Abstract
The phylum Heterolobosea comprises a morphologically diverse and ecologically versatile assemblage of free-living microbial eukaryotes, yet genus-level boundaries remain difficult to resolve due to limited diagnostic characters and extensive phenotypic plasticity. Here, we apply a reproducible 18S rDNA divergence framework to quantify genus-level divergence in Heterolobosea and to evaluate taxonomic placement of a newly discovered isolate from coastal sediments of Mombasa, Kenya. Microscopic observations reveal a highly plastic amoeba exhibiting monopodial limax-type locomotion, episodic eruptive activity, and the formation of large multinucleate and polyploid stages that fragment into smaller cells, suggesting an unusual parasexual-like life cycle. Phylogenetic analyses recover the isolate in a strongly supported clade with Orodruina flavescens and an uncultured environmental lineage from the Lost City hydrothermal field. Pairwise 18S rDNA distance analyses show a clear bimodal separation between intragenus and intergenus comparisons with divergence values among these lineages consistently exceed empirical intrageneric thresholds across multiple analytical frameworks. Substitution saturation diagnostics confirm that these divergences occur within the phylogenetically informative region of the SSU rDNA gene. Together, the molecular, morphological, and ecological evidence support recognition of the Mombasa lineage as a distinct genus and species, Mombasina parasexualis gen. nov. et sp. nov., within Orodruinidae. This study reveals previously underappreciated diversity within Tetramitia and demonstrates the broader utility of quantitative divergence-based frameworks for resolving genus-level boundaries in microbial eukaryotes.
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Data availability
The 18S rDNA sequence generated in this study is deposited in GenBank under an accession number PX620421. All alignments, divergence-analysis scripts, and phylogenetic datasets used in this study are available from the corresponding author upon request. Additional materials, including raw microscopy files and ICC image stacks, will be made available through a public data repository upon request. Video documentation of cellular behavior is available through the principal investigator’s YouTube channel.
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Acknowledgements
We thank the members of the Department of Biology at the University of Nairobi for their assistance with fieldwork and logistical support. We are also grateful to Priyal Patel for help with data collection and laboratory work, and to Christon Jairus Marquez Racoma for assisting with manuscript review.
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Y.I.T. designed the study, performed field sampling, conducted molecular and microscopy analyses, developed the divergence framework, supervised data interpretation, and wrote the manuscript. V.W.W. contributed to project design, assisted in organizing the field expedition, and edited the manuscript. S.G. assisted with generating molecular and morphological data and contributed to manuscript editing. K.S.C. assisted in the generation of morphological and molecular data, and contributed to manuscript editing. All authors reviewed, edited, and approved the final version of the manuscript.
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Tekle, Y.I., Wang’ondu, V.W., Ghebezadik, S. et al. Quantifying genus-level divergence using 18S rDNA and its application to heterolobosea with discovery of a novel genus from Mombasa Kenya.
Sci Rep (2026). https://doi.org/10.1038/s41598-026-45864-9
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DOI: https://doi.org/10.1038/s41598-026-45864-9
Keywords
- Tetramitia
- 18S rDNA divergence
- DNA barcode
- Molecular taxonomy
- Species delimitation
- Marine protists
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