop, 2019). Here, few genes had shared responses to consecutive droughts or common responses across populations.…”