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 2..., , , # Supplementary data from: Phylogenomic insights into the evolution and origin of nematoda [https://doi.org/10.5061/dryad.b2rbnzsnt](https://doi.org/10.5061/dryad.b2rbnzsnt) This repository is associated with Qing X, Zhang YM, Sun S, Ahmed M, Lo W-S, Bert W, Holovachov O, Li H. Phylogenomic Insights into the Evolution and Origin of Nematoda. Systematic Biology, syae073, [https://doi.org/10.1093/sysbio/syae073](https://doi.org/10.1093/sysbio/syae073) In this study we used BUSCOs extracted from various genomes and transcriptomes of nematodes (and various outgroups) to reconstruct the phylogeny of Nematoda. We performed a series of analyses in IQ-TREE (regular analysis, filtered using SRH + concordance factors, GHOST model, and PMSF models for amino acid datasets) and ASTRAL-III (individual gene trees calculated using IQ-TREE) on a total of four matrices: 50% complete and 70% complete matrix for amino acid and nucleotide data. We also performed a divergence dating analysis using fossil...