The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support

Molecular Biology and Evolution
Thomas R Buckley, Clifford W Cunningham

Abstract

The use of parameter-rich substitution models in molecular phylogenetics has been criticized on the basis that these models can cause a reduction both in accuracy and in the ability to discriminate among competing topologies. We have explored the relationship between nucleotide substitution model complexity and nonparametric bootstrap support under maximum likelihood (ML) for six data sets for which the true relationships are known with a high degree of certainty. We also performed equally weighted maximum parsimony analyses in order to assess the effects of ignoring branch length information during tree selection. We observed that maximum parsimony gave the lowest mean estimate of bootstrap support for the correct set of nodes relative to the ML models for every data set except one. For several data sets, we established that the exact distribution used to model among-site rate variation was critical for a successful phylogenetic analysis. Site-specific rate models were shown to perform very poorly relative to gamma and invariable sites models for several of the data sets most likely because of the gross underestimation of branch lengths. The invariable sites model also performed poorly for several data sets where this model ha...Continue Reading

References

Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Feb 1, 1993·Journal of Molecular Evolution·N Goldman
Nov 1, 1994·Addiction·H Ashton
Jul 1, 1994·Journal of Molecular Evolution·Z Yang
Feb 1, 1996·Molecular Phylogenetics and Evolution·J ShoshaniG F Gunnell
Jul 9, 1996·Proceedings of the National Academy of Sciences of the United States of America·B EfronS Holmes
Mar 5, 1996·Proceedings of the National Academy of Sciences of the United States of America·P J LockhartD Penny
Feb 1, 1996·Journal of Molecular Evolution·Z Yang
Jan 1, 1997·Molecular Biology and Evolution·Z Yang
Feb 1, 1997·Journal of Molecular Evolution·F FratiD L Swofford
Nov 21, 1997·Computer Applications in the Biosciences : CABIOS·Z Yang
May 16, 1998·Nature·J L BooreW M Brown
Jul 21, 1998·Molecular Phylogenetics and Evolution·M GoodmanC P Groves
Jan 27, 1999·Bioinformatics·D Posada, K A Crandall
Mar 3, 1999·Molecular Phylogenetics and Evolution·R A Van Den BusscheD M Hillis
Mar 20, 1999·Molecular Phylogenetics and Evolution·E ZietkiewiczD Labuda
May 20, 1999·Molecular Biology and Evolution·W J Bruno, A L Halpern
Jun 16, 1999·Journal of Molecular Evolution·E García-MachadoM Monnerot
Jun 25, 1999·Molecular Phylogenetics and Evolution·J G Groth, G F Barrowclough
Feb 19, 2000·Molecular Phylogenetics and Evolution·Y SattaN Takahata
Mar 29, 2000·Journal of Mathematical Psychology·L Wasserman
Mar 29, 2000·Journal of Mathematical Psychology·M R Forster
Jun 1, 2000·Molecular Biology and Evolution·M Steel, D Penny
Dec 9, 2000·Molecular Biology and Evolution·J García-Moreno, D P Mindell
Jan 13, 2001·International Journal of Systematic and Evolutionary Microbiology·Y InagakiT Ohama
Feb 24, 2001·Nature·W J MurphyS J O'Brien
Mar 7, 2001·Journal of Molecular Evolution·J P Bollback, J P Huelsenbeck
Jun 26, 2001·Molecular Phylogenetics and Evolution·J C Regier, J W Shultz

❮ Previous
Next ❯

Citations

Mar 17, 2004·Molecular Phylogenetics and Evolution·Robert G Moyle
Apr 10, 2008·Molecular Biology and Evolution·David Posada
Oct 3, 2014·AIDS Research and Human Retroviruses·Vlad NovitskyMyron Essex
Dec 10, 2009·Molecular Phylogenetics and Evolution·Carl H Oliveros, Robert G Moyle
Feb 6, 2007·Molecular Phylogenetics and Evolution·Jon Mallatt, Christopher J Winchell
Dec 2, 2004·Developmental and Comparative Immunology·David H Bos, David Posada
Dec 1, 2015·Epidemics·Vlad NovitskyM Essex
Oct 20, 2006·Trends in Ecology & Evolution·Scot A Kelchner, Michael A Thomas
Sep 23, 2006·Fungal Genetics and Biology : FG & B·Markus GökerFranz Oberwinkler
Sep 25, 2009·The Journal of General Virology·Mark Kinnear, Celeste C Linde
Jul 24, 2013·Molecular Phylogenetics and Evolution·Matthew A CampbellJ Andrés López
Feb 11, 2015·Molecular Biology and Evolution·David Kainer, Robert Lanfear
Sep 18, 2012·Molecular Phylogenetics and Evolution·Patrícia Luz RibeiroCássio van den Berg
Feb 8, 2014·Molecular Phylogenetics and Evolution·Mark P Simmons, Andrew P Norton
Dec 23, 2008·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Joern Klein
Jul 21, 2010·Molecular Phylogenetics and Evolution·Ioana C Chintauan-MarquierFrançois Pompanon
Jan 13, 2006·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Baozhen QiaoRonald M Weigel
Feb 16, 2010·Molecular Phylogenetics and Evolution·Joan PonsMichael Balke
Apr 22, 2006·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Marcos Pérez-LosadaKeith A Crandall
Jul 21, 2006·Molecular Phylogenetics and Evolution·Jonathan C Banks, James B Whitfield
Feb 9, 2005·Evolution; International Journal of Organic Evolution·Thomas J Near, Michael F Benard
Jun 19, 2004·Systematic Biology·Bryan N DanforthAdam Pearson
Apr 23, 2008·Current Protocols in Bioinformatics·David Posada
May 30, 2019·International Journal of Systematic and Evolutionary Microbiology·Philippe M de LajudiePeter Young
Jun 22, 2019·BMC Bioinformatics·Wei ChenHong Gu
Aug 23, 2019·Molecular Biology and Evolution·Diego DarribaTomas Flouri
Jun 26, 2020·Molecular Biology and Evolution·Shiran AbadiItay Mayrose
Jun 15, 2007·Genome Biology·Jaime Huerta-CepasToni Gabaldón
Mar 2, 2006·Systematic Biology·Michael E Alfaro, John P Huelsenbeck
Nov 25, 2003·Evolution; International Journal of Organic Evolution·Anna Bartosch-HärlidHans Ellegren
Oct 27, 2004·Systematic Biology·Karl M Kjer
Oct 27, 2004·Systematic Biology·Todd A CastoeChristopher L Parkinson
Sep 24, 2005·Molecular Biology and Evolution·Beth ShapiroAlexei J Drummond

❮ 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.