Benchmarking multi-rate codon models.

PloS One
Wayne DelportSergei L Kosakovsky Pond

Abstract

The single rate codon model of non-synonymous substitution is ubiquitous in phylogenetic modeling. Indeed, the use of a non-synonymous to synonymous substitution rate ratio parameter has facilitated the interpretation of selection pressure on genomes. Although the single rate model has achieved wide acceptance, we argue that the assumption of a single rate of non-synonymous substitution is biologically unreasonable, given observed differences in substitution rates evident from empirical amino acid models. Some have attempted to incorporate amino acid substitution biases into models of codon evolution and have shown improved model performance versus the single rate model. Here, we show that the single rate model of non-synonymous substitution is easily outperformed by a model with multiple non-synonymous rate classes, yet in which amino acid substitution pairs are assigned randomly to these classes. We argue that, since the single rate model is so easy to improve upon, new codon models should not be validated entirely on the basis of improved model fit over this model. Rather, we should strive to both improve on the single rate model and to approximate the general time-reversible model of codon substitution, with as few paramete...Continue Reading

References

Jun 1, 1992·Computer Applications in the Biosciences : CABIOS·D T JonesJ M Thornton
Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Jul 1, 1969·Scientific American·M O Dayhoff
Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Nov 21, 1996·Journal of Theoretical Biology·L E Stanfel
May 29, 2002·Molecular Biology and Evolution·Ziheng Yang, Rasmus Nielsen
Oct 16, 2004·Molecular Biology and Evolution·Sergei L Kosakovsky Pond, Simon D W Frost
Oct 29, 2004·Molecular Biology and Evolution·Sergei L Kosakovsky Pond, Simon D W Frost
Feb 11, 2005·Molecular Biology and Evolution·Sergei L Kosakovsky Pond, Simon D W Frost
Feb 17, 2005·Bioinformatics·Sergei L Kosakovsky Pond, Simon D W Frost
Mar 18, 2006·BMC Bioinformatics·Wendy S W WongRasmus Nielsen
Oct 14, 2006·Molecular Biology and Evolution·Sergei L Kosakovsky PondSimon D W Frost
Nov 18, 2006·Molecular Biology and Evolution·Adi Doron-Faigenboim, Tal Pupko
Apr 3, 2007·Molecular Biology and Evolution·Carolin KosiolNick Goldman
Sep 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·Shozo YokoyamaLyle Britt
Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·John P HuelsenbeckFredrik Ronquist
Oct 17, 2008·Molecular Biology and Evolution·Maria Anisimova, Carolin Kosiol
Oct 31, 2008·Briefings in Bioinformatics·Wayne DelportCathal Seoighe
Feb 24, 2009·Molecular Biology and Evolution·Gavin C Conant, Peter F Stadler
Jul 31, 2010·Bioinformatics·Wayne DelportSergei L Kosakovsky Pond
Aug 7, 2010·PloS One·Sergei Kosakovsky PondKonrad Scheffler
Sep 3, 2010·PLoS Computational Biology·Wayne DelportSergei L Kosakovsky Pond

❮ Previous
Next ❯

Citations

Sep 13, 2012·BMC Evolutionary Biology·Michael P ScherrerClaus O Wilke
Jan 20, 2016·Nature Reviews. Genetics·Julian EchaveClaus O Wilke
Sep 3, 2010·PLoS Computational Biology·Wayne DelportSergei L Kosakovsky Pond
Jan 23, 2019·Molecular Biology and Evolution·Claudia C Weber, Simon Whelan

❮ Previous
Next ❯

Software Mentioned

REV
Datamonkey

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.