Genetic population structure and distribution of a fungal polypore,<i>Datronia caperata</i>(Polyporaceae), in mangrove forests of Central America
Bibliographic record
Abstract
Abstract Aim We examine the genetic structure of a fungal polypore,Datronia caperata(Berk.) Ryvarden (Polyporaceae), colonizing white mangrove,Laguncularia racemosa(L.) Gaertn. f. (Combretaceae), of Central America. Location Mangrove forests of Costa Rica and Panama. Methods Sequences of elongation factor alpha (EFA), beta tubulin (BTUB) and nuclear ribosomal internal transcribed spacer (ITS) regions were obtained from 54 collections ofD.caperatacollected from Caribbean and PacificL. racemosaforests in Central America. Measures of haplotype and nucleotide diversity, nested clade analyses and coalescent analyses were used to estimate the direction and extent of migration of the fungus, and the factors promoting population divergence. We also conducted phylogenetic analyses using Bayesian estimation to test whether putativeD. caperatacollected fromL. racemosawas conspecific withD. caperatacolonizing other hosts from diverse Neotropical forests. Results Our results demonstrate that there is genetic isolation betweenD. caperatapopulations from Caribbean mangroves and those from Pacific mangroves. Our data suggest that the best explanation for the observed haplotype distribution is a recent range expansion from the Caribbean to the Pacific coasts, with subsequent isolation. This is supported by the infrequent overlap of haplotypes, unidirectional migration estimates from the Caribbean to the Pacific and the older estimated age of mutations in the Caribbean low‐copy BTUB and EFA loci. In addition, our data suggest thatD. caperatafrom mangroves are not conspecific with collections from other hosts found in diverse Neotropical forests. Main conclusions The low frequency of shared haplotypes between coasts, coupled with the incomplete lineage sorting after cessation of gene flow, is consistent with isolation during the last Pleistocene glaciation. We hypothesize that the greater haplotype and nucleotide diversity in the Pacific occurs either because larger effective population sizes ofD. caperataare maintained in Pacific mangroves or becauseD. caperatapopulations underwent a significant bottleneck as a result of local extinction followed by recolonization. In addition, we found thatD. caperatafound onL. racemosawas not conspecific withD. caperatafrom non‐mangrove hosts and suggest thatD. caperatafound onL. racemosamay be a host specialist.
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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) | 0.001 | 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".