An updated phylogeny of Boraginales based on the Angiosperms353 probe set: a roadmap for understanding morphological evolution
Bibliographic record
Abstract
BACKGROUND AND AIMS: Boraginales, a subcosmopolitan order with ~2700 species in currently 11 families, has seen fluctuating classification at the family and generic levels. Gynoecium and fruit morphology have been pivotal in morphological classifications, but a systematic evaluation based on anatomical and ontogenetic data has not been attempted. METHODS: We revisited the phylogenetic relationships in Boraginales by analysing 162 newly sequenced samples using the Angiosperms353 probe set, together with existing data from 88 samples. Our sampling covers >80 % of the genera and all currently and previously recognized families. A morphological assessment of taxonomically important gynoecial and fruit characters was done to guide our proposed family-level classification. KEY RESULTS: The phylogenies are largely consistent with previous phylogenetic studies, with better resolution overall and support from both datasets (exons, supercontigs) and all analyses implemented (coalescence, ASTRAL-Pro3, concatenation). The placement of Hydrophyllaceae as nested within Namaceae is a novel result, while the placement of the parasitic Lennoaceae as nested within Ehretiaceae is confirmed with maximum confidence. The placement of Codonaceae remains ambiguous: retrieved within Boraginales I, as sister to the clade comprising Wellstediaceae and Boraginaceae based on exons, and as sister branch to all remaining Boraginales II based on supercontigs. We propose the recognition of a total of nine families in Boraginales. Tribal relationships in Boraginaceae subfam. Cynoglossoideae are fully resolved for the first time. Our data show that shifts in placentation and ovule number are instrumental for the arisal of complex internal ovary architectures. CONCLUSIONS: The results highlight the effectiveness of the Angiosperms353 probe set for understanding the evolutionary history of Boraginales and pave the way for resolving remaining unresolved nodes and taxonomic issues. Complex modifications of bicarpellate ovaries led to an extreme and lineage-specific diversification of fruits that probably played a crucial role in Boraginales macroevolution. Combining this highly resolved phylogeny with future critical morphological analyses promises a deep understanding of evolutionary trajectories in Boraginales.
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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) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.005 | 0.002 |
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".