Dynamic Birth and Death of Argonaute Gene Family Functional Repertoire Across <i>Caenorhabditis</i> Nematodes
Bibliographic record
Abstract
Diverse small RNA pathways, composed of Argonaute effector proteins and their bound small RNA molecules, define critical systems for regulating gene expression in all domains of life. Some small RNA pathways have experienced significant evolutionary change across metazoans, including gains of novel Argonaute genes and losses of entire pathways. Differences in Argonaute functional complement among species therefore profoundly influence the available repertoire of mechanisms for gene regulation. Despite intensive study of Argonaute function in the nematode roundworm Caenorhabditis elegans, the extent of Argonaute gene family dynamism and functional breadth remains unknown. We therefore comprehensively surveyed Argonautes across 51 Caenorhabditis species, yielding over 1,200 genes from 11 subfamilies. We documented multiple cases of diversification, including the birth of a potentially novel Argonaute subfamily and the origin of the ALG-5 microRNA Argonaute near the base of the Caenorhabditis phylogeny, as well as evidence of adaptive sequence evolution and gain of a new CSR-1 splice isoform in a clade of 31 species. We detected repeated independent losses of multiple piRNA pathway components, mirroring within this one genus other instances of piRNA pathway loss across the phylum. We experimentally verified several Argonaute gene gains and losses, supporting their validity. Gene gain and loss occur significantly faster than expected within several Argonaute subfamilies, potentially associated with transposable element proliferation coevolving with WAGO-9/10/12 copy number variation. Our characterization of Argonaute diversity across Caenorhabditis demonstrates exceptional functional dynamism in the evolution of gene regulation, with broad implications for mechanisms of control over ontogenetic development and genome integrity.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| 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) | 0.000 | 0.000 |
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 teacher head, 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".