Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)

BMC Evolutionary Biology
Tobias MüllerMatthias Wolf

Abstract

In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns cannot be unambiguously estimated by the usual methods (maximum parsimony (MP), neighbor-joining (NJ), or maximum likelihood (ML)), nor are they well supported. We represent each subclade by a sequence profile and estimate evolutionary distances between profiles to obtain a matrix of distances between subclades. Our estimator of profile distances generalizes the maximum likelihood estimator of sequence distances. The basal branching pattern can be estimated by any distance-based method, such as neighbor-joining. Our method (profile neighbor-joining, PNJ) then inherits the accuracy and robustness of profiles and the time efficiency of neighbor-joining. Phylogenetic analysis of Chlorophyceae with traditional methods (MP, NJ, ML and MrBayes) reveals seven well supported subclades, but the methods disagree on the basal branching pattern. The tree reconstructed by our method is better supported and can be confirmed by known morphological characters. Moreover the accuracy is significantly improved as shown by parametric bootstrap.

References

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Citations

Aug 30, 2008·Bioinformatics·Matthias WolfTobias Müller
Jul 13, 2013·The Journal of Heredity·Paul V HicknerDavid W Severson
Apr 21, 2009·Molecular Biology and Evolution·Morgan N PriceAdam P Arkin
Aug 14, 2009·Proceedings. Biological Sciences·Arnaud BatailleSimon J Goodman
Aug 10, 2005·BMC Bioinformatics·Chunlin Wang, Elliot J Lefkowitz
Jul 29, 2008·BMC Evolutionary Biology·Alexander KellerMatthias Wolf
Jan 7, 2011·PloS One·Roland F SchwarzFlorian Markowetz
Mar 22, 2012·Journal of Visualized Experiments : JoVE·Benjamin MergetMatthias Wolf
Feb 19, 2011·Parkinson's Disease·Sara VaraneseAlessandro Di Rocco
Nov 27, 2010·BMC Research Notes·Benjamin Merget, Matthias Wolf
Nov 30, 2019·The Plant Journal : for Cell and Molecular Biology·Eva L von der Heyde, Armin Hallmann
Dec 1, 2012·Journal of Phycology·Nicholas P TipperyLouise A Lewis

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Software Mentioned

WEIGHBOR
Rose
BIONJ
FASTME
NJ
MrBayes
PNJ

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