Data from: Phylogenomic insights into the evolution and origin of nematoda

The phylum Nematoda represents one of the most cosmopolitan and abundant
metazoan groups on Earth. In this study, we reconstructed the phylogenomic
tree for phylum Nematoda. A total of 60 genomes, belonging to eight
nematode orders, were newly sequenced, providing the first low-coverage
genomes for the orders Dorylaimida, Mononchida, Monhysterida,
Chromadorida, Triplonchida, and Enoplida. The resulting phylogeny is
well-resolved across most clades, with topologies remaining consistent
across various reconstruction parameters. The subclass Enoplia is placed
as a sister group to the rest of Nematoda, agrees with previous published
phylogenies. While the order Triplonchida is monophyletic, it is not
well-supported, and the order Enoplida is paraphyletic. Taxa possessing a
stomatostylet form a monophyletic group; however, the superfamily
Aphelenchoidea does not constitute a monophyletic clade. The genera
Trichinella and Trichuris are inferred to have shared a common ancestor
approximately 202 mya, a considerably later period than previously
suggested. All stomatostylet-bearing nematodes are proposed to have
originated ~305 mya, corresponding to the transition from the Devonian to
the Permian period. The genus Thornia is placed outside of Dorylaimina and
Nygolaimina, disagreeing with its position in previous studies.
Additionally, we tested the whole genome amplification method and
demonstrated that it is a promising strategy for obtaining sufficient DNA
for phylogenomic studies of microscopic eukaryotes. This study
significantly expanded the current nematode genome dataset, and the
well-resolved phylogeny enhances our understanding of the evolution of
Nematoda.