First genomic analysis of Platycopioida and phylogenomics across six copepod orders
Jeon D, Song C, Ko J, Kondo Y, Toyota K, Jeong MK, Soh HY, Ohtsuka S, Eyun S
Cladistics 42 
— Figures and Tables (Colored and High resolution) —
Figure 1. Phylogenetic tree of 22 copepods and seven other arthropods inferred based on 40 single-copy orthologous BUSCO genes (i.e., Full Matrix), using RAxML-NG, IQ-TREE2, MrBayes, and PhyloBayes. Nodal support values are provided in the following order: BPR, BPI, PPM, PPP. Red dots at nodes indicate maximum support in all analyses. Three different arthropod taxa (Insecta, Malacostraca, and Thecostraca) were analysed, and the final tree was rooted using two non-crustacean insect species, fruit fly (Drosophila melanogaster) and red flour beetle (Tribolium castaneum), as outgroups. Scale bar represents amino acid substitutions per site.
Figure 2. Phylogenetic trees reconstructed based on (A) alignment excluding incomplete taxa (Matrix A), (B) alignment excluding Monstrilloida taxa (Matrix B), and (C) alignment excluding Harpacticoida taxa (Matrix C). The inset accompanying panel A depicts a different monstrilloid subtree resulting from the BI analysis. Each tree was inferred using IQ-TREE2 and PhyloBayes. Nodal support values are provided in the order of BPI, PPP. Nodes without support values indicate those with maximum support in both analyses. Branch colour indexes for copepod orders: red, Platycopioida; orange, Calanoida; yellow, Siphonostomatoida; green, Cyclopoida; blue, Harpacticoida; and purple, Monstrilloida.
Table 1. Statistical result of alternative tree topology tests.
— Supplemental Figures and Tables (Colored and High resolution) —
Supplementary Figure S1. MCMC trace plots for PhyloBayes-MPI analyses of full dataset. Trace plots for continuous parameters (logL, statent, length, alpha, Nmode, and rrent) comparing two independent MCMC chains for the full dataset (~3,810 cycles). All chains rapidly reached stationarity within the first 100 iterations and showed tight overlap throughout the remaining cycles.
Supplementary Figure S2. MCMC trace plots for PhyloBayes-MPI analyses of dataset excluding incomplete taxa. Trace plots for continuous parameters (logL, statent, length, alpha, Nmode, and rrent) comparing two independent MCMC chains for the dataset excluding incomplete taxa (~5,641 cycles). All chains rapidly reached stationarity within the first 100 iterations and showed tight overlap throughout the remaining cycles.
Supplementary Figure S3. MCMC trace plots for PhyloBayes-MPI analyses of dataset excluding monstrilloid taxa. Trace plots for continuous parameters (logL, statent, length, alpha, Nmode, and rrent) comparing two independent MCMC chains for the dataset excluding monstrilloid taxa (~5,433 cycles). All chains rapidly reached stationarity within the first 100 iterations and showed tight overlap throughout the remaining cycles.
Supplementary Figure S4. MCMC trace plots for PhyloBayes-MPI analyses of dataset excluding harpacticoid taxa. Trace plots for continuous parameters (logL, statent, length, alpha, Nmode, and rrent) comparing two independent MCMC chains for the dataset excluding harpacticoid taxa (~3,867 cycles). All chains rapidly reached stationarity within the first 100 iterations and showed tight overlap throughout the remaining cycles.
Supplementary Table S1. Fourty complete single-copy BUSCO genes used for this study.
Supplementary Table S2. Information on PhyloBayes analysis for different datasets.
[Platycopioid Movie]
— Sequences used in phylogenetic inference—
