Genetic variability in microbial eukaryotes reshapes marine biodiversity assessment in the age of amplicon sequencing

PLOS One | https://doi.org/10.1371/journal.pone.0326053 June 20, 2025 15 / 29 (2) Highlighting taxonomic concepts in need of revision. Results from specimens in the Sphaerozoidae (Collodaria) clearly indicated that a taxonomic revision is needed at the genus level. Each of the Sphaerozoidae genera, Collozoum (no spicules), Rhaphidozoum (simple spicules), and Sphaero- zoum (branching spicules) were found to be polyphyletic (Fig 8). Their dominant ASVs were scattered throughout the family Sphaerozoidae, indicating that spicule presence and shape may have evolved independently in multiple clades and should not be considered diagnostic characters at the genus level. These results align with the findings of Biard et al. Fig 7. Mean p-distances of ASVs within individual specimens and morphospecies, and between morphospecies of the same taxonomic order. Panel (a) shows the average intragenomic, intraspecies, and interspecies p-distances for each taxonomic order, based on full-length ASV compositions. Results of the same analyses are shown for the extracted V4-region sequences in panel (b). Only the ASVs derived from specimens morphologically- classified to the species level were used in this analyses. All data underlying this figure is given in S2 Data. https://doi.org/10.1371/journal.pone.0326053.g007