Common garden experiments in the genomic era: new perspectives and opportunities

Abstract

The study of local adaptation is rendered difficult by many evolutionary confounding phenomena (for example, genetic drift and demographic history). When complex traits are involved in local adaptation, phenomena such as phenotypic plasticity further hamper evolutionary biologists to study the complex relationships between phenotype, genotype and environment. In this perspective paper, we suggest that the common garden experiment, specifically designed to deal with phenotypic plasticity, has a clear role to play in the study of local adaptation, even (if not specifically) in the genomic era. After a quick review of some high-throughput genotyping protocols relevant in the context of a common garden, we explore how to improve common garden analyses with dense marker panel data and recent statistical methods. We then show how combining approaches from population genomics and genome-wide association studies with the settings of a common garden can yield to a very efficient, thorough and integrative study of local adaptation. Especially, evidence from genomic (for example, genome scan) and phenotypic origins constitute independent insights into the possibility of local adaptation scenarios, and genome-wide association studies in the context of a common garden experiment allow to decipher the genetic bases of adaptive traits.

Genetic and morphological differentiation of Porphyra and Pyropia species (Bangiales, Rhodophyta) coexisting in a rocky intertidal in Central Chile

“…We also propose that transplant experiments and/or common garden experiments should be considered to complement the population genetic analyses and to test for adaptation (e.g., de Villemereuil et al. ).…”

Tree hydraulic traits are coordinated and strongly linked to climate‐of‐origin across a rainfall gradient

“…Under field conditions, however, it is impossible to separate the relative contribution of genetics and environment to the observed phenotypic variation (Nicotra et al, ). Furthermore, species might be exposed to variable environmental conditions even when growing in a common site, resulting in phenotypic shifts unrelated to genetic composition (de Villemereuil, Gaggiotti, Mouterde, & Till‐Bottraud, ). Consequently, field‐based trait variance may be misleading if applied to conservation and breeding efforts.…”

The importance of phenotypic plasticity and local adaptation in driving intraspecific variability in thermal niches of marine macrophytes

“…By using the phenotypically rich data provided by ecological methods (e.g. thermal tolerance) and the large number of markers provided by genome scans it is possible to conduct effective GWA studies without the confounding effects of plasticity seen in wild populations (de Villemereuil et al 2016). A single experiment would yield not only two lines of evidence (phenotypic and genotypic) to infer adaptation but allow both genotype and phenotype to be effectively linked together (Fig.…”

“…Therefore, there is real scope to not only use ecological genomics and common garden/transplant experiments to yield insights into adaptation, but to directly link phenotypic traits with the underlying genomic variation (de Villemereuil et al 2016). By using the phenotypically rich data provided by ecological methods (e.g.…”