Virtual Genomes in Flux: An Interplay of Neutrality and Adaptability Explains Genome Expansion and Streamlining

Abstract

The picture that emerges from phylogenetic gene content reconstructions is that genomes evolve in a dynamic pattern of rapid expansion and gradual streamlining. Ancestral organisms have been estimated to possess remarkably rich gene complements, although gene loss is a driving force in subsequent lineage adaptation and diversification. Here, we study genome dynamics in a model of virtual cells evolving to maintain homeostasis. We observe a pattern of an initial rapid expansion of the genome and a prolonged phase of mutational load reduction. Generally, load reduction is achieved by the deletion of redundant genes, generating a streamlining pattern. Load reduction can also occur as a result of the generation of highly neutral genomic regions. These regions can expand and contract in a neutral fashion. Our study suggests that genome expansion and streamlining are generic patterns of evolving systems. We propose that the complex genotype to phenotype mapping in virtual cells as well as in their biological counterparts drives genome size dynamics, due to an emerging interplay between adaptation, neutrality, and evolvability.

A Synergism between Adaptive Effects and Evolvability Drives Whole Genome Duplication to Fixation

“…Nevertheless, successful re-adaptation was more prevalent in lineages with WGD, and consequently larger genomes. This corroborates our previous research, showing that large genome increases early during adaptation benefit long term adaptation [38] and is in accordance with a similar inference drawn by Van de Peer and co-workers [21], [20] based on parallel paleopolyploidy events in plants and frequent species radiation in the wake of WGD [40], [33], [41], [5]. A particular case in point of long term evolvability due to WGD is the evolution of novel signaling and developmental pathways in vertebrates [42], [43], [24].…”

“…Strong genome streamlining occurred in all simulations, irrespective of environmental change and the fixation of WGD, indicating that maintenance of large genomes comes at a considerable mutational cost [44], [38], [45]. However, WGDs create “irremediable complexity” [46], [28], [47], enforcing the maintenance of larger genomes, which would put lineages that evolve to equal fitness without WGD at an advantage.…”

In silico experimental evolution: a tool to test evolutionary scenarios

“…Other outputs like genealogical trees can be used to analyze the mutations that occurred in the line of descent of the final best individual (see for example [19]). Additional tests can be performed on this final best individual, like mutagenesis experiments to measure its mutational robustness or the level of epistasis in its genome (see for example [20]).…”

Genomics, evolution, and molecular epidemiology of the Streptococcus bovis / Streptococcus equinus complex (SBSEC)

“…Sgp ATCC 43144 seems to have undergone a gene lost compared to Sgg strains, which reduces the ability of ATCC 43144 to survive in the rumen. Events of gene lost and gain are considered typical for genome evolution and are observed frequently in the genus Streptococcus (Cuypers and Hogeweg, 2012;Richards et al, 2014). However, Sgp ATCC 43144 has some unique region such as a glucuronic acid utilization cluster and a nisin like immunity and production operon.…”