Copepod phylogenomics supports Canuelloida as a valid order separate from Harpacticoida

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.