ArticleBMC evolutionary biology2016
Models for gene duplication when dosage balance works as a transition state to subsequent neo-or sub-functionalization.
Article in BMC evolutionary biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Evolutionary causes and consequences of gene duplication.Nature reviews. Genetics · 2026Review
- Pan-Genome and Transcriptome-Guided Analysis Reveals Duplication-Driven Evolution and Candidate MYB-bHLH Modules Associated with Fruit Development in Pear.Plants (Basel, Switzerland) · 2026Article
- Genomic perplexity and the evolution of context-dependent function.Molecular biology and evolution · 2026Article
- Characteristics of duplicated gene expression and DNA methylation regulation in different tissues of allopolyploid Brassica napus.BMC plant biology · 2024Article
- Expectations of duplicate gene retention under the gene duplicability hypothesis.BMC ecology and evolution · 2023Article
- Dosage balance acts as a time-dependent selective barrier to subfunctionalization.BMC ecology and evolution · 2023Article
- Evolutionary trade-off and mutational bias could favor transcriptional over translational divergence within paralog pairs.PLoS genetics · 2023Article
- WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events.BMC bioinformatics · 2022Article
- WRKY transcription factors and ethylene signaling modify root growth during the shade-avoidance response.Plant physiology · 2022Article
- Diversity in olfactory receptor repertoires is associated with dietary specialization in a genus of frugivorous bat.G3 (Bethesda, Md.) · 2021Article
- Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data.Molecular biology and evolution · 2021Article
- Article
- A Phylogenetic Rate Parameter Indicates Different Sequence Divergence Patterns in Orthologs and Paralogs.Journal of molecular evolution · 2020Article
- Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants.Molecular biology and evolution · 2020Article
- Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates.BMC evolutionary biology · 2020Article
- The Many Nuanced Evolutionary Consequences of Duplicated Genes.Molecular biology and evolution · 2019Article
- Evolution of intrinsic disorder in eukaryotic proteins.Cellular and molecular life sciences : CMLS · 2017Review
- Constraining the timing of whole genome duplication in plant evolutionary history.Proceedings. Biological sciences · 2017Article
- Enzyme sub-functionalization driven by regulation.EMBO reports · 2017Article
- Novel Genomic and Evolutionary Perspective of Cyanobacterial tRNAs.Frontiers in genetics · 2017Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDosage balance has been described as an important process for the retention of duplicate genes after whole genome duplication events. However, dosage balance is only a temporary mechanism for duplicate gene retention, as it ceases to function following the stochastic loss of interacting partners, as dosage balance itself is lost with this event. With the prolonged period of retention, on the other hand, there is the potential for the accumulation of substitutions which upon release from dosage balance constraints, can lead to either subsequent neo-functionalization or sub-functionalization. Mechanistic models developed to date for duplicate gene retention treat these processes independently, but do not describe dosage balance as a transition state to eventual functional change.
resultsHere a model for these processes (dosage plus neofunctionalization and dosage plus subfunctionalization) has been built within an existing framework. Because of the computational complexity of these models, a simpler modeling framework that captures the same information is also proposed. This model is integrated into a phylogenetic birth-death model, expanding the range of available models.
conclusionsIncluding further levels of biological reality in methods for gene tree/species tree reconciliation should not only increase the accuracy of estimates of the timing and evolutionary history of genes but can also offer insight into how genes and genomes evolve. These new models add to the tool box for characterizing mechanisms of duplicate gene retention probabilistically.
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