ArticleGenome biology and evolution2012
Virtual genomes in flux: an interplay of neutrality and adaptability explains genome expansion and streamlining.
Article in Genome biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Trade-offs between receptor modification and fitness drive host-bacteriophage co-evolution leading to phage extinction or co-existence.The ISME journal · 2024Article
- Evolution of Complex Regulation for Cell-Cycle Control.Genome biology and evolution · 2022Article
- Contingent evolution of alternative metabolic network topologies determines whether cross-feeding evolves.Communications biology · 2020Article
- Transcriptional Mutagenesis Prevents Ribosomal DNA Deterioration: The Role of Duplications and Deletions.Genome biology and evolution · 2019Article
- Adapting the engine to the fuel: mutator populations can reduce the mutational load by reorganizing their genome structure.BMC evolutionary biology · 2019Article
- Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences.PLoS computational biology · 2019Article
- Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery.Biology direct · 2017Review
- Conservation of Nonsense-Mediated mRNA Decay Complex Components Throughout Eukaryotic Evolution.Scientific reports · 2017Article
- Correlated duplications and losses in the evolution of palmitoylation writer and eraser families.BMC evolutionary biology · 2017Article
- Evolution of evolvability and phenotypic plasticity in virtual cells.BMC evolutionary biology · 2017Article
- Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level.Frontiers in microbiology · 2016Article
- Reductive genome evolution at both ends of the bacterial population size spectrum.Nature reviews. Microbiology · 2014Article
- Mutation rates and evolution of multiple coding in RNA-based protocells.Journal of molecular evolution · 2014Article
- Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics.Current opinion in structural biology · 2014Review
- A synergism between adaptive effects and evolvability drives whole genome duplication to fixation.PLoS computational biology · 2014Article
- Phylogenomics and the dynamic genome evolution of the genus Streptococcus.Genome biology and evolution · 2014Article
- In silico experimental evolution: a tool to test evolutionary scenarios.BMC bioinformatics · 2013Article
- What Can Phages Tell Us about Host-Pathogen Coevolution?International journal of evolutionary biology · 2012Article
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2 authors.
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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.
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