DOI: 10.5061/dryad.b2rbnzsnt
title: Data from: Phylogenomic insights into the evolution and origin of nematoda

description: 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.
description: # 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 calibrations in MCMCTree, using the 50% amino acid matrix as input guide tree and extensively filtered the input data to select for genes that are most clock-like. ### **Assembled Contigs:** new_nematoda_assemblies.tar.gz: Assembled contigs for new genomes generated in this study. ### **Alignments:** Nem_aa50_spruceup95.fasta: Matrix for amino acid 50 percent complete matrix, trimmed using Spruceup at 95% confidence interval. Nem_nuc50_spruceup95.fasta: Matrix for nucleotide 50 percent complete matrix, trimmed using Spruceup at 95% confidence interval. Nem_nuc70_spruceup95.fasta: Matrix for nucleotide 70 percent complete matrix, trimmed using Spruceup at 95% confidence interval. Nem_aa70_spruceup95.fasta: Matrix for amino acid 70 percent complete matrix, trimmed using Spruceup at 95% confidence interval. Nem_aa50.part: Partition file for Nem_aa50_spruceup95.fasta Nem_nuc50.part: Partition file for Nem_nuc50_spruceup95.fasta Nem_aa70.part: Partition file for Nem_aa70_spruceup95.fasta Nem_nuc70.part: Partition file for Nem_nuc70_spruceup95.fasta ### **Trees:** Nem_50p_aa_ASTRAL.treefile: Output tree from ASTRAL for the amino acid 50 percent complete matrix. Nem_50p_aa_concord.cf.treefile: Output tree from IQTREE for amino acid 50 percent complete matrix, with concordance factors and filtered using SRH test. Nem_50p_aa_ghost.treefile: Output tree from IQTREE for amino acid 50 percent complete matrix, using GHOST model. Nem_50p_aa_loci.treefile: Output individual gene trees from IQTREE for amino acid 50 percent complete matrix. Nem_50p_aa_PMSFC20.treefile: Output tree from IQTREE for amino acid 50 percent complete matrix, using PMSF C20 model, and Nem_50p_aa_reg.treefile as guide tree. Nem_50p_aa_reg.treefile: Output tree from IQTREE for amino acid 50 percent complete matrix. Nem_50p_nuc_ASTRAL.treefile: Output tree from ASTRAL for the nucleotide 50 percent complete matrix. Nem_50p_nuc_concord.cf.treefile: Output tree from IQTREE for nucleotide 50 percent complete matrix, with concordance factors and filtered using SRH test. Nem_50p_nuc_ghost.treefile: Output tree from IQTREE for nucleotide 50 percent complete matrix, using GHOST model. Nem_50p_nuc_loci.treefile: Output individual gene trees from IQTREE for nucleotide 50 percent complete matrix. Nem_50p_nuc_reg.treefile: Output tree from IQTREE for nucleotide 50 percent complete matrix. Nem_70p_aa_ASTRAL.treefile: Output tree from ASTRAL for the amino acid 70 percent complete matrix. Nem_70p_aa_concord.cf.treefile: Output tree from IQTREE for amino acid 70 percent complete matrix, with concordance factors and filtered using SRH test. Nem_70p_aa_ghost.treefile: Output tree from IQTREE for amino acid 70 percent complete matrix, using GHOST model. Nem_70p_aa_loci.treefile: Output individual gene trees from IQTREE for amino acid 70 percent complete matrix. Nem_70p_aa_PMSFC60.treefile: Output tree from IQTREE for amino acid 70 percent complete matrix, using PMSF C60 model, and Nem_70p_aa_reg.treefile as guide tree. Nem_70p_aa_reg.treefile: Output tree from IQTREE for amino acid 70 percent complete matrix. Nem_70p_nuc_ASTRAL.treefile: Output tree from ASTRAL for the nucleotide 70 percent complete matrix. Nem_70p_nuc_concord.cf.treefile: Output tree from IQTREE for nucleotide 70 percent complete matrix, with concordance factors and filtered using SRH test. Nem_70p_nuc_ghost.treefile: Output tree from IQTREE for nucleotide 70 percent complete matrix, using GHOST model. Nem_70p_nuc_loci.treefile: Output individual gene trees from IQTREE for nucleotide 70 percent complete matrix. Nem_70p_nuc_reg.treefile: Output tree from IQTREE for nucleotide 70 percent complete matrix. ### **Dating:** Nem_50p_aa_MCMCinput.tree: Input guide tree for MCMCTree, a modified version of the Nem_50p_aa_PMSFC20.treefile. Nem_50p_aa_MCMCfilter.fasta: Filtered amino acid 50 percent complete matrix used for MCMCTree analysis. Nem_50p_aa_MCMCresult.tree: Output tree from MCMCTree. mcmctree.ctl: Control file for MCMCTree. in.BV: Normal approximation file used by MCMCTree. MCMCTreePlot.r: R script used to generate final figure. ### **Supplementary figures and tables:** Supplement figures.docx: contains supplementary figures S1-S5. Supplementary tables_final.xlsx: contains supplementary table S1-S4. Node Numbers.xlsx: contains the node numbers and corresponding estimated time. ## Version changes **4-March-2025:** Added Assembled Contigs, updated Supplemental Tables to include S3b to show the age of all nodes