Phylogenomic analysis demonstrates a pattern of rare and long-lasting concerted evolution in prokaryotes
Bibliographic record
Abstract
Concerted evolution, where paralogs in the same species show higher sequence similarity to each other than to orthologs in other species, is widely found in many species. However, cases of concerted evolution that last for hundreds of millions of years are very rare. By genome-wide analysis of a broad selection of prokaryotes, we provide strong evidence of recurrent concerted evolution in 26 genes, most of which have lasted more than ~500 million years. We find that most concertedly evolving genes are key members of important pathways, and encode proteins from the same complexes and/or pathways, suggesting coevolution of genes via concerted evolution to maintain gene balance. We also present LRCE-DB, a comprehensive online repository of long-lasting concerted evolution. Collectively, our study reveals that although most duplicated genes may diverge in sequence over a long period, on rare occasions this constraint can be breached, leading to unexpected long-lasting concerted evolution in a recurrent manner.
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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 | 0.001 |
| 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".