ArticleMolecular biology and evolution2010
A novel method to detect proteins evolving at correlated rates: identifying new functional relationships between coevolving proteins.
Article in Molecular biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 53 citations in OpenAlex.
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- Female membrane proteins regulate postmating ovulation inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- ERCnet: Phylogenomic Prediction of Interaction Networks in the Presence of Gene Duplication.Molecular biology and evolution · 2025Article
- Mutation pressure, drift, and the pace of molecular coevolution.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The oxoglutarate dehydrogenase complex is involved in myofibril growth and Z-disc assembly in Drosophila.Journal of cell science · 2023Article
- Incompatibility and Interchangeability in Molecular Evolution.Genome biology and evolution · 2023Review
- Genome-wide signatures of plastid-nuclear coevolution point to repeated perturbations of plastid proteostasis systems across angiosperms.The Plant cell · 2021Article
- Post-ejaculatory modifications to sperm (PEMS).Biological reviews of the Cambridge Philosophical Society · 2020Review
- Ancient convergent losses ofScience (New York, N.Y.) · 2018Article
- Genomic Signatures of Sexual Conflict.The Journal of heredity · 2017Article
- Filamin actin-binding and titin-binding fulfill distinct functions in Z-disc cohesion.PLoS genetics · 2017Article
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- The Budding Yeast Ubiquitin Protease Ubp7 Is a Novel Component Involved in S Phase Progression.The Journal of biological chemistry · 2016Article
- Adaptive selection and coevolution at the proteins of the Polycomb repressive complexes in Drosophila.Heredity · 2016Article
- Overlapping Patterns of Rapid Evolution in the Nucleic Acid Sensors cGAS and OAS1 Suggest a Common Mechanism of Pathogen Antagonism and Escape.PLoS genetics · 2015Article
- Article
- Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae.The Plant cell · 2015Article
- Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene-based networks.PLoS genetics · 2015Article
- Sexual conflict and seminal fluid proteins: a dynamic landscape of sexual interactions.Cold Spring Harbor perspectives in biology · 2014Review
- A test of double interspecific introgression of nucleoporin genes in Drosophila.G3 (Bethesda, Md.) · 2014Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Interacting proteins evolve at correlated rates, possibly as the result of evolutionary pressures shared by functional groups and/or coevolution between interacting proteins. This evolutionary signature can be exploited to learn more about protein networks and to infer functional relationships between proteins on a genome-wide scale. Multiple methods have been introduced that detect correlated evolution using amino acid distances. One assumption made by these methods is that the neutral rate of nucleotide substitution is uniform over time; however, this is unlikely and such rate heterogeneity would adversely affect amino acid distance methods. We explored alternative methods that detect correlated rates using protein-coding nucleotide sequences in order to better estimate the rate of nonsynonymous substitution at each branch (d(N)) normalized by the underlying synonymous substitution rate (d(S)). Our novel likelihood method, which was robust to realistic simulation parameters, was tested on Drosophila nuclear pore proteins, which form a complex with well-documented physical interactions. The method revealed significantly correlated evolution between nuclear pore proteins, where members of a stable subcomplex showed stronger correlations compared with those proteins that interact transiently. Furthermore, our likelihood approach was better able to detect correlated evolution among closely related species than previous methods. Hence, these sequence-based methods are a complementary approach for detecting correlated evolution and could be applied genome-wide to provide candidate protein-protein interactions and functional group assignments using just coding sequences.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.