Comparative genomics in ecological physiology: toward a more nuanced understanding of acclimation and adaptation

Abstract

SummaryOrganisms that live in variable environments must adjust their physiology to compensate for environmental change. Modern functional genomics technologies offer global top-down discovery-based tools for identifying and exploring the mechanistic basis by which organisms respond physiologically to a detected change in the environment. Given that populations and species from different niches may exhibit different acclimation abilities, comparative genomic approaches may offer more nuanced understanding of acclimation responses, and provide insight into the mechanistic and genomic basis of variable acclimation. The physiological genomics literature is large and growing, as is the comparative evolutionary genomics literature. Yet, expansion of physiological genomics experiments to exploit taxonomic variation remains relatively undeveloped. Here, recent advances in the emerging field of comparative physiological genomics are considered, including examples of plants, bees and fish, and opportunities for further development are outlined particularly in the context of climate change research. Elements of robust experimental design are discussed with emphasis on the phylogenetic comparative approach. Understanding how acclimation ability is partitioned among populations and species in nature, and knowledge of the relevant genes and mechanisms, will be important for characterizing and predicting the ecological and evolutionary consequences of human-accelerated environmental change.

Reciprocal osmotic challenges reveal mechanisms of divergence in phenotypic plasticity in the killifish Fundulus heteroclitus

“…S1). These genes were consistently up-regulated in response to hypo-osmotic challenge in multiple populations of F. heteroclitus (Whitehead et al, 2011(Whitehead et al, , 2012, as well as in other euryhaline Fundulus species (Whitehead et al, 2013), highlighting their importance for osmotic acclimation.…”

“…By combining the global approach of transcriptomics with physiology, we infer mechanisms underlying osmotic phenotypes through the identification of evolutionarily conserved responses. Because changes in selective pressures in different osmotic niches may lead to divergence in acclimation responses between populations, this study provides insight into the mechanisms responsible for adaptive divergence between osmotic niches (Whitehead, 2012).…”

Current Knowledge and Recent Advances in Marine Dinoflagellate Transcriptomic Research

“…Currently, a number of transcriptomic studies that are trying to elucidate dinoflagellates' stress responses are only using a single-species approach under different levels of stress. However, comparative gene expression from more than one species offers significant improvement for elucidation of dinoflagellates' transcriptome responses, as genes responsible for environment adaptation are more likely under strong evolutionary constraints and share common responses or adaptation strategies for coping with stress environments [109]. Comparative transcriptome analysis of toxic metal responses in the plants Arabidopsis thaliana and Arabidopsis halleri produces reliable results as 87% of the genes upregulated under excess copper in A. halleri are also upregulated in A. thaliana, indicating stable and functionally-relevant changes conserved among some plant species [110].…”

Biophysics, environmental stochasticity, and the evolution of thermal safety margins in intertidal limpets

“…For example, it is possible (perhaps likely) that constitutive and acute thermal tolerance costs are associated with different gene products and pathways or that different levels of thermal stress require different suites of responses (e.g. Logan and Somero, 2010;Logan and Somero, 2011;Whitehead, 2012). Similarly, an investigation of the ratio of induced to constitutive thermal tolerance costs, and how that ratio might vary as a function of genotype and thermal history, would provide crucial information.…”