Molecular systematics and population genomics of the tree-pathogenic fungus Grosmannia clavigera
Bibliographic record
Abstract
Ophiostomatoid fungi increasingly damage forests, but understanding their interactions with vectors and hosts is hampered by uncertainty over the validity of genera, relationships between genera, and species boundaries. To address some of these issues, I first generated a new multigene dataset from 67 taxa that represent the genus Grosmannia and other related genera. The multigene phylogeny resolved the Grosmannia fungi into a clade that was separated from previously intermixed species of the genera Ambrosiella and Raffaelea, and that corresponded to distinct ecological niches and vector associates, i.e. bark versus wood-boring beetles. Second, I generated and used 15 gene genealogies to define species boundaries in G. clavigera. This destructive pine pathogen is vectored by two beetle species: mountain and Jeffrey pine beetles (MPB, JPB). MPB and its fungal associates have expanded into the largest epidemic in western North American history. I identified two phylogenetic species: Gs and Gc. Gc is present in the phylogenetically close Pinus species ponderosa and jeffreyi, which are infested by localized populations of their respective beetles. In contrast, Gs is an exclusive associate of MPB and its primary host P. contorta, although it is found in other pine species in current epidemic regions. These results suggest that host-tree species and beetle population dynamics are important factors in the genetic divergence and diversity of fungal associates in the beetle-tree ecosystems. Finally, we generated new genomic sequences for eleven Gs and Gc strains to further assess evidence for divergence in these fungi as they adapt to different pine species, and to find genes that may be involved in species divergence. Aligning these genome sequences to the reference genome, we identified 103,430 SNPs that supported the Gs and Gc lineages and divided each lineage into two subclades. Genome-wide scans identified truncated genes and potential pseudogenes that differed between Grosmannia lineages, as well as seven genes that show evidence of positive selection. The seven genes are involved in secondary metabolism and in detoxifying host-tree defense chemicals (e.g. polyketide synthases, oxidoreductases), and their variants may reflect adaptation to the specific chemistries of P. contorta, ponderosa, and jeffreyi.
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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 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| 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 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".