DOI: 10.5061/dryad.8mp17
title: Data from: Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction

description: 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.
description: Figure
 S1Figure S1. Phylogenetic
 hypothesis of the interrelationships of Pauropoda, Symphyla, Diplopoda and
 Chilopoda inferred from a 4-gene data set using
 ExaBayes.FigS1_tree_with_pauropoda.pdfFigure S2Figure S2. Phylogenetic informativeness profile of the genes included in supermatrices III (a), VI (b) and V (c) during the interval of time corresponding to the diversification of all myriapod clades (as delimited by blue lines in the ultrametric tree in (a)).FigS2.pdfFigure S3Figure S3. Phylogenetic hypothesis of Myriapoda based on 232 morphological characters coded for both extant and extinct species (see Material and Methods for further details). Strict consensus of 2515 shortest cladograms (420 steps). Fossil taxa are marked with a dagger symbol.FigS3.pdfFigure S4Figure S4. Topologies recovered in the SAW analyses to test for LBA between a) Symphyla and Polyxenida, and b) Scutigeromorpha and Craterostigmomorpha.FigS4_new.pdfFigure S5Figure S5. BaCoCa results showing compositional homogeneity values per taxon and per gene in supermatrices II and III (results in supermatrix I not shown due to a lack of resolution related to the high number of genes included in the matrix).FigS5_Comp_Homog.pdfFigure S6Figure S6. Supernetwork representation of quartets derived from individual ML gene trees, for the genes concatenated in supermatrices I (a), II (b) and III (c). Phylogenetic conflict is represented by reticulations and short branches.FigS6.pdfSources of codings and dates for fossils and supplementary referencesSupplementary_Fossil codings.pdf