Ancient reticulation, incomplete lineage sorting and the evolution of the pyrenoid at the dawn of hornwort diversification
Bibliographic record
Abstract
BACKGROUND AND AIMS: Resolving the phylogeny of hornworts is critical in understanding the evolution of key morphological characters that are unique to the group, including the pyrenoid. Extensive phylogenomic analyses have revealed unexpected complexities in the placement of Leiosporoceros, the previously identified sister taxon to other hornworts. We explore the role of incomplete lineage sorting (ILS) and ancient reticulation in resolving interrelationships and understanding the diversification and evolutionary processes within hornworts. METHODS: Using the GoFlag probe set, we sequenced 405 exons representing 234 nuclear genes, sampling 79 hornwort specimens, including representatives of all hornwort genera. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed ancient reticulation and ILS, and estimated the timing of divergences based on fossil calibrations. KEY RESULTS: Extreme levels of gene tree incongruence challenge the sister relationship of Leiosporoceros to other hornworts. This phylogenetic discordance is due to ILS and ancient reticulation, the latter revealed using a network approach to identify evidence of gene flow among hornwort lineages. Hornwort diversification began in the Carboniferous with widespread family-level divergences during the mid-Cretaceous and Palaeogene. CONCLUSIONS: ILS and ancient reticulation are identified as important in hornwort evolution. Patterns of hornwort diversification parallel those in other plants groups (e.g. liverworts, mosses, ferns and gymnosperms). Two scenarios on pyrenoid evolution are plausible based on the variable position of the pyrenoid-free Leiosporoceros. Pyrenoids were retained from a green algal ancestor and are plesiomorphic, or they evolved in response to the substantial drop in atmospheric CO2 levels during the Carboniferous as has been hypothesized in other photosynthetic organisms. Both hypotheses require losses and gains during hornwort speciation.
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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 | 0.001 | 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".