Phylogenomic Insights into the Evolution and Origin of Nematoda

2024/12/30 by Xue Qing, Y. Miles Zhang, Sidi Sun +5 · 1 voice · 42 citations
Agricultural and Biological Sciences · Earth and Planetary Sciences · Environmental Science · #Biological evolution #Biology #Evolutionary biology #Genetics #Macroevolution #Marine Biology and Ecology Research #Nematode management and characterization studies #Paleontology #Parasite Biology and Host Interactions #Phylogenetics #Zoology

paper · open access · doi:10.1093/sysbio/syae073

published in Systematic Biology 74(3), 349-358 (Oxford University Press)

openalex publication_date 2024/12/30 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/22

Abstract

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 8 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, agreeing with previously 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 millions of years ago (Ma), a considerably later period than previously suggested. All stomatostylet-bearing nematodes are proposed to have originated ~305 Ma, 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. In addition, 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.

Citations

• Interactions of Bacteria, Fungi, and their Nematode Grazers: Effects on Nutrient Cycling and Plant Growth

Cited by

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• The timescale of nematode evolution reveals late and convergent radiations of parasitism
• Ultraconserved Elements and Machine Learning Classifiers Enable Robust Phylogenetics and Taxonomy in Model and Non‐Model Nematodes
• Molecular phylogeny of Chromadorea supports genus reclassification of Desmodorida and Microlaimida with the description of two new species from the Yellow Sea, China
• Phylogenetic analysis within Monhysteridae and Thoracostomopsidae based on rDNA sequences and two new species from the Yellow Sea, China
• Divergence in neuronal signaling pathways despite conserved neuronal identity among Caenorhabditis species. [europepmc]
• The immunomodulatory p43 secreted protein of Trichuris whipworm parasites is a lipid carrier that binds signalling lipids and precursors. [europepmc]
• Comparative connectomics of two distantly related nematode species reveals patterns of nervous system evolution. [europepmc]
• Functional divergence of conserved developmental plasticity genes between two distantly related nematodes. [europepmc]
• Ghosts of symbionts past: the hidden history of the dynamic association between filarial nematodes and their Wolbachia endosymbionts. [europepmc]
• Ultraconserved Elements and Machine Learning Classifiers Enable Robust Phylogenetics and Taxonomy in Model and Non-Model Nematodes. [europepmc]
• A bacterial food source for effective laboratory cultivation of the freshwater nematode Plectus sambesii . [europepmc]
• Resolving tissue and cellular functions of parasitic nematodes. [europepmc]
• Molecular phylogenies provide insights into the evolutionary relationships of the Spirurida (Nematoda), with special emphasis on the superfamily Physalopteroidea. [europepmc]
• Ultrastructural Description of Amphid Neurons in the Pine Wood Nematode Indicates Concurrent Evolution of the Stylet and Specific Neurons. [europepmc]
• Convergent genome evolution shaped the emergence of terrestrial animals. [europepmc]
• Developmental dynamic transcriptomics reveals multiple effectors and transcription factors critical for Ditylenchus destructor parasitism. [europepmc]
• Genomic and Transcriptomic Insights into the Evolution and Parasitic Strategy of the Woody-Plant Nematode Pratylenchus vulnus . [europepmc]
• The rewiring of a terminal selector regulatory cascade generates convergent neuronal laterality. [europepmc]
• Bacterial diet influences mutation rate in Pristionchus pacificus. [europepmc]
• Computational Analysis of Telomerase RNA Evolution in Caenorhabditis Species. [europepmc]
• Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response. [europepmc]
• Analysis of Nematode Ventral Nerve Cords Suggests Multiple Instances of Evolutionary Changes to Neuron Number. [europepmc]
• Evolution of Animal Parasitism in Nematodes of the Suborder Spirurina. [europepmc]
• Calibrating and documenting host-switching and evolution of incompatibility loci for two closely related Wolbachia clades. [europepmc]
• Multiple losses of ecdysone receptor genes in nematodes: an alternative evolutionary scenario of molting regulation. [europepmc]
• Developmental constraints in the repeated evolution of male tail characters in rhabditid and diplogastrid nematodes. [europepmc]
• Origins of Self-Fertility in Three Caenorhabditis Nematodes. [europepmc]

Discussions

• Our paper on the phylogeny of Nematoda 🪱came out on the last day of 2024 in @systbiol.bsky.social. Well at least the link is, the PDF will come later... What started off as a collaboration invitati [bsky, 116 points, 7 comments]

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