Signatures of Endosymbiosis in Mitochondrial Genomes of Rhabdocoel Flatworms
Bibliographic record
Abstract
The transition from a free-living lifestyle to endosymbiosis represents a large evolutionary shift, impacting various aspects of any organism's biology, including its molecular-genetic groundwork. So far, it has been impossible to generalise the impact this lifestyle shift has on genomic architecture. This study explores this phenomenon using a new model system: neodalyellid flatworms (Rhabdocoela), a diverse assemblage of free-living and independently evolved endosymbiotic lineages. A uniquely comprehensive mitochondrial genomic dataset, consisting of 50 complete or partial mitogenome sequences (47 of which are new to science), is constructed, increasing the genomic resources available for rhabdocoel flatworms over tenfold. A robust phylogenomic framework is built, enabling an in-depth exploration of the molecular-genetic signatures associated with evolutionary shifts towards endosymbiosis. To understand speciation influenced by host phylogeny, first steps are taken to unravel the host-switching history of the largest endosymbiotic group of neodalyellids. We test several hypotheses regarding the potential consequences of a symbiotic lifestyle and find marginally heightened AT content, more pronounced GC skew and relaxed selection on specific protein-coding genes in endosymbionts compared to their free-living counterparts. Numerous substitutions have accumulated in certain endosymbiotic lineages; however, the correlation with lifestyle remains uncertain. A high frequency of genetic rearrangements across all studied lineages is observed. Our findings affirm the variable nature of rhabdocoel mitogenomes and, for the first time, reveal distinct signatures of an endosymbiotic lifestyle in neodalyellid flatworms. This effort lays the groundwork for future research into the evolutionary and genomic consequences of a symbiotic lifestyle in this and other animal systems.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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 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".