Björn M von Reumont *1, Karen Meusemann 1, Nikolaus U Szucsich 2, Emiliano Dell' Ampio 2,
Vivek Gowri-Shankar, Daniela Bartel 2, Sabrina Simon 3, Harald O Letsch 1, Roman R Stocsits 1,
Yun-xia Luan 4, Johann Wolfgang Wägele 1, Günther Pass 2, Heike Hadrys 3,5 and Bernhard
Misof 6

Can comprehensive background knowledge be incorporated into substitution models to
improve phylogenetic analyses?
A case study on major arthropod relationships

Address:
1) Molecular Lab, Zoologisches Forschungsmuseum A. Koenig, Bonn, Germany,
2) Department of Evolutionary Biology, University Vienna, Vienna, Austria,
3) ITZ, Ecology & Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany,
4) Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese
Academy of Sciences, Shanghai, PR China,
5) Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA and
6) UHH Biozentrum Grindel und Zoologisches Museum, University of Hamburg, Hamburg,
Germany

Email: Björn M von Reumont* This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ; KarenMeusemann This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ;

Nikolaus U Szucsich This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ; Emiliano Dell'Ampio
This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ; Vivek Gowri Shankar This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ; Daniela Bartel
This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ; Sabrina Simon This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ; Harald O Letsch This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ;
Roman R Stocsits This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ; Yun-xia Luan This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ;

Johann Wolfgang Wägele This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ; Günther Pass This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ;

Heike Hadrys This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ; Bernhard Misof This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
* Corresponding author   

Published: 27 May 2009
BMC Evolutionary Biology 2009, 9:119 doi:10.1186/1471-2148-9-119

This article is available from: http://www.biomedcentral.com/1471-2148/9/119

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Abstract
Background: Whenever different data sets arrive at conflicting phylogenetic hypotheses, only
testable causal explanations of sources of errors in at least one of the data sets allow us to critically
choose among the conflicting hypotheses of relationships. The large (28S) and small (18S) subunit
rRNAs are among the most popular markers for studies of deep phylogenies. However, some
nodes supported by this data are suspected of being artifacts caused by peculiarities of the
evolution of these molecules. Arthropod phylogeny is an especially controversial subject dotted
with conflicting hypotheses which are dependent on data set and method of reconstruction. We
assume that phylogenetic analyses based on these genes can be improved further i) by enlarging the
taxon sample and ii) employing more realistic models of sequence evolution incorporating non-
stationary substitution processes and iii) considering covariation and pairing of sites in rRNA-genes.
Results: We analyzed a large set of arthropod sequences, applied new tools for quality control of
data prior to tree reconstruction, and increased the biological realism of substitution models.
Although the split-decomposition network indicated a high noise content in the data set, our
measures were able to both improve the analyses and give causal explanations for some
incongruities mentioned from analyses of rRNA sequences. However, misleading effects did not
completely disappear.