Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales<sup>1</sup>
Bibliographic record
Abstract
The order Poales comprises a substantial portion of plant life (7% of all angiosperms and 33% of monocots) and includes taxa of enormous economic and ecological significance. Molecular and morphological studies over the past two decades, however, leave uncertain many relationships within Poales and among allied commelinid orders. Here we present the results of an initial project by the Monocot AToL (Angiosperm Tree of Life) team on phylogeny and evolution in Poales, using sequence data for 81 plastid genes (exceeding 101 aligned kb) from 83 species of angiosperms. We recovered highly concordant relationships using maximum likelihood (ML) and maximum parsimony (MP), with 98.2% mean ML bootstrap support across monocots. For the first time, ML resolves ties among Poales and other commelinid orders with moderate to strong support. Analyses provide strong support for Bromeliaceae being sister to the rest of Poales; Typhaceae, Rapateaceae, and cyperids (sedges, rushes, and their allies) emerge next along the phylogenetic spine. Graminids (grasses and their allies) and restiids (Restionaceae and its allies) are well supported as sister taxa. MP identifies a xyrid clade (Eriocaulaceae, Mayacaceae, Xyridaceae) sister to cyperids, but ML (with much stronger support) places them as a grade with respect to restiids graminids. The conflict in resolution between these analyses likely reflects long-branch attraction and highly elevated substitution rates in some Poales. All other familial relationships within the order are strongly supported by both MP and ML analyses. Character-state mapping implies that ancestral Poales lived in sunny, fire-prone, at least seasonally damp/wet, and possibly nutrient-poor sites, and were animal pollinated. Five subsequent shifts to wind pollination—in Typhaceae, cyperids, restiids, Ecdeiocoleaceae, and the vast PACCMAD-BEP clade of grasses—are significantly correlated with shifts to open habitats and small, inconspicuous, unisexual, and nectar-free flowers. Prime ecological movers driving the repeated evolution of wind pollination in Poales appear to include open habitats combined with the high local dominance of conspecific taxa, with the latter resulting from large-scale disturbances, combined with tall plant stature, vigorous vegetative spread, and positive ecological feedback. Reproductive assurance in the absence of reliable animal visitation probably favored wind pollination in annuals and short-statured perennials of Centrolepidaceae in ephemerally wet depressions and windswept alpine sites.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 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 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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".