Experiments on the role of deleterious mutations as stepping stones in adaptive evolution

Abstract

Many evolutionary studies assume that deleterious mutations necessarily impede adaptive evolution. However, a later mutation that is conditionally beneficial may interact with a deleterious predecessor before it is eliminated, thereby providing access to adaptations that might otherwise be inaccessible. It is unknown whether such sign-epistatic recoveries are inconsequential events or an important factor in evolution, owing to the difficulty of monitoring the effects and fates of all mutations during experiments with biological organisms. Here, we used digital organisms to compare the extent of adaptive evolution in populations when deleterious mutations were disallowed with control populations in which such mutations were allowed. Significantly higher fitness levels were achieved over the long term in the control populations because some of the deleterious mutations served as stepping stones across otherwise impassable fitness valleys. As a consequence, initially deleterious mutations facilitated the evolution of complex, beneficial functions. We also examined the effects of disallowing neutral mutations, of varying the mutation rate, and of sexual recombination. Populations evolving without neutral mutations were able to leverage deleterious and compensatory mutation pairs to overcome, at least partially, the absence of neutral mutations. Substantially raising or lowering the mutation rate reduced or eliminated the long-term benefit of deleterious mutations, but introducing recombination did not. Our work demonstrates that deleterious mutations can play an important role in adaptive evolution under at least some conditions. epistasis | experimental evolution | genetic drift

Intermediate Migration Yields Optimal Adaptation in Structured, Asexual Populations

“…Fitness valleys are created by mutations that are individually deleterious but jointly beneficial (Weinreich et al 2005). Several recent works have found examples of fitness valleys formed by individually deleterious but jointly beneficial mutations in both organic and in silico study systems (Covert et al 2013, Cowperthwaite et al 2006, Lenksi et al 2003, Weinreich et al 2006. If such fitness valleys are common enough then they could play an important role in the evolution of structured populations, as originally postulated by Wright (1932).…”

“…The 9 logical functions range in complexity from relatively simple to relatively difficult , Lenski et al 2003, Covert et al 2012a, Covert et al, 2013. Organisms that perform more complex logical functions receive a larger share of instruction executions per update than those that execute easier logical functions.…”

“…Experiments with digital organisms have previously shown that passages through fitness valleys can drastically improve the long term adaptive fate of populations (Covert et al 2013). These works have measured the long-term adaptive effects of deleterious mutations by preventing them from entering the population (Covert et al 2013, Covert et al 2012a, and Covert et al 2012b.…”

“…These works have measured the long-term adaptive effects of deleterious mutations by preventing them from entering the population (Covert et al 2013, Covert et al 2012a, and Covert et al 2012b. To prevent deleterious mutations, we proceed as follows (RpD protocol from Covert et al 2013): Whenever a new digital organism is created, it is placed in an isolated test environment to measure its fitness.…”

“…By using the replace deleterious (RpD) protocol from Covert et al (2013), we can prevent structured populations of digital organisms from crossing fitness valleys. This replacement method allows us to control for the effects of increased drift in the evolution of structured populations, by observing how well the populations evolve on a rugged landscape when they are unable to cross through fitness valleys.…”