Science AI Journal
Biochemistry, Genetics and Molecular Biology · Research topic

Open research questions in Protist diversity and phylogeny

25 unresolved questions extracted from the limitations and future-work sections of 166 Protist diversity and phylogeny papers in our library. Each links back to the study that raised it.

What the literature leaves open

  • Molecular phylogeny analyses based on SSU rDNA sequence data support previous inferences that Cyclotrichium should be removed from Litostomatea; however, its final class-level affiliation remains to be investigated.

    Taxonomy and Phylogeny of the Little-Known Ciliate Genus Cyclotrichium: With Special Reference to Two New Species · 2026 · DOI

  • While the involvement of some enzymes in the biogenesis and function of the 1°siRNAs is not surprising, like Dicer1, the necessity of RNA-dependent-RNA-Polymerase (RdRP) activity remains unknown. The reason for such differences remains unclear. Our findings highlight the diversity of feeding strategies in the Vampyrellida and demonstrate how much remains to be discovered about these widespread and fascinating microbes. However, the phylogenetic relationships of major groups within stramenopiles are poorly resolved, due to both lack of massive sequence data, especially for heterotrophic representatives, and lack of data on yet undescribed diversity of stramenopiles, including many predicted by metagenomic studies (e. I will discuss the open questions and main conclusions from these findings for future scenarios (global warming).

    Contributions to the mobilid genus Leiotrocha Fabre-Domergue, 1888 · 2026 · DOI

  • Here, we sequenced transcriptomes of poorly studied flagellates23,24 (14 apusomonads,25,26 7 ancyromonads,27 and 1 cultured Mediterranean strain of Meteora sporadica17) and conducted comprehensive phylogenomics analyses with an expanded taxon sampling of early-branching protists.

    Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life · 2024 · DOI

  • RESULTS AND DISCUSSION To contribute to solving the deepest evolutionary relationships among eukaryotic taxa, we sought to enrich the available taxon sampling in early-diverging lineages of flagellates, many of which are understudied grazers dwelling on benthos.

    Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life · 2024 · DOI

  • Despite the fact that picoplankton is prevalent, its diversity and spatial distribution from the Straits of Malacca (SM) to the South China Sea (SCS) remain poorly investigated.

    Diversity and biogeography of picoplankton communities from the Straits of Malacca to the South China Sea · 2020 · DOI

  • By contrast, similarly ancient gene clusters have not been reported among the other classes of homeobox genes (that is, the LIM, POU, PRD and SIX classes).

    A conserved cluster of three PRD-class homeobox genes (homeobrain, rx and orthopedia) in the Cnidaria and Protostomia · 2010 · DOI

  • It remains to be seen whether the mechanisms responsible for the evolutionary conservation of the HRO cluster are the same mechanisms responsible for cohesion of the Hox cluster and other ANTP-class homeobox clusters that have been widely conserved throughout animal evolution.

    A conserved cluster of three PRD-class homeobox genes (homeobrain, rx and orthopedia) in the Cnidaria and Protostomia · 2010 · DOI

  • Even if the date on the latter stela referred, not to the erection of that monument, but to the king's arrival at Memphis, or even Sile, it is scarcely possible that southern Palestine and the Sinai desert could have been traversed in nine days. Although Edel's second objection is scarcely cogent, the first is damn ing.

    The Coregency of Tuthmosis III and Amenophis II · 1965 · DOI

  • Rhizaria, one of the most species-rich and ecologically important eukaryotic supergroups, accommodates a newly discovered osmotrophic species, yet high-quality genomic resources remain scarce, limiting our understanding of their metabolic diversity and ecological functions.

    A rhizarian genome reveals an osmotrophic route to extracellular digestion in eukaryotes · 2026 · DOI

  • The newly generated assemblies (nuclear and organelle) will add to a growing body of genomic resources for underrepresented and understudied animal parasitic nematodes from the Clade 3, enabling comprehensive studies in their phylogeny and trait evolution in the future.

    Morphogenomic description of Cranifera cranifera (Chitwood, 1932) Kloss, 1960 from captive Blaptica dubia Serville, 1838 cockroach · 2026 · DOI

  • We then examined co-occurrence between protists and prokaryotes, predicting putative symbiotic or predator-prey relationships, particularly among understudied protist groups with bacteria such as Verrucomicrobia and Rickettsiales.

    Global Environmental Genomics Reveals Vast Uncultivated Protist Diversity and Taxonomic Blind Spots · 2026 · DOI

  • Free-living kinetoplastids are greatly understudied compared to their parasitic relatives, but are ecologically important microbivores, and collectively comprise the great majority of kinetoplastid diversity.

    Phylogenomics of free-living neobodonids reveals they are a paraphyletic group from which all other metakinetoplastids are descended · 2026 · DOI

  • Introduction Marine microbial eukaryotes are major contributors to oceanic biodiversity and biogeochemical cycling in both surface and deep waters, yet their functional diversity and distribution remain incompletely understood.

    Taxonomy as an indicator of trophic diversity in microbial eukaryotic plankton in an Arctic outflow gateway · 2026 · DOI

  • Recent work has provided evidence for additional genetic input from other prokaryotes to the eukaryotic proteome yet the extent and sources of these contributions remain debated.

    Origins of eukaryotic metabolism · 2026 · DOI

  • Irrigation practices and water salinity significantly affect eukaryotic communities, yet the interactive effects of drip irrigation depth and water salinity on these communities remain unclear.

    Drip Irrigation Depth and Water Salinity Synergistically Drive the Rhizosphere Soil Eukaryotic Community and Key Microbial Groups of Wheat · 2026 · DOI

  • The fossil record for this time interval is demonstrably incomplete but is actively being studied with supergroup candidates being suggested, indicating gaps in fossil discovery and classification.

    Clade dynamics support an early origin of crown eukaryotes · 2026 · DOI

  • Even if crown eukaryotes and supergroups have not yet been unambiguously identified in the proposed time interval, some of the fossils are likely to be crown-group members, indicating a validation gap.

    Clade dynamics support an early origin of crown eukaryotes · 2026 · DOI

  • Early crown members are expected to be rare, ecologically marginal, and consequently poorly preserved and difficult to identify, making identification challenging.

    Clade dynamics support an early origin of crown eukaryotes · 2026 · DOI

  • Anhydrobiotic animals protect cellular architecture and metabolic machinery in the dry state, yet the molecular repertoire supporting this profound dehydration tolerance is not fully understood.

    Using Scientific Enquiry to Make Sense of Global Challenges. · 2010 · DOI

Most-cited papers in Protist diversity and phylogeny

Most recent work

Find a gap in your own Protist diversity and phylogeny sub-topic

This page shows what the Protist diversity and phylogeny literature already flags as unresolved. To narrow it to your specific question, run the guided finder — it searches the gap library on demand and checks candidates against 250M+ OpenAlex works.

Open the Research Gap Finder →

Related topics in Biochemistry, Genetics and Molecular Biology

Gut microbiota and health
289 open questions
Single-cell and spatial transcriptomics
185 open questions
dental development and anomalies
121 open questions
Mitochondrial Function and Pathology
110 open questions
Genetic Associations and Epidemiology
106 open questions
Human-Animal Interaction Studies
105 open questions
Genomics and Chromatin Dynamics
97 open questions
Inflammatory Bowel Disease
91 open questions
25 open questions have been extracted from the limitations and future-work passages of 166 Protist diversity and phylogeny papers in our library. Each one below links back to the study that raised it, so you can read the original claim in context.

Tools for your next paper

Gaps & Literature SearchFind open questions in any field — 120,000+ open gaps mined from our own library.Pre-CheckIs your paper ready? A Tier 1–5 acceptance probability in seconds.Journal FinderA ranked shortlist of target journals from a 17,500-venue index.Duplicate Publication CheckerCheck prior-publication & salami-slicing risk across 8 sources.Citation GeneratorFreeA DOI or title → APA, MLA, Vancouver, Chicago, BibTeX, RIS. No signup.Graphical Abstract MakerFreeTurn your findings into a colorblind-safe graphical abstract.

Compare the category — Honest roundups of the AI research tools, ours listed alongside the alternatives.

Command palette

Jump anywhere, run any action.