Model-Based Inference of Punctuated Molecular Evolution.

Molecular Biology and Evolution
Marc ManceauAmaury Lambert

Abstract

In standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a rate that can vary (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary timescale. Here, we develop a model, which we call the Relaxed Clock with Spikes model, combining basal, clock-like molecular substitutions with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) cooccurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular substitutions and from variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on wh...Continue Reading

References

Sep 21, 1979·Proceedings of the Royal Society of London. Series B, Containing Papers of a Biological Character·S J Gould, R C Lewontin
Jan 1, 1991·Critical Reviews in Toxicology·J Meier, K Stocker
Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
May 28, 1994·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·S NeeP H Harvey
Dec 29, 1998·Molecular Biology and Evolution·J L ThorneI S Painter
Jul 26, 2003·Science·Andrea J WebsterMark Pagel
Aug 21, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey L FederMartin Aluja
Jan 13, 2004·Science·Christopher C Witt, Robb T Brumfield
Aug 11, 2004·Toxicon : Official Journal of the International Society on Toxinology·Yasuo Yamazaki, Takashi Morita
Oct 6, 2005·Genetics·Mark Kirkpatrick, Nick Barton
May 11, 2006·PLoS Biology·Alexei J DrummondAndrew Rambaut
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
Sep 13, 2007·Systematic Biology·Wayne P MaddisonSarah P Otto
Sep 25, 2007·Molecular Biology and Evolution·Thomas LepageNicolas Lartillot
Oct 4, 2008·Nature·Ole SeehausenNorihiro Okada
Jul 31, 2010·Toxicon : Official Journal of the International Society on Toxinology·R Manjunatha Kini, Robin Doley
Sep 3, 2010·BMC Biology·Alexei J Drummond, Marc A Suchard
Oct 12, 2010·Molecular Biology and Evolution·Nicolas Lartillot, Raphaël Poujol
Mar 30, 2011·Proceedings of the National Academy of Sciences of the United States of America·Tanja Stadler
Sep 21, 2011·Proceedings of the National Academy of Sciences of the United States of America·Hélène MorlonJoshua B Plotkin
Oct 14, 2011·Proceedings. Biological Sciences·Rampal S EtienneAlbert B Phillimore
Mar 1, 2012·Molecular Biology and Evolution·Alexei J DrummondAndrew Rambaut
Mar 27, 2012·Toxicon : Official Journal of the International Society on Toxinology·Bryan G FryTimothy N W Jackson
Nov 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Koichiro TamuraSudhir Kumar
Apr 24, 2013·Proceedings of the National Academy of Sciences of the United States of America·Sam Yeaman
Aug 28, 2013·Trends in Ecology & Evolution·Matthew W PennellJosef C Uyeda
Oct 26, 2013·Theoretical Population Biology·Amaury Lambert, Tanja Stadler
Feb 19, 2014·Nature Reviews. Genetics·Ole SeehausenAlex Widmer
Mar 13, 2014·Journal of Mathematical Biology·Amaury LambertRampal S Etienne
Apr 25, 2014·Evolution; International Journal of Organic Evolution·Rampal S EtienneAmaury Lambert
Jan 21, 2015·Systematic Biology·Daniel L Rabosky, Emma E Goldberg
Sep 26, 2015·Systematic Biology·Helen K AlexanderTanja Stadler
Dec 29, 2015·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·James MalletMatthew W Hahn
Mar 2, 2016·Systematic Biology·Fábio K Mendes, Matthew W Hahn

❮ Previous
Next ❯

Citations

Jul 13, 2020·Journal of Evolutionary Biology·Julie MarinAmaury Lambert
Oct 22, 2021·Systematic Biology·Thijs JanzenRampal S Etienne

❮ 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.