A morphological cell atlas of the freshwater sponge Ephydatia muelleri with key insights from targeted single-cell transcriptomes
Bibliographic record
Abstract
How animal cell types, tissues, and regional body plans arose is a fundamental question in EvoDevo. Many current efforts attempt to link genetic information to the morphology of cells, tissues and regionalization of animal body plans using single-cell sequencing of cell populations. However, a lack of in-depth understanding of the morphology of non-bilaterian animals remains a considerable block to understanding the transitions between bilaterian and non-bilaterian cells and tissues. Sponges (Porifera), one of the earliest diverging animal phyla, pose a particular challenge to this endeavour, because their body plans lack mouths, gut, conventional muscle and nervous systems. With a goal to help bridge this gap, we have studied the morphology, behaviour and transcriptomics of cells and tissue types of an easily accessible and well-studied species of freshwater sponge, Ephydatia muelleri. New features described here include: a polarized external epithelium, a new contractile sieve cell that forms the entry to incurrent canals, motile cilia on apopyle cells at the exit of choanocyte chambers, and non-motile cilia on cells in excurrent canals and oscula. Imaging cells in vivo shows distinct behavioural characteristics of motile cells in the mesohyl. Transcriptomic phenotypes of three cell types (cystencytes, choanocytes and archaeocytes) captured live indicate that cell-type transcriptomes are distinct. Importantly, individual archaeocytes show a range of transcriptomic phenotypes which is supported by the distinct expression of different genes by subsets of this cell type. In contrast, all five choanocyte cells sampled live revealed highly uniform transcriptomes with significantly fewer genes expressed than in other cell types. Our study shows that sponges have tissues whose morphology and cell diversity are both functionally complex, but which together enable the sponge, like other metazoans, to sense and respond to stimuli.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.004 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".