Integrating Phenotypic Plasticity Within an Ecological Genomics Framework: Recent Insights from the Genomics, Evolution, Ecology, and Fitness of Plasticity

Abstract

E.B. Ford's 1964 book Ecological Genetics was a call for biologists to engage in multidisciplinary work in order to elucidate the link between genotype, phenotype, and fitness for ecologically relevant traits. In this review, we argue that the integration of an ecological genomics framework in studies of phenotypic plasticity is a promising approach to elucidate the causal links between genes and the environment, particularly during colonization of novel environments, environmental change, and speciation. This review highlights some of the questions and hypotheses generated from a mechanistic, evolutionary, and ecological perspective, in order to direct the continued and future use of genomic tools in the study of phenotypic plasticity.

Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs

“…The genomics revolution has spawned powerful tools for studying relatedness of populations and species, the connections between genetic and phenotypic variation, for example, how variations in the form of feeding structures are caused by differential expression of key developmental genes (Abzhanov et al, ; Guðbrandsson et al, ), and to determine to what extent these differences are due to genetic differences (and how they are distributed in genomes; Wolf & Ellegren, ). These methods have enabled studies evaluating feedback between the organism and its environment, the role of plasticity in generating functional variation and possibly promoting adaptation (Abouheif et al, ; Morris & Rogers, ). Central to this study, genomic methods can reveal differences between populations and ecotypes, and highlight genes and pathways that may be under positive selection in natural populations (Malinsky et al, ; Wolf & Ellegren, ).…”

Differentially Expressed microRNAs and Target Genes Associated with Plastic Internode Elongation in Alternanthera philoxeroides in Contrasting Hydrological Habitats

“…Investigating the development of plastic traits in ecological context has revealed an association between environmentally contingent phenotypic expression and the environmental sensitivity of gene expression ( Morris and Rogers, 2014 ). This environmental sensitivity of gene expression is, in turn, driven by the flexibility of epigenetic gene regulation in fluctuating environments ( Bossdorf et al, 2008 ; Richards et al, 2017 ).…”

“…This environmental sensitivity of gene expression is, in turn, driven by the flexibility of epigenetic gene regulation in fluctuating environments ( Bossdorf et al, 2008 ; Richards et al, 2017 ). Epigenetic variations triggered by environmental perturbations can lead to inducible phenotypic changes by altering transcriptional profiles and eventually altering ontogenetic trajectory in response to environmental variation, even in the complete absence of genetic variability ( Kalisz and Kramer, 2008 ; Aubin-Horth and Renn, 2009 ), and thus serve as a mechanistic link between genes and environment ( Schlichting and Smith, 2002 ; Morris and Rogers, 2014 ). A suite of epigenetic mechanisms, including DNA methylation, histone modifications and small RNAs, have been shown to be able to control the temporal, spatial and abundance patterns of gene expression and RNA-translation under varied environments ( Schlichting and Smith, 2002 ; Chinnusamy and Zhu, 2009 ).…”

Non-adaptive phenotypic plasticity: the effects of terrestrial and aquatic herbicides on larval salamander morphology and swim speed

“…This GBH‐induced morphology is likely non‐adaptive because (1) it occurs in the absence of dragonfly predators and (2) deep‐tailed tadpoles grow more slowly and have a reduced survival relative to ‘normal’ tadpoles when dragonflies are absent (Van Buskirk & Relyea, ). Because non‐adaptive plasticity can lead to population extinction (Ghalambor et al ., ; Morris & Rogers, ; Morris et al ., ), amphibians are already experiencing global population declines (Houlahan et al ., ; Stuart et al ., ), and GBH use is so widespread, an understanding of the implications of this novel stressor on induced phenotypes in amphibians is relevant for conservation efforts, as well as our general understanding of the role of plasticity in evolution.…”