Phylogenetic Diversity and Taxonomy of Marine Protists

Marine protists encompass a vast array of unicellular eukaryotes that form the foundation of oceanic food webs and drive global biogeochemical cycles. Recent advances in environmental sequencing and single-cell genomics have uncovered deep phylogenetic lineages previously obscured by morphological convergence and cryptic diversity. Integrative taxonomy now combines molecular phylogenies, ultrastructural observations and ecological traits to delineate new clades across dinoflagellates, radiolarians, ciliates, diplonemids and kinetoplastids. Phylogenomic analyses of conserved marker genes reveal both ancient radiations and rapid diversifications linked to key innovations such as novel feeding modes, organellar specialisations and horizontal gene transfers. This growing phylogenetic framework refines higher-level classification, informs evolutionary models of genome architecture and underpins ecological assessments of protist contributions to carbon export, nutrient regeneration and marine ecosystem resilience.

Research from Nature Portfolio

Recent studies have revealed remarkable mitochondrial genome plasticity across diplonemid protists, highlighting an unusual multipartite organisation of nearly a hundred chromosomes. Comparative analyses of closely related species demonstrate that although the number and arrangement of gene fragments remain broadly conserved, the total complement of distinct mitochondrial chromosomes can vary two-fold. Overlapping coding modules and lineage-specific patterns of RNA editing and trans-splicing underscore an evolutionary balance between sequence divergence and maintenance of essential gene functions. These findings refine the internal taxonomy of diplonemids and illuminate general principles of organellar genome evolution in early eukaryotes.

Phylogenetic Diversity and Taxonomy of Marine Protists publication trend

The graph below shows the total number of articles in phylogenetic diversity and taxonomy of marine protists across all publications each year (not limited to Nature Index journals).

Technical terms

Phylogenomic analysis: Reconstruction of evolutionary relationships using large sets of conserved genes or whole-genome data.

Multipartite genome: An organellar or nuclear genome organised into multiple distinct DNA molecules rather than a single chromosome.

Trans-splicing: Post-transcriptional joining of RNA segments encoded on separate genome fragments to form a mature transcript.

RNA editing: Enzymatic alteration of nucleotide sequences in RNA molecules, often by insertion, deletion or substitution, to generate functional messages.

Ultrastructure: Fine cellular architecture revealed by high-resolution electron microscopy, critical for morphological classification and functional inference.

References

1. Ultrastructure and 3D reconstruction of a diplonemid protist (Diplonemea) and its novel membranous organelle. mBio (2023).
2. Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes. BMC Biology (2023).
3. Keeping it complicated: Mitochondrial genome plasticity across diplonemids. Scientific Reports (2017).