Contingency and entrenchment in protein evolution under purifying selection

Abstract

The phenotypic effect of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations and shape the patterns of protein divergence across species. Whereas epistasis between adaptive substitutions has been studied extensively, relatively little is known about epistasis under purifying selection. Here we use computational models of thermodynamic stability in a ligand-binding protein to explore the structure of epistasis in simulations of protein sequence evolution. Even though the predicted effects on stability of random mutations are almost completely additive, the mutations that fix under purifying selection are enriched for epistasis. In particular, the mutations that fix are contingent on previous substitutions: Although nearly neutral at their time of fixation, these mutations would be deleterious in the absence of preceding substitutions. Conversely, substitutions under purifying selection are subsequently entrenched by epistasis with later substitutions: They become increasingly deleterious to revert over time. Our results imply that, even under purifying selection, protein sequence evolution is often contingent on history and so it cannot be predicted by the phenotypic effects of mutations assayed in the ancestral background.intragenic epistasis | coevolution | near neutrality | protein stability W hether a heritable mutation is advantageous or deleterious to an organism often depends on the evolutionary history of the population. A mutation that is beneficial at the time of its introduction may confer its beneficial effect only in the presence of other potentiating or permissive mutations (1-9). Thus, the fate of a mutation arising in a population may be contingent on previous mutations (10-13). Conversely, once a mutation has fixed in a population, the mutation becomes part of the genetic background onto which subsequent modifications are introduced. Because the beneficial effects of the subsequent modifications may depend on the focal mutation, as time passes reversion of the focal mutation may become increasingly deleterious, leading to a type of evolutionary conservatism, or entrenchment (14-18).In the context of protein evolution, the effects of contingency and entrenchment are most easily studied by considering a sequence of single amino acid changes (19) that extends both forward and backward in time from some focal substitution. To assess the roles of contingency and entrenchment we can study the degree to which each focal substitution was facilitated by previous substitutions, and the degree to which the focal substitution influences the subsequent course of evolution (Fig. 1A).Dependencies within a sequence of substitutions are closely connected to the concept of epistasis-that is, the idea that the phenotypic effect of a mutation at a particular genetic site may depend on the genetic background in which it arises (20-24). In the absence of epistasis, a mutation has the same effect ...

Epistasis and the Dynamics of Reversion in Molecular Evolution

“…Our results help bring clarity to a recent controversy concerning site-specific amino acid preferences during protein evolution (Naumenko et al 2012;Pollock et al 2012;Ashenberg et al 2013;Pollock and Goldstein 2014;Bazykin 2015;Doud et al 2015;Goldstein et al 2015;Risso et al 2015;Shah et al 2015;Usmanova et al 2015). First, our results show that in the presence of epistasis, reversion rates will be decreasing in time and that the longer a population has left a set of genotypic states, the longer the expected time until reversion.…”

“…This issue has been especially important recently, due to ongoing debate in the field of protein evolution about how position-specific preferences for amino acids may change over time (Naumenko et al 2012;Pollock et al 2012;Ashenberg et al 2013;Pollock and Goldstein 2014;Bazykin 2015;Doud et al 2015;Goldstein et al 2015;Risso et al 2015;Shah et al 2015;Usmanova et al 2015). Specifically, several groups have suggested that once an amino acid substitution occurs at a particular position, epistatic interactions with subsequent substitutions at other positions should tend to increase the selective preference for the derived amino acid relative to the ancestral state (Naumenko et al 2012;Pollock et al 2012;Shah et al 2015; cf. Fisher 1930, p. 95), a phenomenon known as entrenchment .…”

Inference of epistatic effects leading to entrenchment and drug resistance in HIV-1 protease

“…We observe strong epistatic effects. The primary mutations are destabilizing in the context of the wildtype background, but become stabilizing on average as other resistance mutations accumulate in the background, similar to the concept of entrenchment in systems biology (Pollock et al 2012;Gong et al 2013;Shah et al 2015). Furthermore, we find that entrenchment is modulated by the collective effect of the entire sequence, including mutations at polymorphic residues, and the variance of the statistical energy cost of introducing a primary mutation increases as resistance mutations accumulate; this heterogeneity is another manifestation of epistasis (McCandlish et al , 2016Barton et al 2016b).…”

Multiple Barriers to the Evolution of Alternative Gene Orders in a Positive-Strand RNA Virus

“…Whether our results will extend to other present-day potyviruses is a valid question, but it is equally important to consider that these results may have only a limited bearing on the potential for gene-order evolution in ancestral potyviruses. As a result of epistasis, adaptive evolution can limit accessible evolutionary trajectories (Salverda et al 2011), while purifying selection can result in entrenchment (Shah et al 2015). It is therefore plausible that evolutionary trajectories to alternative gene orders may have been more accessible to ancestral viruses.…”