Nonadaptive Amino Acid Convergence Rates Decrease over Time

Abstract

Convergence is a central concept in evolutionary studies because it provides strong evidence for adaptation. It also provides information about the nature of the fitness landscape and the repeatability of evolution, and can mislead phylogenetic inference. To understand the role of adaptive convergence, we need to understand the patterns of nonadaptive convergence. Here, we consider the relationship between nonadaptive convergence and divergence in mitochondrial and model proteins. Surprisingly, nonadaptive convergence is much more common than expected in closely related organisms, falling off as organisms diverge. The extent of the convergent drop-off in mitochondrial proteins is well predicted by epistatic or coevolutionary effects in our “evolutionary Stokes shift” models and poorly predicted by conventional evolutionary models. Convergence probabilities decrease dramatically if the ancestral amino acids of branches being compared have diverged, but also drop slowly over evolutionary time even if the ancestral amino acids have not substituted. Convergence probabilities drop-off rapidly for quickly evolving sites, but much more slowly for slowly evolving sites. Furthermore, once sites have diverged their convergence probabilities are extremely low and indistinguishable from convergence levels at randomized sites. These results indicate that we cannot assume that excessive convergence early on is necessarily adaptive. This new understanding should help us to better discriminate adaptive from nonadaptive convergence and develop more relevant evolutionary models with improved validity for phylogenetic inference.

Contingency and entrenchment in protein evolution under purifying selection

“…This is precisely what would be expected if the entrenchment observed in our simulations occurs in nature. Similarly, Goldstein et al (90) studied the probability of parallel evolution along two lineages as a function of the evolutionary distance between those two lineages. They found that the larger the evolutionary distance between the two lineages, the lower the rate of convergent evolution.…”

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution

“…If the model and parameter values used are exactly correct, and if all possible reconstructions are considered in the averaging, the AWP method will recover the correct base compositions in the ancestral nodes. Note that AWP is very similar to the approach of sampling ancestral reconstructions according to their posterior probabilities (Williams et al 2006;Goldstein et al 2015); indeed, averaging over all possible ancestral reconstructions (AWP) is equivalent to sampling if the number of samples is infinite. Used to count substitutions along a branch, the AWP method may suffer from two sources of errors.…”

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

“…Instead, they tend to be located at exposed positions to an extent comparable to divergent substitutions ( Fig. 3c), despite the prediction that more exposed positions result in lower convergence probability 28 . Exposed sites are structurally less constrained, and substitutions in such sites are likely to change their interactions with other molecules in solution, rather than changing protein conformation [25][26][27] .…”

“…10). Substitution pairs that result in the same descendant amino acid at the same alignment position in both branches were categorized as convergent changes, whereas the remaining substitution pairs were counted as divergent changes 21,28 .…”