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


CONCLUSIONS
Analyses of data sets that result in ambiguous phylogenetic hypotheses demand for methods, which do not only filter stochastic noise, but likewise allow to differentiate phylogenetic signal from systematic biases. Such methods can only rely on our findings regarding the evolution of the analyzed data. Analyses on independent data sets then are crucial to test the plausibility of the results. Our approach can easily be extended to genomic data, as well, whereby layers of quality assessment are set up applicable to phylogenetic reconstructions in general.
von Reumont
Björn M
BM
Molecular Lab, Zoologisches Forschungsmuseum A, Koenig, Bonn, Germany. bmvr@arcor.de
Meusemann
Karen
K
Szucsich
Nikolaus U
NU
Dell'Ampio
Emiliano
E
Gowri-Shankar
Vivek
V
Bartel
Daniela
D
Simon
Sabrina
S
Letsch
Harald O
HO
Stocsits
Roman R
RR
Luan
Yun-xia
YX
Wägele
Johann Wolfgang
JW
Pass
Günther
G
Hadrys
Heike
H
Misof
Bernhard
B
D000818:Animals; D001181:Arthropods / Q000235:genetics*; D019143:Evolution, Molecular; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods
D012337:RNA, Ribosomal, 18S; D012339:RNA, Ribosomal, 28S