Genotype network intersections promote evolutionary innovation

Abstract

Evolutionary innovations are qualitatively novel traits that emerge through evolution and increase biodiversity. The genetic mechanisms of innovation remain poorly understood. A systems view of innovation requires the analysis of genotype networks—the vast networks of genetic variants that produce the same phenotype. Innovations can occur at the intersection of two different genotype networks. However, the experimental characterization of genotype networks has been hindered by the vast number of genetic variants that need to be functionally analyzed. Here, we use high-throughput sequencing to study the fitness landscape at the intersection of the genotype networks of two catalytic RNA molecules (ribozymes). We determined the ability of numerous neighboring RNA sequences to catalyze two different chemical reactions, and we use these data as a proxy for a genotype to fitness map where two functions come in close proximity. We find extensive functional overlap, and numerous genotypes can catalyze both functions. We demonstrate through evolutionary simulations that these numerous points of intersection facilitate the discovery of a new function. However, the rate of adaptation of the new function depends upon the local ruggedness around the starting location in the genotype network. As a consequence, one direction of adaptation is more rapid than the other. We find that periods of neutral evolution increase rates of adaptation to the new function by allowing populations to spread out in their genotype network. Our study reveals the properties of a fitness landscape where genotype networks intersect and the consequences for evolutionary innovations. Our results suggest that historic innovations in natural systems may have been facilitated by overlapping genotype networks.

Experimental Resurrection of Ancestral Mammalian CPEB3 Ribozymes Reveals Deep Functional Conservation

“…A common sequence was added to the 3′-end of the transcript to act as a universal primer binding site during reverse transcription ( Wilkinson et al. 2006 ; Bendixsen et al. 2019 ).…”

Big on Change, Small on Innovation: Evolutionary Consequences of RNA Sequence Duplication

“…And in vitro evolution experiments that exhaustively map the fitness of all possible sequences for very short RNAs, reveal disconnected networks of functional sequences that cannot be connected by continuous paths of fit mutations (Jiménez et al 2013; Pressman et al 2019). In at least one system, continuous paths of fit mutations connecting two different structures have been identified (Schultes and Bartel 2000; Bendixsen et al 2019). However, because these paths were discovered between sequences that were specifically designed by the experimenter to be connected through a continuous path of fit point mutations (Schultes and Bartel 2000) and the subsequent exploration of paths between them was highly restricted (Bendixsen et al 2019), it is unclear how likely it is that freely evolving RNA population would follow such paths.…”

A two-step PCR assembly for construction of gene variants across large mutational distances

“…Although local neighbourhoods provide important insights into changes in fitness, they fail to capture full evolutionary trajectories occurring over deep evolutionary times. Uncovering the phenotypes of genotypes at large mutational distances can provide unprecedented insights into the interactions between large number of mutations [ 10 , 12 , 41 , 48 , 52–54 ], their impact on fitness [ 33 , 43 , 44 , 49 , 55–59 ] and into evolution of novel phenotypes [ 7 , 40 , 51 , 60 , 61 ].…”