Multilevel Evolution and the Emergence of Function

Abstract

In this thesis we have researched how novel functions arise through Darwinian Evolution. Evolution has been generating novel traits, forms and functions since its inception, about four billion years ago. Cellular life did not exist at such an early evolutionary stage and instead, according to the RNA world hypothesis, RNAs functioned both as information storage medium (the role of DNA today) and as chemical reaction catalyst (the role of proteins). Because such RNAs catalysed each other's replication (i.e. replication is an altruistic trait), parasites that were replicated but did not spend any time replicating others should have been selected. Was the survival of replicators threatened by this? How could stronger replicators evolve if selection favoured parasites? In Chapter 2 we show that stronger parasites aid indirectly the evolution of stonger replicators thanks to a feedback process driven by the spatial self-organsation of the two species. The problem of the evolution of altruistic and cooperative traits is not limited to the RNA world, but extends to present day organisms as well. One example is the production of shared but costly, useful substances - so called public good - by many microorganisms. Selfish individuals that do not produce public good can thrive by exploiting cooperative individuals, but the system collapses if nobody produces public good. Should public good production be counter-selected when costs are larger because selection for selfishness intensifies? In Chapter 3 we show that selfish individuals evolve at higher costs and organise in space with cooperators. Spatial self-organisation feeds back on the evolution of public good production of cooperators, that become more cooperative, and selfish individuals, that become more selfish. In Chapter 4 we endow interacting RNA-like replicators with genotype and phenotype, respectively nucleotide sequence and secondary structure, and we study the evolutionary consequences of a complex genotype to phenotype map (RNA folding) at high mutation rates. We find that a functional ecosystem emerges, in which novel functions are associated to sequences that cannot be replicated. Such ecosystem enhances the survival of a single (master) sequence. In turn, this sequence contains the entire information to generate the functional ecosystem, and this information is decoded via the mutational process. The stabilising effect of mutations was experimentally observed in yeast's rRNA gene cluster, where mutations ensuing from transcription-replication conflicts are exploited to increase rRNA gene copy number depending on resource availability. In Chapter 5 we model yeast's rRNA mutational dynamics and find that larger rates of mutations are beneficial for long term genome integrity when they are biased towards gene duplications and deletions, even though their short term effect is near-neutral, as is the the case for yeast's rRNA. In conclusion, the results presented in this thesis highlight the merit of a multilevel approach for understanding evolution and its endless inventivity.