Rates of molecular evolution and the fraction of nucleotide positions free to vary

Journal of Molecular Evolution
S R Palumbi

Abstract

Selective constraints on DNA sequence change were incorporated into a model of DNA divergence by restricting substitutions to a subset of nucleotide positions. A simple model showed that both mutation rate and the fraction of nucleotide positions free to vary are strong determinants of DNA divergence over time. When divergence between two species approaches the fraction of positions free to vary, standard methods that correct for multiple mutations yield severe underestimates of the number of substitutions per site. A modified method appropriate for use with DNA sequence, restriction site, or thermal renaturation data is derived taking this fraction into account. The model also showed that the ratio of divergence in two gene classes (e.g., nuclear and mitochondrial) may vary widely over time even if the ratio of mutation rates remains constant. DNA sequence divergence data are used increasingly to detect differences in rates of molecular evolution. Often, variation in divergence rate is assumed to represent variation in mutation rate. The present model suggests that differing divergence rates among comparisons (either among gene classes or taxa) should be interpreted cautiously. Differences in the fraction of nucleotide positio...Continue Reading

References

Sep 1, 1978·Cell·H C HeindellW A Salser
Jan 29, 1986·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·W M Fitch
Feb 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·K M Helm-Bychowski, A C Wilson
Jan 1, 1987·Journal of Molecular Evolution·G F Shields, A C Wilson
Dec 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·J R PowellC Yoon
Jan 1, 1987·Journal of Molecular Evolution·R DeSalleA C Wilson
Jan 1, 1987·Journal of Molecular Evolution·H Ochman, A C Wilson
Jan 1, 1987·Journal of Molecular Evolution·P Perrin, G Bernardi
Jan 1, 1987·Journal of Molecular Evolution·K NicoghosianR Cedergren
May 1, 1987·Genetics·N Takahata
Aug 1, 1986·Genetics·J H Gillespie
Mar 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·C I Wu, W H Li
Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Jan 1, 1971·Journal of Molecular Evolution·R E Dickerson
Feb 28, 1972·Journal of Molecular Biology·T H Jukes, R Holmquist
Jan 1, 1982·Journal of Molecular Evolution·W M BrownA C Wilson
Aug 14, 1981·Science·T A Kunkel, L A Loeb
Dec 1, 1984·Proceedings of the National Academy of Sciences of the United States of America·J H Gillespie
Jul 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·M Kimura
Aug 27, 1982·Science·P Cloud, M F Glaessner
Jul 1, 1987·Trends in Ecology & Evolution·R Desalle, J A Hunt

❮ Previous
Next ❯

Citations

Sep 1, 1994·Journal of Molecular Evolution·H BurgerL C Dorssers
Apr 1, 1996·Mathematical Biosciences·C Kelly, J Rice
Sep 1, 1996·Trends in Ecology & Evolution·Z Yang
Jun 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·D W Winkler, F H Sheldon
Jan 20, 1999·Proceedings of the National Academy of Sciences of the United States of America·R P HirtT M Embley
Jun 1, 1997·Molecular Phylogenetics and Evolution·C S Griffiths
Feb 16, 1995·Nature·G J NaylorW M Brown
Apr 7, 2010·Critical Reviews in Clinical Laboratory Sciences·Tommy Tsan-Yuk LamJulian W Tang
Feb 26, 2019·Nature Communications·Shiran AbadiItay Mayrose
Mar 1, 1990·Evolution; International Journal of Organic Evolution·Stephen R Palumbi, Allan C Wilson
Aug 1, 1998·Evolution; International Journal of Organic Evolution·C W CunninghamD M Hillis
Jul 15, 2021·Current Biology : CB·Michael S Y Lee, Alessandro Palci

❮ 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.