Phenotypic plasticity: how ecology modulates the genome
Phenotypic plasticity can be defined as re-programming of the genome in response to the environment. A trait is plastic when the same genotype results in the development of a different phenotype depending on the environment the organism faces (Pigliucci 2001; West-Eberhard 2003). Plastic responses range from morphological modifications to drastic changes in physiology, life history and behaviour, and often involve changes in a suite of traits (Pigliucci 2001; West-Eberhard 2003). In many cases, it has been shown that not only is a plastic response adaptive and allows individuals to meet the challenges brought about by a variable environment, but that it can also be costly compared to the constitutive expression of the trait (Pigliucci 2001, 2005). Phenotypic plasticity can be illustrated with the concept of a reaction norm, which is the representation of values that a trait takes in each environment (Fig. 1). Different genotypes may have different reaction norms, meaning that they respond differently to the same environmental conditions. Indeed, it is possible that one genotype responds to a change in an environmental variable while another does not change, or changes in another direction (Cote et al. 2007). The presence of genetic variation for a trait, along with the force of selection, determines whether selection acting on that trait will result in an evolutionary response. Therefore, if different genotypes in a population produce different reaction norms, and if the slope of the reaction norm is positively correlated with fitness, increased plasticity should evolve in that population for that particular trait (Schlichting & Pigliucci 1998). The amount of plasticity can thus evolve differently in distinct populations and species, depending on the selection pressures they each face (for an experimental evolution example, see Suzuki & Nijhout 2006). Furthermore, if certain genotypes are plastic within a population and others are not, it is possible that genetic variation for the trait will be measured as null in one environment (all genotypes develop the same phenotype) and high in another (where plasticity is expressed and genotypes differ in phenotypes, Fig. 1, and see Landry et al. 2006). Therefore, the response to selection on the same trait can vary among environments, for the same set of genotypes (Schlichting & Pigliucci 1998). Finally, it has been proposed that plasticity can accelerate evolution by allowing individuals to exploit a novel environment if they possess the capacity to develop a new phenotype when faced with that novel environment (Price et al. 2003; Yeh & Price 2004). Implicit in this hypothesis is the idea that plastic individuals will be favoured over nonplastic ones by natural selection. Eventually, the new phenotype may become fixed through genetic assimilation, or there may be an evolutionary shift in the elevation or the slope of the reaction norm, a process referred to as genetic accommodation (West-Eberhard 2003; Pigliucci et al. 2006; Suzuki & Nijhout 2006; Crispo 2007).
Determining how plastic developmental changes that occur in response to environmental conditions are coordinated at the molecular and cellular levels is a challenge that combines ecology with developmental biology (Gilbert 2005). Perhaps unsurprisingly, the historic lack of interaction between these fields means that the mechanisms that underlie the development of the alternative phenotypes are still largely unknown for many systems. In the few systems in which they have been studied, the identified mechanisms include changes in gene expression as well as changes in protein and hormone activity (Gilbert 2005). The mechanisms by which an environmental cue is detected and triggers a plastic response at the molecular and cellular level are also largely unknown, especially in animals. Although understanding which changes in gene expression are related to a plastic response would clearly enlighten our comprehension of plasticity and its evolution, these changes are partially or completely unknown in many cases.
Fortunately, novel genome-level molecular approaches that have been developed in genetic model organisms are increasingly available for nonmodel species. These approaches come at an opportune time to address many long-standing questions regarding the processes and mechanisms of phenotypic plasticity. These questions can be broadly categorized into three groups: (i) determining the genomic make-up of plastic traits; (ii) understanding the higher-level biological processes involved and their conservation across species; and (iii) determining the molecular machinery that interfaces the genotype and the environment. For many of these questions, the answers require molecular studies of species that have served as models for specific questions, but have not been the focus of past genetic analysis. These will be referred to as ‘nonmodel’ species.
Until recently, there was a partition between the study of plasticity from an ecological and an evolutionary perspective (using nonmodel species) and the study of plasticity from a molecular and genetic angle (using genetic model species). Recently, however, these disparate fields have been united in the new discipline of integrative biology. This discipline examines the molecular and cellular mechanisms underlying traits of interest in ecology and evolution, particularly in species previously unstudied with molecular and genetic tools. It also takes genetic model species out of the laboratory and extends knowledge of these systems to include the effects of their natural habitat. Integrative biology employs techniques and approaches to study several different levels of biological organization within a single research programme. It often requires the collaboration of several complementary researchers, each with specific disciplinary expertise, to tackle a unified problem from many angles (Wake 2003). Several integrative biology studies published in recent years have provided insights on the molecular basis of interspecific variation in phenotypes by borrowing concepts and tools from the fields of functional genomics and systems biology (Carleton & Kocher 2001; Toma et al. 2002; Reed & Serfas 2004; Abzhanov et al. 2006; Derome et al. 2006; Diz & Skibinski 2007; Jordan et al. 2007; Landry et al. 2007). In this review, we present the implementation of this strategy for the study of plastic variation in phenotypes. This discovery-driven approach that employs high-throughput molecular tools to study genomic reaction norms has proven to be a powerful approach for uncovering hundreds of new candidate genes and new biological processes.
Ecological annotation of genes
The integrative biology approach associates molecular results with traits of ecological and evolutionary interest. It gives us a better understanding of the function of genes in relevant environments and therefore results in ecological annotation for genes and processes. Furthermore, the relationship between molecular and ecological knowledge is a two-way interaction. On the one hand, molecular techniques promise to further our understanding of gene functions and molecular mechanisms underlying ecologically important traits. On the other hand, ecological studies are necessary for a comprehensive understanding of functional genomics, as many genes in genetic model species show no phenotype when knocked out or manipulated in the laboratory (Carroll & Potts 2006; Pena-Castillo & Hughes 2007). For example, some genes may not have effects on survival in the laboratory, yet might be essential when mounting a plastic stress response to an environmental variable. Quantifying the contribution of genes to a phenotype in ecological (as opposed to laboratory) environments will allow an ‘ecological annotation of genes and genomes’ (Landry & Aubin-Horth 2007) and will thus fill gaps in our knowledge of gene function. Indeed, studying how ecology modulates genome activity will not only enhance our understanding of this pervasive process, but also document the molecular functions and biological processes with which a gene is associated (Fig. 2).
However, to distinguish causation from consequence, one must eventually go beyond simply correlating phenotypes with gene expression patterns. Indeed, gene expression is itself a trait that can be plastic (it is affected by the genotype and by the environment) and can be the result of a response to a change in the environment (Cote et al. 2007). It is thus possible to represent the different levels of expression of a gene in different environments as a reaction norm. Furthermore, it has been shown that different genotypes can have different reaction norms of gene expression (Landry et al. 2006; Li et al. 2006). Distinguishing transcriptional changes that are the cause rather than the consequence of plastic development can be achieved using time series that track the development of the plastic trait after manipulating the internal and/or external environment. This time series approach reveals the progression of transcriptional variation and allows the identification of genes whose transcription changes early and potentially transitively. Such early, transient changes are the most probable triggers of the plastic phenotypic changes. Below, we present examples of this type of developmental series in the study of plasticity in animals.
The comparative method
Another means by which to study the relationship between gene expression and phenotype is the comparative method. For example, techniques to examine expression profile changes have been developed for the medical field and applied to comparative studies of environmental stress (Gasch et al. 2000; Cossins et al. 2006; Gasch 2007; Reinius et al. 2008; Kassahn et al. 2009). The comparison may examine a given tissue for several species, a response to different environmental cues in the same species or a response to the same environmental cue but in different tissues. Beyond understanding the molecular mechanisms of a particular instance of plastic development, comparative studies collectively draw a more complete picture of which molecular networks are rearranged (and how they are rearranged), which molecular networks are reused in different species and how ecology modulates genome-wide processes. We further discuss the comparative approach in the second part of this review.
We also present how integrative biology has answered, or has the potential to answer, the above questions about phenotypic plasticity. We reveal how newer techniques will grow in importance for the study of these molecular processes. These techniques include (i) heterologous hybridization on DNA microarrays; (ii) new sequencing technologies applied to transcriptomics; (iii) techniques for the study of small RNAs for gene regulation and epigenetic effects; as well as (iv) proteomic techniques. We also review recent studies in genetic model systems that have uncovered mechanisms by which the environmental cues that trigger different plastic responses are sensed and integrated by the organism and result in a plastic change. Finally, we showcase a subset of the recent studies in order to demonstrate that plastic changes in gene expression in response to an environmental cue can persist after this cue is removed and that this long-term response is made possible by several epigenetic molecular mechanisms, including DNA methylation. We finally outline future advances that may arise through the study of plasticity using the above approaches.