Molecular Biology of Mechanostransduction: Transduction of environmentally imposed signals proceeds through a progression of stages that receive and integrate environmental signals ultimately generating a physiological response. The gene expression profiles provided in this study cleverly capture these distinct stages of mechanotransduction. Animals are raised to maturity on diets differing in hardness inducing the development of the two distinct morphs. Once morphs are established, jaws of mature individuals are dissected within 30 min of feeding on their respective hard or soft diets. Thus, the differentially expressed genes identified in their analysis can be putatively assigned to the distinct stages of mechanotransduction based on their predicted function (Fig. 2). This recreates the ontogeny of signal transduction that translates mechanical strain into a LPJ phenotype (for expanded discussions of the molecular biology of mechanotransduction, see Mantila Roosa et al. 2011; Nomura & Takano-Yamamoto 2000). Briefly, mechanical strain causes damage and other changes to the physical environment of the cell eliciting a chemical cellular response. At this stage, the intracellular response and intercellular communication are mediated by the action of mechanosensitive ion channels and gap junctions that cause an influx of calcium, activation of calcium-signalling pathways and induction of GTPases (Nomura & Takano-Yamamoto 2000; Mantila Roosa et al. 2011). This cellular response leads to a rapid activation of immediate early genes. These broad-acting transcription factors integrate the environmental signal into a molecular level response resulting in the activation (or repression) of signalling molecules and transcription factors that regulate the downstream physiological response that builds the structural change. Specifically, action of growth factors and specific transcription factors results in increases in cell proliferation and differentiation as well as matrix secretion and cytoskeleton organization (ibid). In addition, repression of other signalling molecules such as cytokines and chemokines minimizes bone remodelling and promotes matrix secretion (Mantila Roosa et al. 2011).
The Role of Immediate and Downstream Genes in Plasticity-Driven Divergence: Plasticity-driven phenotypic divergence can result from genetic accommodation and/or genetic assimilation of environmentally induced phenotypes among populations (West-Eberhard 2003; Pfennig et al. 2010). Genetic accommodation is a mechanism by which an induced phenotype becomes evolutionarily adaptive through quantitative genetic changes (Suzuki & Nijhout 2006). This can result in either increases or decreases in environmental responsiveness of phenotype development. Genetic assimilation is the specific case in which the development of an induced phenotype loses environmental responsiveness and is constitutively expressed even in the absence of the original trigger (Waddington 1953). Whereas loss of responsiveness to environmental signals results in the consistent development of the ground state phenotype, genetic assimilation results in the consistent development of the induced phenotype. Thus, when variation among environments favours the evolution of distinct developmental strategies, phenotypic divergence among populations can become fixed. For example, populations of A. alluaudi may differ in their developmental responsiveness to diet with some populations exhibiting fixed development of the papilliform morph and others the molariform morph regardless of diet hardness (see discussion in Gunter et al. 2013).
The genes and developmental pathways that make up the immediate and downstream components of the response to mechanical strain (Fig. 2) should play different roles in genetic assimilation versus genetic accommodation. The immediate-level genes trigger the plastic response by modulating existing pathways–the downstream genes–that regulate skeletal development, growth and metabolism both in the presence and in the absence of mechanical strain. Loss of environment dependence associated with genetic assimilation requires decoupling of the external signal from phenotype development. Thus, at the transcriptional level, genetic assimilation should reflect fixation of expression patterns in the downstream genes rather than the immediate genes. On the other hand, adjustments to the level of environmental responsiveness associated with genetic accommodation can result from changes in reactivity of immediate-level genes to environmental signals, from interpretation of this response by downstream genes or a combination. The relative importance of these mechanisms for plasticity evolution is an empirical question open for investigation.
Hypothesis Testing Using Comparative Transcriptomics: Next-generation sequencing techniques are increasingly applied in a diversity of taxa including ecological and evolutionary model systems like cichlids. These methods generate an unprecedented wealth of data that can inform longstanding debates on the mechanisms and evolutionary significance of developmental plasticity (Aubin-Horth & Renn 2009; Beldade et al. 2011). Evidence will come in part by showing that the mechanisms that underlie the response to environmental signals also result in phenotypic divergence among taxa (Pfennig et al. 2010). However, what this means at the transcriptional level is unclear. In fact, the sheer number of genes differentially expressed, even between intraspecific morphs, can be overwhelming (Aubin-Horth & Renn 2009). How can we sift through similarities and differences in gene expression profiles to find evidence of a role for plasticity in evolutionary diversification? It will certainly require hypotheses of what broad gene expression patterns looks like under different mechanisms of plasticity-driven diversification (e.g. see Renn & Schumer 2013). For plastic phenotypes like the A. alluaudi LPJ, the environmental trigger is clear, and the ontogeny of the molecular response can be tracked. In this case, assigning differentially expressed genes to their specific roles in generating the phenotypic response to the environment highlights gene expression patterns expected to associate with distinct models of plasticity-driven diversification. This type of approach enables the use of comparative transcriptomic data–for example comparisons of LPJ transcriptomes of fixed molariform and plastic populations of A. alluaudi–as evidence of genetic assimilation.