10.5061/DRYAD.CVDNCJT2R
Szucsich, Nikolaus U.
University of Vienna
Bartel, Daniela
University of Vienna
Blanke, Alexander
University of Bonn
Böhm, Alexander
University of Vienna
Donath, Alexander
Zoological Research Museum Alexander Koenig
Fukui, Makiko
Ehime University
Grove, Simon
Tasmanian Museum and Art Gallery
Liu, Shanlin
China Agricultural University
Macek, Oliver
University of Vienna
Machida, Ryuichiro
University of Tsukuba
Misof, Bernhard
Zoological Research Museum Alexander Koenig
Nakagaki, Yasutaka
University of Tsukuba
Podsiadlowski, Lars
Zoological Research Museum Alexander Koenig
Sekiya, Kaoru
University of Tsukuba
Tomizuka, Shigekazu
University of Tsukuba
von Reumont, Björn M.
University of Giessen
Waterhouse, Robert M.
University of Lausanne
Walzl, Manfred
University of Vienna
Meng, Guanliang
Zoological Research Museum Alexander Koenig
Zhou, Xin
China Agricultural University
Pass, Günther
University of Vienna
Meusemann, Karen
0000-0002-7590-4851
University of Freiburg
Data from: Four myriapod relatives – but who are sisters? No end to
debates on relationships among the four major myriapod subgroups
Dryad
dataset
2020
Evolutionary Biology, Phylogenomics
FWF Austrian Science Fund
https://ror.org/013tf3c58
P 20497-B17, P 23251-B17
Swiss National Science Foundation*
PP00P3_170664
European Research Council
https://ror.org/0472cxd90
No. 754290, “Mech-Evo-Insect”
Swiss National Science Foundation
https://ror.org/00yjd3n13
PP00P3_170664
2020-10-03T00:00:00Z
2020-10-03T00:00:00Z
en
https://doi.org/10.1186/s12862-020-01699-0
208165990 bytes
4
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Background: Phylogenetic relationships among the myriapod subgroups
Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly
resolved. The first phylogenomic study covering all subgroups resolved
phylogenetic relationships congruently to morphological evidence but is in
conflict with most previously published phylogenetic trees based on
diverse molecular data. Outgroup choice and long-branch attraction effects
were stated as possible explanations for these incongruencies. In this
study, we addressed these issues by extending the myriapod and outgroup
taxon sampling using transcriptome data. Results: We generated new
transcriptome data of 42 panarthropod species, including all four myriapod
subgroups and additional outgroup taxa. Our taxon sampling was
complemented by published transcriptome and genome data resulting in a
supermatrix covering 59 species. We compiled two data sets, the first with
a full coverage of genes per species (292 single-copy protein-coding
genes), the second with a less stringent coverage (988 genes). We inferred
phylogenetic relationships among myriapods using different data types,
tree inference, and quartet computation approaches. Our results
unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses
clearly showed that there is strong signal for a single unrooted topology,
but a sensitivity of the position of the internal root on the choice of
outgroups. However, we observe strong evidence for a clade
Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda.
Conclusions: Our best quartet topology is incongruent with current
morphological phylogenies which were supported in another phylogenomic
study. AU tests and quartet mapping reject the quartet topology congruent
to trees inferred with morphological characters. Moreover, quartet mapping
shows that confounding signal present in the data set is sufficient to
explain the weak signal for the quartet topology derived from
morphological characters. Although outgroup choice affects results, our
study could narrow possible trees to derivatives of a single quartet
topology. For highly disputed relationships, we propose to apply a series
of tests (AU and quartet mapping), since results of such tests allow to
narrow down possible relationships and to rule out confounding signal.
Material collection, generation of RNASeqdata and processing was done as
described in the corresponding paper and supplementary text. Details are
provided in the README.