Development of genomic resources for cattails ( <i>Typha</i> ), a globally important macrophyte genus
Bibliographic record
Abstract
Abstract 1. Background A critical knowledge gap in freshwater plants research is the lack of genetic tools necessary to answer fundamental questions about their demographic histories, adaptation, and phylogenetic relationships. One example of this is Typha , a global genus of freshwater plants foundational to wetlands that is also becoming an increasingly problematic biological invader in numerous regions worldwide; while important insights have been discovered for this genus, existing markers are insufficient to answer fundamental questions about their demographic histories, adaptation, and phylogenetic relationships, to identify introduced and hybrid lineages, and to examine patterns of hybridisation and introgression. 2. Methods We optimised a library preparation and data processing protocol to develop genome–wide nuclear and plastid resources for studying the evolutionary history, genetic structure and diversity, hybridisation, local adaptation, invasiveness, and geographic expansion dynamics of Typha . 3. Main results We sequenced 140 Typha samples and identified ∼120K nuclear SNPs that differentiate T. angustifolia , T. domingensis and T. latifolia and retrieved their plastome sequences. We observed genetic introgression among the three species. 4. Conclusions Following a fast, straightforward, and cost–efficient genomic library preparation protocol, we produced a suite of genome–wide resources to facilitate investigations into the taxonomy and population genetics of Typha and to advance the genomic understanding of wetland plants. 5. Contributions The protocol described, the updated chromosome–level genome assembly of T. latifolia , the catalogue of species-specific SNPs, and the chloroplast sequences produced in this study comprise permanent resources that can be applied to study the genetic composition of multiple populations and hybrid zones and will be incorporated into future studies of Typha, an ecologically important and globally invasive macrophyte.
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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 | 0.002 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.007 | 0.006 |
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".