Data for: Phylogenetic resolution and conflict in the species-rich flowering plant family Leguminosae
Bibliographic record
Abstract
The Tree of Life is central to evolutionary biology, yet resolving deep, recalcitrant phylogenetic relationships remains challenging due to complex processes such as incomplete lineage sorting (ILS), hybridization, and polyploidization. Although previous phylogenetic studies have advanced our understanding of Leguminosae (Fabaceae), a species-rich and ecologically diverse family, many deep relationships at the tribal and higher levels remain unresolved. Integrating newly generated genome skimming data for 231 species with previously issued plastid genomic, mitochondrial genomic and transcriptomic data, we reconstructed a phylogeny of the family using whole plastome, 39 mitochondrial genes, and 1559 low-copy nuclear genes, achieving dense taxonomic sampling across almost all recognized tribes and major unplaced lineages. Our results supported the monophyly of the six subfamilies and 49 recognized tribes, resolved ten clades worthy of recognition as new tribes in subfamily Papilionoideae, and clarified many contentious relationships. However, nuclear-nuclear and cytonuclear conflicts persists at multiple nodes among trees inferred from different datasets and analytical methods. We propose the most probable resolution for 22 contentious nodes by applying nuclear gene-tree quartet analysis and corroboration from support of nuclear Maximum Likelihood (ML) and ASTRAL trees. Our results indicate ILS significantly contributes to observed phylogenetic conflicts, while gene flow represents an additional and previously underappreciated factor that mainly contributes to cytonuclear conflicts, particularly along the branches of the Angylocalyceae + Dipterygeae + Amburaneae (ADA) clade and Wisterieae. Both processes likely underlie recalcitrant phylogenetic relationships, such as those within the 50-kb inversion clade of Papilionoideae. Our study uses multiple data partitions and analytical methods to resolve contentious phylogenetic relationships in Leguminosae, resulting in a robust phylogenomic framework to guide further investigations in this economically important and exceptionally diverse family.
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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 | 0.003 | 0.013 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.005 | 0.009 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.072 | 0.040 |
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".