Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences.

Journal of Molecular Evolution
Guy BaeleStijn Vansteelandt

Abstract

We discuss the importance of non-reversible evolutionary models when analyzing context-dependence. Given the inherent non-reversible nature of the well-known CpG-methylation-deamination process in mammalian evolution, non-reversible context-dependent evolutionary models may be well able to accurately model such a process. In particular, the lack of constraints on non-reversible substitution models might allow for more accurate estimation of context-dependent substitution parameters. To demonstrate this, we have developed different time-homogeneous context-dependent evolutionary models to analyze a large genomic dataset of primate ancestral repeats based on existing independent evolutionary models. We have calculated the difference in model fit for each of these models using Bayes Factors obtained via thermodynamic integration. We find that non-reversible context-dependent models can drastically increase model fit when compared to independent models and this on two primate non-coding datasets. Further, we show that further improvements are possible by clustering similar parameters across contexts.

References

Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Jan 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·M Kimura
Jan 1, 1984·Journal of Molecular Evolution·C LanaveG Serio
Feb 29, 2000·FEBS Letters·A J MighellA F Markham
Aug 26, 2000·Molecular Biology and Evolution·K J Fryxell, E Zuckerkandl
Apr 12, 2002·Systematic Biology·John P HuelsenbeckAmy M Levine
Mar 4, 2003·Nature Genetics·Phil GreenEric D Green
Nov 18, 2003·Annual Review of Genetics·Evgeniy S Balakirev, Francisco J Ayala
Dec 6, 2003·Genome Research·Elliott H MarguliesEric D Green
Dec 9, 2003·Molecular Biology and Evolution·Adam Siepel, David Haussler
Apr 3, 2004·Genome Research·Mathieu BlanchetteWebb Miller
Aug 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·Dick G Hwang, Phil Green
Jun 1, 2005·Trends in Genetics : TIG·Mike Steel
Feb 28, 2006·Trends in Genetics : TIG·Elliott H MarguliesEric D Green
Mar 9, 2006·Systematic Biology·Nicolas Lartillot, Hervé Philippe
Jun 22, 2006·Molecular Biology and Evolution·Nicolas RodrigueNicolas Lartillot
Dec 8, 2009·Annual Review of Entomology·Fredrik Ronquist, Andrew R Deans
Sep 1, 1996·Trends in Ecology & Evolution·Z Yang

❮ 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.