ArticleMolecular biology and evolution2012
Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Tracing the paths of modular evolution by quantifying rearrangement events of protein domains.BMC ecology and evolution · 2025Article
- Approaches to increase the validity of gene family identification using manual homology search tools.Genetica · 2023Review
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- Annotation-free delineation of prokaryotic homology groups.PLoS computational biology · 2022Article
- Improved inference of tandem domain duplications.Bioinformatics (Oxford, England) · 2021Article
- Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study.Genome biology and evolution · 2020Article
- Evolution of the extracytoplasmic function σ factor protein family.NAR genomics and bioinformatics · 2020Article
- Alien Domains Shaped the Modular Structure of Plant NLR Proteins.Genome biology and evolution · 2019Article
- Shaping the regulation of the p53 mRNA tumour suppressor: the co-evolution of genetic signatures.BMC cancer · 2019Review
- CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection.Molecular biology and evolution · 2018Article
- Review
- DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.Genome biology and evolution · 2017Article
- PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya.Database : the journal of biological databases and curation · 2016Article
- The inference of gene trees with species trees.Systematic biology · 2015Review
- Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies.BMC bioinformatics · 2015Article
- Event inference in multidomain families with phylogenetic reconciliation.BMC bioinformatics · 2015Article
- The robustness of a signaling complex to domain rearrangements facilitates network evolution.PLoS biology · 2014Article
- Big data and other challenges in the quest for orthologs.Bioinformatics (Oxford, England) · 2014Article
- Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey.Briefings in bioinformatics · 2014Review
- Computational approaches to species phylogeny inference and gene tree reconciliation.Trends in ecology & evolution · 2013Review
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3 authors.
Funding
Abstract
Although the possibility of gene evolution by domain rearrangements has long been appreciated, current methods for reconstructing and systematically analyzing gene family evolution are limited to events such as duplication, loss, and sometimes, horizontal transfer. However, within the Drosophila clade, we find domain rearrangements occur in 35.9% of gene families, and thus, any comprehensive study of gene evolution in these species will need to account for such events. Here, we present a new computational model and algorithm for reconstructing gene evolution at the domain level. We develop a method for detecting homologous domains between genes and present a phylogenetic algorithm for reconstructing maximum parsimony evolutionary histories that include domain generation, duplication, loss, merge (fusion), and split (fission) events. Using this method, we find that genes involved in fusion and fission are enriched in signaling and development, suggesting that domain rearrangements and reuse may be crucial in these processes. We also find that fusion is more abundant than fission, and that fusion and fission events occur predominantly alongside duplication, with 92.5% and 34.3% of fusion and fission events retaining ancestral architectures in the duplicated copies. We provide a catalog of ∼9,000 genes that undergo domain rearrangement across nine sequenced species, along with possible mechanisms for their formation. These results dramatically expand on evolution at the subgene level and offer several insights into how new genes and functions arise between species.
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