Taxonomy and phylogeny of the leaf–inhabiting sooty molds in family Metacapnodiaceae
Bibliographic record
Abstract
Metacapnodiaceae is one of the families of sooty molds in Ascomycota. Sooty mold fungi inhabit plant leaves, twigs, and trunks as spongy subicula composed of loosely tangled, black hyphae, usually in association with insect honeydew or plant leachates. Before my studies, DNA sequences were available from only two species in Metacapnodiaceae. Sooty molds' phylogenetic relationships have been difficult to study because they are difficult to culture. Further, they grow intermingled with other fungi and are difficult to separate for DNA extraction. To characterize Metacapnodium diversity at the species level, I collected two local species and borrowed specimens from international herbaria. I applied DNA sequence barcoding of ribosomal internal transcribed spacer regions of 16 collections, using a Metacapnodium-specific primer, followed by phylogenetic analyses. I describe and illustrate diagnostic morphological characters of 15 species of Metacapnodium. Using this combination of morphology and barcode phylogeny, I describe two new species and propose two new combinations. Earlier morphological study had led to two alternative hypotheses about relationships of Metacapnodiaceae in Ascomycota--it could be accommodated in class Dothideomycetes, order Capnodiales, or else in class Eurotiomycetes, order Chaetothyriales. To resolve the deeper relationships of Metacapnodiaceae, I sequenced partial nuclear ribosomal large subunit gene regions from five specimens and elongation factor 1-alpha gene regions from two specimens. I aligned my sequences with publicly available sequences from ribosomal DNA, RPB2 and Ef1-alpha gene regions. My analysis revealed that Metacapnodium is a sister group to the order Verrucariales, class Eurotiomycetes, contrary to earlier suggestions. These results are surprising because Verrucariales, the closest relatives of Metacapnodiaceae, are lichenized fungi and have little in common with Metacapnodium species. Resolving family relationships is relevant to age estimates of Ascomycota, as a fossilized Metacapnodium specimen in 24 million-year-old Bitterfeld amber has been inappropriately used to date Capnodiales. I can now infer that 24 million years ago is the most recent date that Metacapnodium could have diverged from Verrucariales. This example shows that by clarifying the phylogenetic position of Metacapnodium, we can gain insights into the evolutionary history and diversification of sooty molds and improve estimates of the timing of diversification of Ascomycota.
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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 | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".