Model misspecification confounds the estimation of rates and exaggerates their time dependency

Molecular Ecology
Brent C EmersonMichael J Hickerson

Abstract

While welcoming the comment of Ho et al. (2015), we find little that undermines the strength of our criticism, and it would appear they have misunderstood our central argument. Here we respond with the purpose of reiterating that we are (i) generally critical of much of the evidence presented in support of the time-dependent molecular rate (TDMR) hypothesis and (ii) specifically critical of estimates of μ derived from tip-dated sequences that exaggerate the importance of purifying selection as an explanation for TDMR over extended timescales. In response to assertions put forward by Ho et al. (2015), we use panmictic coalescent simulations of temporal data to explore a fundamental assumption for tip-dated tree shape and associated mutation rate estimates, and the appropriateness and utility of the date randomization test. The results reveal problems for the joint estimation of tree topology, effective population size and μ with tip-dated sequences using BEAST. Given the simulations, BEAST consistently obtains incorrect topological tree structures that are consistent with the substantial overestimation of μ and underestimation of effective population size. Data generated from lower effective population sizes were less likely to ...Continue Reading

References

May 15, 1991·Proceedings of the National Academy of Sciences of the United States of America·W M FitchP Palese
Jan 1, 1987·Journal of Molecular Evolution·G F Shields, A C Wilson
Mar 23, 2002·Science·D M LambertC Baroni
Nov 27, 2004·Bioinformatics·Christian N K AndersonElizabeth A Hadly
Nov 30, 2004·Science·Beth ShapiroAlan Cooper
Jun 15, 2007·Systematic Biology·Simon Y W HoAlexei J Drummond
Sep 6, 2007·Biology Letters·Simon Y W HoRobin G Allaby
Oct 4, 2008·PLoS Genetics·Craig D MillarDavid M Lambert
Oct 17, 2008·Molecular Biology and Evolution·Cadhla RamsdenMichael A Charleston
Sep 9, 2009·Molecular Ecology·Miguel Navascués, Brent C Emerson
Jun 9, 2010·Systematic Biology·Regis Debruyne, Hendrik N Poinar
Mar 1, 2012·Molecular Biology and Evolution·Alexei J DrummondAndrew Rambaut
Sep 12, 2012·Nature Reviews. Genetics·Aylwyn Scally, Richard Durbin
Nov 10, 2013·Molecular Biology and Evolution·Gregg W C Thomas, Matthew W Hahn
Nov 6, 2014·Molecular Biology and Evolution·Peter D KeightleyChris D Jiggins
Feb 3, 2015·Molecular Ecology·Brent C Emerson, Michael J Hickerson
Mar 17, 2015·Molecular Biology and Evolution·Sebastián DuchêneSimon Y W Ho
Jan 16, 2016·Molecular Ecology·Simon Y W HoBeth Shapiro

❮ Previous
Next ❯

Citations

Feb 18, 2016·Molecular Ecology·Adrien Rieux, François Balloux
Apr 4, 2018·Proceedings of the National Academy of Sciences of the United States of America·Simon MöllerTanja Stadler

❮ 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.