An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids
Bibliographic record
Abstract
Plastids originated as a cyanobacterium that was engulfed by the ancestral lineage of the major photosynthetic eukaryotic group (Archaeplastida). Although the ancestral cyanobacterial lineage of these organelles is not known, Archaeplastida still retain remnants of the ancestral cyanobacterial genome, inherited through the plastid. As a result, it should be possible to constrain the origin of plastids within Cyanobacteria through phylogenetic analyses. To date, such phylogenetic studies have produced conflicting results and two competing hypotheses: 1) plastids diverged relatively recently in cyanobacterial evolution and are most closely related to nitrogen-fixing cyanobacteria, or 2) plastids diverged early in the evolutionary history of cyanobacteria, before the divergence of most crown group lineages. Here, we differentiate between these competing hypotheses using a phylogenetic analysis of ribosomal proteins from an expanded data set of cyanobacterial genomes and representative plastid sequences. Our results robustly support a deep rooting of the plastid ancestor lineage as sister to Gloeomargarita, with a divergence from other cyanobacterial groups before that of Pseudanabaena. The results of our study are especially important for future molecular clock studies, which are highly dependent upon tree topologies and distances for modeling accurate branch rates. The deeper rooting of plastids in our phylogenies and increased cyanobacterial sequence coverage provide an improved tree topology and enable the use of well-informed fossil calibrations.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".