fungi / yeast convergence / comparison. Design and run log: studies/fungi/yeast_convergence (PR #43).
yeast_convergence: cross-contrast comparison
Sixteen contrasts test whether yeast growth form evolved independently with the same functional gene families. 9 origin contrasts compare a yeast lineage with its filamentous sister. 5 pseudo-origin controls (filamentous lineages with large gene loss and no change in growth form) and 2 reversal contrasts have enrichment tables. A term counts as recurrent when at least 3 origins call it significant (Pfam and Pfam clan; BH q ≤ 0.05 against a Poisson-binomial null). Terms that a pseudo-origin control also calls are labelled streamlining_generic.
Result
0 terms are recurrent and absent from all controls (class yeast_convergent). 4 terms are recurrent and also called in at least one control. This does not show that convergence is absent. The analysis has few origins, small ingroups for some contrasts, and a null model that ignores family size.
| direction | vocab | term | name | origins sig/tested | origins | q | controls sig/tested | class |
|---|---|---|---|---|---|---|---|---|
| loss | pfam_clan | CL0219 | RNase_H | 4/9 | yc_tremellomycetes, yc_ustilaginomycotina, yc_pucciniomycotina, yc_mucoromycota | 0.00277 | 1/5 | streamlining_generic |
| novelty | pfam_clan | CL0271 | F-box | 3/8 | yc_dothideales, yc_pucciniomycotina, yc_mucoromycota | 0.0248 | 3/5 | streamlining_generic |
| novelty | pfam | PF00646 | F-box: F-box domain | 3/8 | yc_dothideales, yc_pucciniomycotina, yc_mucoromycota | 0.0478 | 3/5 | streamlining_generic |
| novelty | pfam | PF12937 | F-box-like: F-box-like | 3/9 | yc_dothideales, yc_pucciniomycotina, yc_mucoromycota | 0.0478 | 1/5 | streamlining_generic |
- Lichen proteomes: Letharia lupina WasteWater1 was screened against NCBI nr (diamond, best hit by bit score): 95.6% of its 12,349 proteins have a fungal best hit, and 0 have a green-plant or algal one. Of 2,666 novelty and loss candidate proteins of the lichen contrast, 0 have a non-fungal best hit and 10 have no hit. The screen is a check, not an assignment. C. rubrotincta was not screened as a whole proteome.
- Pfam is the primary vocabulary for every contrast: from UniProt records, or from a HMMER search for proteomes without UniProt annotation. GO and InterPro are used only for contrasts whose species are all UniProt proteomes. 0 terms are recurrent in those secondary vocabularies.
- 6 proteomes score under 85% BUSCO complete (fungi_odb10) and are kept. Loss calls for those species may include missing genes, not only losses.
- The arbuscular mycorrhizal control has 31,206 novelty candidates. About half of its proteins have no diamond hit in the Mucoromycota outgroups. Whether this is real expansion is not tested. Several of its top Pfam bars are transposon families.
yc_rev_neolectahas one ingroup species. The pipeline builds the presence matrix from proteins with a hit to another proteome, so it cannot call novelty candidates there. This contrast adds loss tables only.yc_saccharomycotinaandyc_taphrinomycotinashare two outgroup species. Neither makes a recurrent call, so the overlap does not change these results.- Growth-form codings for some species are predicted or unsourced (issue 44).
Definitions
Novelty: a gene family present in at least 75% of the ingroup (IN) species and absent from all outgroup (OUT) species. Loss: the reverse, present in at least 75% of the OUT species and absent from all IN species. Calls come from pairwise diamond searches (E-value < 1e-5). Enrichment is a one-sided hypergeometric test per Pfam family, BH-corrected within each vocabulary.
Contrasts
| id | role | lineage | ingroup / outgroup | pages |
|---|---|---|---|---|
| yc_saccharomycotina | origin | Saccharomycotina | 5 / 4 | novelty · loss · report |
| yc_taphrinomycotina | origin | Taphrinomycotina | 6 / 3 | novelty · loss · report |
| yc_chaetothyriales | origin | Chaetothyriales black yeasts | 5 / 3 | novelty · loss · report |
| yc_dothideales | origin | Dothideales (Aureobasidium) | 4 / 3 | novelty · loss · report |
| yc_capnodiales | origin | Capnodiales (Hortaea) | 2 / 3 | novelty · loss · report |
| yc_tremellomycetes | origin | Tremellomycetes | 4 / 3 | novelty · loss · report |
| yc_ustilaginomycotina | origin | Ustilaginomycotina | 4 / 4 | novelty · loss · report |
| yc_pucciniomycotina | origin | Pucciniomycotina (red yeasts) | 5 / 3 | novelty · loss · report |
| yc_mucoromycota | origin | Mucorales (dimorphic Mucor) | 3 / 4 | novelty · loss · report |
| yc_pseudo_powdery_mildew | pseudo | none (control) | 4 / 3 | novelty · loss · report |
| yc_pseudo_ectomycorrhizal | pseudo | none (control) | 4 / 4 | novelty · loss · report |
| yc_pseudo_dermatophyte | pseudo | none (control) | 4 / 2 | novelty · loss · report |
| yc_pseudo_arbuscular_mycorrhizal | pseudo | none (control) | 4 / 4 | novelty · loss · report |
| yc_pseudo_lichen | pseudo | none (control) | 4 / 4 | novelty · loss · report |
| yc_rev_eremothecium | reversal | Eremothecium (filamentous reversal within Saccharomycetaceae) | 3 / 4 | novelty · loss · report |
| yc_rev_neolecta | reversal | Neolecta (fruiting lineage within Taphrinomycotina) | 1 / 6 | novelty · loss · report |
Files and provenance
Inputs, script commit, parameters and SHA-256 of every input and output are in PROVENANCE.yaml.