Where does all of this epistasis come from in the first place? Is there something about the evolution of genetic systems that yields epistasis as a by-product? Because evolutionary change is predicated on the current state of a genetic system, functional epistasis is in fact an extremely likely outcome of the evolutionary process. Since future changes are built upon past changes, the “tinkering” nature of evolution74
has the potential to build somewhat baroque systems. As solutions to one functional problem become fixed within an evolutionary lineage, future functional changes will frequently be built by adding additional elements to these existing systems, as for example when new effector molecules attach themselves to the backbone of an existing signal transduction pathway. This will be true whether or not epistatic variation is present or important while selection is operating ().
Figure 4 Four different views of the generation of epistasis under natural selection. Each figure shows a hypothetical adaptive landscape in which the mean fitness of a population is a function of underlying variation at two or more loci. Lines display points (more ...)
Under this view, evolving genetic systems are something of a house of cards. Removing one central component can bring the whole house down (i.e., be epistatic to many other genes) more because of the overall structural dependence induced by historical contingency than because it is a result of some intricately pieced together machine75
. Indeed, Crow76
has conjectured that alleles with more severe effects, such as knockouts, will be more likely to display epistasis than alleles with more subtle genetic effects because larger perturbations are more likely to disrupt the overall structure of the genetic system. Thus, the fact that perturbation approaches, as outlined above, commonly reveal epistasis does not necessarily mean that the alleles responsible for evolutionary change also tend to be epistatic. Each allelic difference, including those generated via induced mutations, needs to be evaluated in its own light. Although epistasis is usually portrayed as a property of a given locus, as we have seen, it is really a property of individual alleles at multiple loci. Unfortunately, allelic variation for epistatic effects has yet to be studied in a systematic fashion2
It is important to remember that most models of the evolution of genetic systems (such as those depicted in ) represent very simple metaphors of complex genetic phenomena. One of the problems in this approach is representing complex, multidimensional processes as three-dimensional cartoons. It is clear that taking these kinds of cartoons too literally can lead to a limited view of possible evolutionary dynamics, such as neglecting the possibility of complex ridges connecting regions of high fitness. Fisher’s77
view was the evolutionary process was so multidimensional that there will always be some axis along which selection can move a population, such that adaptive valleys, even if they exist, will be very localized in their impacts. Kauffman78
has emphasized the opposite, showing that the number of valleys can rapidly increase with increasing dimensions. To a large extent, this is an empirical question—albeit one that is extremely difficult to address adequately.
The bottom line here is that epistasis and genetic interactions are an inevitable consequence of the evolutionary process, no matter how it is conceived. This means that functional biologists have to confront the reality of complex genetic systems no matter what their ultimate cause. This is the exquisite—and sometimes frustrating—result of 3.5 billion years of descent with modification.
Epistasis and the path of evolutionary change
Epistasis can have an important influence on a number of evolutionary phenomena, including the genetic divergence between species79
, the evolution of sexual reproduction4
, and the evolution of the structure of genetic systems80
. One of the more interesting long term questions in evolutionary biology is whether or not epistasis determines the path of evolutionary change. Although the focus here has traditionally been on interactions between disparate loci, currently the best systems for investigating this question are derived from functional studies of interactions operating within individual proteins (Box 3
). Thus far, these studies81-85
have shown that epistasis can play a strong role in limiting the possible paths that evolution can take, but not in limiting its eventual outcome. Of course this might be due in part to the fact that inaccessible evolutionary outcomes may never be observed, but this in itself is an important result. These studies have been especially valuable in helping to build a bridge between the functional analysis of epistasis that has characterized molecular genetics and the long term impact of epistasis on genetic change that has characterized much of the debate in evolutionary biology.
Box 3. Epistasis within a locus
One of the best systems for rigorously testing the functional and evolutionary consequences of epistasis is in the within-locus interactions that characterize protein folding and activity. The nicest example of this thus far comes from Ortlund et al.’s82
investigation of the evolution of novel function in vertebrate steroid receptors. The first step here was to use phylogenetic methods to reconstruct the inferred ancestral protein sequence that predates the separate evolution of the mineralcorticoid and glucocorticoid steroid receptors and to test its function81
. It turns out that the ancestral protein is fairly promiscuous and interacts with a variety of steroid ligands, even with ligands not present within the ancestral organism at that time. Specialization therefore occurred via the evolution of a glucocorticoid-specific receptor from a more general mineralcorticoid ancestor, which was achieved via changes at two interacting sites, S106P and L111Q. By itself, S106P essentially destroys receptor function, while L111Q by itself has little functional effect. Together, however, S106P changes the architecture of the protein in such a way that allows L111Q move down to form a novel hydrogen bond with cortisol, which is a clear case of functional epistasis (a
). Ortlund et al. call these two changes “group X”. Three more amino acid changes (group Y) are needed to yield the final specificity to cortisol, but these substitutions destabilize the protein. They must therefore be preceded by two other amino acid changes (group Z) that stable the purturbation in protein structure induced by changes in the X and Y groups. Ortlund et al. call the Z group substitutions “permissive” mutations, because they appear to have little effect on receptor function, but are a critical first step for allowing the other functional changes to occur. There is another permissive mutation, Y27R (b
), which precedes all of these other changes and which generates a novel cation-π interaction (replacing a weaker hydrogen bond) that stabilizes portions of the structure that would have otherwise been destabilized by the subsequent changes.
Together, these structural interactions create a specific order in which the evolutionary substitutions must occur. There are a number of possible pathways for these changes (c
), but only a few are functionally viable because the so-called “conformational epistasis” generated by structural failure of the protein limits the evolutionary options. Here the evolution is from a generalized response in the ancestor (AncGR1) to the hormones aldosterone (green), cortisone (purple) and DOC (orange) to specificity to cortisone alone (+XYZ). In this example we have a direct tie between specific amino acid changes, epistatic interactions generated by their influence on protein structure, and the impact that these interactions have on subsequent evolutionary change. Figure reprinted with permission from Ref 82
The evolution of regulatory complexity
One consequence of a systematic search for gene interactions is that the consequences of linkage may tend to be overlooked. As seen in the case of the histocompatibility loci in multiple sclerosis, linkage can facilitate the maintenance of epistatic interactions (and visa versa)86
and could help explain how molecular complexity evolves. Such linkage is self evident when looking at evolution of protein function, but recent analysis of patterns of gene regulation suggest that there can be very complex patterns of gene regulation within localized genomic regions87
that may be the result of similar types of evolutionary constraints. We need to look at interactions between promoters and coding genes, micro RNAs, chromatin remodeling, and other factors that Bateson would never have dreamed of, as being parts of epistatic networks whose evolutionary dynamics may be guided by complex sets of genetic interactions and their genomic relationship with one another.