Adaptive evolvability through direct selection instead of indirect, second-order selection

Experimental evolution of evolvability

Evolvability-the capacity to generate adaptive variation-is a trait that can itself evolve through natural selection. However, the idea that mutation can become biased toward adaptive outcomes remains controversial. In this work, we report the evolution of enhanced evolvability through localized hypermutation in experimental populations of bacteria. The evolved mechanism is analogous to the mutation-prone sequences of contingency loci observed in pathogenic bacteria. Central to this outcome was a lineage-level selection process, where success depended on the capacity to evolve between two phenotypic states. Subsequent evolution showed that the hypermutable locus is itself evolvable with respect to alterations in the frequency of environmental change. Lineages with localized hypermutability were more likely to acquire additional adaptive mutations, revealing an unanticipated benefit.

Evolvability: filling the explanatory gap between adaptedness and the long-term mathematical conception of fitness

The new foundation for the propensity interpretation of fitness (PIF), developed by Pence and Ramsey (Br J Philos Sci 64:851-881, 2013), describes fitness as a probability distribution that encompasses all possible daughter populations to which the organism may give rise, including daughter populations in which traits might change and the possible environments that members of the daughter populations might encounter. This long-term definition of fitness is general enough to avoid counterexamples faced by previous mathematical conceptions of PIF. However, there seem to be downsides to its generality: the ecological role of fitness involves describing the degree of adaptedness between an organism and the specific environment it inhabits. When all possible changes in traits and all possible environments that a daughter population may encounter are included in the concept, it becomes difficult to see how fitness can fulfill this role. In this paper, we argue that this is a feature of Pence and Ramsey's view rather than a bug: long-term fitness accommodates evolvability considerations, which concern the role that variation plays in evolutionary processes. Building on the foundations, we show that Pence and Ramsey's fitness-F-can be partitioned into fourths: adaptedness, robustness of adaptedness, and two facets of evolvability. Conceptualizing these last three components forces us to consider the role played by grains of description of both organisms and the environment when thinking about long-term fitness. They track the possibility that there could be a change in type in a daughter population as a way of responding to environmental challenges, or that the type persists in the face of novel environments. We argue that these components are just as salient as adaptedness for long-term fitness. Together, this decomposition of F provides a more accurate picture of the factors involved in long-term evolutionary success.

Evolvability-enhancing mutations in the fitness landscapes of an RNA and a protein

Can evolvability-the ability to produce adaptive heritable variation-itself evolve through adaptive Darwinian evolution? If so, then Darwinian evolution may help create the conditions that enable Darwinian evolution. Here I propose a framework that is suitable to address this question with available experimental data on adaptive landscapes. I introduce the notion of an evolvability-enhancing mutation, which increases the likelihood that subsequent mutations in an evolving organism, protein, or RNA molecule are adaptive. I search for such mutations in the experimentally characterized and combinatorially complete fitness landscapes of a protein and an RNA molecule. I find that such evolvability-enhancing mutations indeed exist. They constitute a small fraction of all mutations, which shift the distribution of fitness effects of subsequent mutations towards less deleterious mutations, and increase the incidence of beneficial mutations. Evolving populations which experience such mutations can evolve significantly higher fitness. The study of evolvability-enhancing mutations opens many avenues of investigation into the evolution of evolvability.

Exploring the expanse between theoretical questions and experimental approaches in the modern study of evolvability

Despite several decades of computational and experimental work across many systems, evolvability remains on the periphery with regards to its status as a widely accepted and regularly applied theoretical concept. Here we propose that its marginal status is partly a result of large gaps between the diverse but disconnected theoretical treatments of evolvability and the relatively narrower range of studies that have tested it empirically. To make this case, we draw on a range of examples-from experimental evolution in microbes, to molecular evolution in proteins-where attempts have been made to mend this disconnect. We highlight some examples of progress that has been made and point to areas where synthesis and translation of existing theory can lead to further progress in the still-new field of empirical measurements of evolvability.