DOI: 10.5061/dryad.7wm37pw3z
title: Data from: Copepod phylogenomics supports Canuelloida as a valid order separate from Harpacticoida

description: Copepods are small crustaceans that are ubiquitous in aquatic
 environments. They are particularly abundant in marine and freshwater
 plankton, marine sediments, and as parasites or commensals of other
 aquatic organisms. Despite their abundance and importance, phylogenetic
 relationships among copepods are poorly resolved. The validity of
 higher-level taxa, including several orders, has continued to be
 controversial throughout the 21st century. This study has two main goals:
 first, to use phylogenomic data to assess relationships among the four
 major copepod orders: Calanoida, Cyclopoida, Harpacticoida, and
 Siphonostomatoida, which together include more than 98% of copepod species
 diversity, and second, to test the validity of the recently proposed order
 Canuelloida. Towards these goals, we sampled 28 copepod transcriptomes and
 genomes spanning 20 families and 5 orders, including the first
 transcriptome of a representative of Canuelloida. We identified 2,527
 single-copy protein-coding genes comprising 939,460 amino acid (aa)
 positions and 530,269 informative sites. All phylogenetic analyses support
 a monophyletic Podoplea (i.e., the superorder comprising all copepod
 orders except for Calanoida and Platycopioida) with Calanoida as its
 sister taxon. We find robust support across all methods for Canuelloida as
 a distinct order separate from the traditionally recognized Harpacticoida
 (Oligoarthra). Contrary to several recent studies of smaller sets of
 nuclear genes or mitochondrial genomes, we recover Cyclopoida and
 Harpacticoida as sister taxa and find that gene tree discordance analysis
 rejects the alternative topologies. Transcriptomic data are promising for
 resolving the backbone of the copepod phylogeny but collecting and
 sequencing the nearly 15,000 species of copepods, many of which are
 infrequently encountered and less than 1 mm in size, remains a major
 hurdle.
description: # Data from: Copepod phylogenomics supports Canuelloida as a valid order
 separate from Harpacticoida This dataset is associated with Bernot et al.
 (2025) "Copepod phylogenomics supports Canuelloida as a valid order
 separate from Harpacticoida". This is the associated phylogenetic
 data comprising: concatenated alignments, individual ortholog alignments,
 and resulting species tree files. ## Description of the data and file
 structure Overview: the dataset includes the following zip files: *
 matrices # super matrices used in this study, based on different
 occupancies described in Bernot et al. (2025) * orthologs # individual
 ortholog alignments before and after trimming with gblocks *
 species_tree_files # newick species tree files resulting from phylogenetic
 analysis of 50% matrix under different models described in Bernot et al.
 (2025) ## Detailed Table of Contents * matrices # concatenated matrices
 based on different taxon occupancy levels described in Bernot et al.
 (2025) * supermatrix_100aa_mintaxa15.phy # phylip file of 50% taxon matrix
 (15/30 taxa) * supermatrix_100aa_mintaxa15_reformatted.nex # nexus file of
 50% taxon matrix (15/30 taxa) * supermatrix_100aa_mintaxa22.phy # phylip
 file of 73% taxon matrix (22/30 taxa) *
 supermatrix_100aa_mintaxa22_reformated.nex # nexus file of 73% taxon
 matrix (22/30 taxa) * supermatrix_100aa_mintaxa24.phy # phylip file of 80%
 taxon matrix (24/30 taxa) * supermatrix_100aa_mintaxa24_reformated.nex #
 nexus file of 80% taxon matrix (24/30 taxa) * orthologs # orthologs.zip
 comprises 2 folders of the individual alignments for the 2,686 orthologs
 used in this study. File naming convention follows
 [https://bitbucket.org/yangya/phylogenomic_dataset_construction/src/master/](https://bitbucket.org/yangya/phylogenomic_dataset_construction/src/master/) * raw_fastas # mafft aligned fasta files for the 2,686 orthologs in the 50% matrix. * gblocks_alignments # mafft alignments after trimming with gblocks for 2,686 orthologs in the 50% matrix. Each file assigned the same unique identifiers as above. "ngaps" file ending appended after alignments were checked to remove any taxon that consisted only of gaps following trimming with gblocks, which can occasionally occur. * species_tree_files # tree files resulting from analyses of 50% taxon matrix under different models described below. * C20_mintax15_goodnames.treefile # tree file from IQTREE2 C20+LG+F+G analysis with 100 BS reps of 50% matrix * iqtree_auto_UFBoot_mintax15_goodnames.iqtree # tree file from IQTREE2 partitioned analysis of 50% matrix as described in manuscript * iqtree_auto_UFBoot_mintax24_goodnames.iqtree # tree file from IQTREE2 partitioned analysis of 73% matrix as described in manuscript * iqtree_auto_UFBoot_mintax22_goodnames.iqtree # tree file from IQTREE2 partitioned analysis of 80% matrix as described in manuscript * ASTRAL_mintax22_raw_goodnames.tre # tree file from ASTRAL analysis of 50% taxon matrix using raw gene trees * ASTRAL_mintax22_BS30_goodnames.tre # tree file from ASTRAL analysis of 50% taxon matrix using gene trees with &lt;30% UFBS support collapsed * ASTRAL_mintax22_BS20_goodnames.tre # tree file from ASTRAL analysis of 50% taxon matrix using gene trees with &lt;20% UFBS support collapsed