Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation
- Harvard University, United States
- University of Bergen, Norway
Figures
Figure 1 with 2 supplements
Phylogenetic relationships of Platyhelminthes, encompassing 25 ‘turbellarian’ species, 8 representatives of Neodermata, and 7 spiralian outgroups.
Phylogram represents results from a maximum likelihood (ML) analysis of 516 predicted orthogroups (120,527 aligned amino acid sites trimmed of nonstationary and poorly aligned residues), analysed in …
Figure 1—figure supplement 1
Maximum likelihood phylogram resulting from analysis of untrimmed 516-gene matrix.
132,299 aligned amino acid sites, analyzed in ExaML under LG4M+F and also in phyML (v20130927) under LG+FR4+F+IL, with support values to the right of each node representing clade frequency in 100 …
Figure 1—figure supplement 2
Majority rule consensus (MRC) phylogram of a Bayesian Markov Chain Monte Carlo sampling with the CAT+GTR+Γ4 model in PhyloBayes-MPI v1.4e.
Phylogram shown represents a summary of 517 and 219 trees sampled from two chains which had run for 4236 and 3638 generations, respectively; the first 3200 trees sampled were discarded as ‘burn-in’, …
Figure 2
Quartet supernetworks built from 516 individual ML gene trees, showing predominant inter-gene conflicts in genes selected for concatenation.
A qualitatively nearly identical topology (not shown) was recovered using bootstrap majority rule consensus trees as input. Edge weights were calculated in SuperQ v1.1, with the ‘balanced’ linear …
Figure 3
ASTRAL species tree.
Constructed under default settings from 516 input unrooted partial gene trees inferred in RAxML v8.0.20. Nodal support values reflect the frequency of splits in trees constructed by ASTRAL from 100 …
Figure 4
ML phylogram inferred from a version of the BMGE-trimmed matrix in which all taxa of Neodermata have been deleted.
Tree inferred in ExaML v1.0.0 under the LG4M+F model; nodal support values represent the frequency of splits in 100 bootstrap replicates.
Figure 5
ML phylogram inferred from a version of the BMGE-trimmed matrix from which Bothrioplana semperi has been deleted.
Tree inferred in ExaML v1.0.0 under the LG4M+F model; nodal support values represent the frequency of splits in 100 bootstrap replicates.
Figure 6
Summary depiction of the phylogenetic results presented in the present study.
All terminal taxa (turbellarian orders, neodermatan classes, and outgroup clades) are shown with equilateral triangles log-scaled in proportion to described species number (largely following [Martín-…
Additional files
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Supplementary file 1
Summary statistics and accession numbers for each species used in this study. Summarizes quality-controlled RNA-Seq data, de novo transcriptome assemblies, peptide predictions (incl. those from published genome data), and gene occupancy in the 516-orthogroup matrix. Libraries marked with a single asterisk represent stranded libraries made using the IntegenX mRNA sample prep kit, whereas those marked with two asterices represent libraries prepared from amplified cDNA made using the PMA method (Pan et al., 2013); all other libraries were produced using the Illumina TruSeq RNA Sample Prep Kit v2.
- https://doi.org/10.7554/eLife.05503.011
