Data from: Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction

Myriapods, including the diverse and familiar centipedes and millipedes,
are one of the dominant terrestrial arthropod groups. Although molecular
evidence has shown that Myriapoda is monophyletic, its internal phylogeny
remains contentious and understudied, especially when compared to those of
Chelicerata and Hexapoda. Until now, efforts have focused on taxon
sampling (e.g., by including a handful of genes from many species) or on
maximizing matrix size (e.g., by including hundreds or thousands of genes
in just a few species), but a phylogeny maximizing sampling at both levels
remains elusive. In this study, we analyzed 40 Illumina transcriptomes
representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and
Symphyla); 25 transcriptomes were newly sequenced to maximize
representation at the ordinal level in Diplopoda and at the family level
in Chilopoda. Ten supermatrices were constructed to explore the effect of
several potential phylogenetic biases (e.g., rate of evolution,
heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%).
Analyses based on maximum likelihood and Bayesian mixture models retrieved
monophyly of each myriapod class, and resulted in 2 alternative
phylogenetic positions for Symphyla, as sister group to Diplopoda +
Chilopoda, or closer to Diplopoda, the latter hypothesis having been
traditionally supported by morphology. Within centipedes, all orders were
well supported, but 2 deep nodes remained in conflict in the different
analyses despite dense taxon sampling at the family level. Relationships
among centipede orders in all analyses conducted with the most complete
matrix (90% occupancy) are at odds not only with the sparser but more
gene-rich supermatrices (75% and 50% supermatrices) and with the matrices
optimizing phylogenetic informativeness or most conserved genes, but also
with previous hypotheses based on morphology, development, or other
molecular data sets. Our results indicate that a high percentage of
ribosomal proteins in the most complete matrices, in conjunction with
distance from the root, can act in concert to compromise the estimated
relationships within the ingroup. We discuss the implications of these
findings in the context of the ever more prevalent quest for completeness
in phylogenomic studies.