Estimating synonymous and nonsynonymous substitution rates

Molecular Biology and Evolution
S V Muse

Abstract

Partitioning the total substitution rate into synnonymous and nonsynonymous components is a key aspect of many analyses in molecular evolution. Numerous methods exist for estimating these rates. However, until recently none of the estimation procedures were based on a sound statistical footing. In this paper, the evolutionary model of Muse and Gaut (1994) is used as the basis for two sets of parameters quantifying silent and replacement substitution rates. The parameters are shown to be equal when the four nucleotides are equally frequent and unequal otherwise. Maximum-likelihood estimation of these parameters is described, and the performance of these estimates is compared to that of existing estimation procedures. It is shown that the estimates of Nei and Gojobori (1986) are not unbiased for either set of parameters, although they provide very good estimates for one set as long as sequence divergence is not too high. However, some disturbing properties are found for the Nei and Gojobori estimates. In particular, it is shown that the expected value of the Nei and Gojobori estimate of silent substitution rate is a function of both the silent and replacement substitution rates. The maximum-likelihood estimates have no such probl...Continue Reading

Citations

Dec 15, 2000·Trends in Ecology & Evolution·Z Yang, J P Bielawski
Nov 23, 2000·Current Opinion in Genetics & Development·J L Thorne
Jul 27, 2007·Proceedings of the National Academy of Sciences of the United States of America·Radek SzklarczykAnton Nekrutenko
Jun 24, 1997·Proceedings of the National Academy of Sciences of the United States of America·B S Gaut, J F Doebley
Apr 29, 1997·Proceedings of the National Academy of Sciences of the United States of America·N Takahata, Y Satta
Jul 22, 1998·Proceedings of the National Academy of Sciences of the United States of America·L BargelloniT Patarnello
Sep 2, 1998·Proceedings of the National Academy of Sciences of the United States of America·E C MetzV D Vacquier
Oct 28, 2010·AIDS Research and Human Retroviruses·Sanjay R MehtaDavey M Smith
Sep 24, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jin JunCraig Nelson
Oct 31, 2008·Briefings in Bioinformatics·Wayne DelportCathal Seoighe
May 31, 2008·Molecular Biology and Evolution·Sergei L Kosakovsky PondSimon D W Frost
Jan 10, 2009·Molecular Biology and Evolution·John D O'BrienMarc A Suchard
May 24, 2006·BMC Bioinformatics·Jason GertzBarak A Cohen
Jun 3, 2006·BMC Evolutionary Biology·Zhang ZhangJun Yu
Jan 1, 2010·Genes & Genetic Systems·Yoshiyuki Suzuki
Sep 13, 2008·PLoS Computational Biology·Elena Rivas, Sean R Eddy
Jan 20, 2016·Nature Reviews. Genetics·Julian EchaveClaus O Wilke
Nov 3, 2007·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Adrian SchneiderGina Cannarozzi
Sep 20, 2001·The Journal of General Virology·C H WoelkD W Brown
Apr 15, 2015·Genome Biology and Evolution·David Roy Smith
Nov 28, 2006·Genomics, Proteomics & Bioinformatics·Zhang Zhang, Jun Yu
Dec 1, 2009·Genomics, Proteomics & Bioinformatics·Dapeng WangJun Yu
Apr 14, 2010·PLoS Pathogens·Melissa R van DijkChris J Janse
Dec 20, 2008·PLoS Pathogens·Wayne DelportCathal Seoighe
Dec 24, 2011·PLoS Genetics·Ernest K LeeRob Desalle
Jul 19, 2012·PLoS Genetics·Ben MurrellSergei L Kosakovsky Pond
Jun 23, 2006·PLoS Computational Biology·Sergei L Kosakovsky PondAndrew J Leigh Brown
Nov 28, 2007·PLoS Computational Biology·Art F Y PoonSimon D W Frost
Aug 20, 2011·PloS One·Yoshikazu FurutaIchizo Kobayashi

❮ Previous
Next ❯

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.