Phylogenetic incongruence arising from fragmented speciation in enteric bacteria
Bibliographic record
Abstract
Evolutionary relationships among species are often assumed to be fundamentally unambiguous, where genes within a genome are thought to evolve in concert and phylogenetic incongruence between individual orthologs is attributed to idiosyncrasies in their evolution. We have identified substantial incongruence between the phylogenies of orthologous genes in Escherichia, Salmonella, and Citrobacter, or E. coli, E. fergusonii, and E. albertii. The source of incongruence was inferred to be recombination, because individual genes support conflicting topology more robustly than expected from stochastic sequence homoplasies. Clustering of phylogenetically informative sites on the genome indicated that the regions of recombination extended over several kilobases. Analysis of phylogenetically distant taxa resulted in consensus among individual gene phylogenies, suggesting that recombination is not ongoing; instead, conflicting relationships among genes in descendent taxa reflect recombination among their ancestors. Incongruence could have resulted from random assortment of ancestral polymorphisms if species were instantly created from the division of a recombining population. However, the estimated branch lengths in alternative phylogenies would require ancestral populations with far more diversity than is found in extant populations. Rather, these and previous data collectively suggest that genome-wide recombination rates decreased gradually, with variation in rate among loci, leading to pluralistic relationships among their descendent taxa.
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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 | 0.002 | 0.008 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.002 |
| Research integrity | 0.001 | 0.001 |
| 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".