Identifying spatially concordant evolutionary significant units across multiple species through DNA barcodes: Application to the conservation genetics of the freshwater fishes of Java and Bali
Bibliographic record
Abstract
Delineating Evolutionary Significant Units for conservation purposes is a crucial step in conservation. Across a distribution range, species frequently display population structure that drives the distribution of genetic diversity. These patterns of genetic structure and diversity result from intricate interactions between biogeographic history and demographic dynamics. Prior biogeographic knowledge, however, is scarcely available, a trend particularly pronounced in the tropics where the taxonomic impediment is hampering biogeographic studies and conservation efforts. DNA barcoding has been initially proposed to foster taxonomic studies through the development of an automated molecular system of species identification. While its utility for species identification is increasingly acknowledged, its usefulness for fast and large-scale delineation of ESU remains to be explored. If proved to be useful for that purpose, DNA barcoding may also open new perspectives in conservation by quickly providing preliminary information about population conservation status. The present study aims at assessing the utility of DNA barcoding for the delineation of ESUs among the most common freshwater fish species of Java and Bali through the comparison of population genetic structures and diversification patterns across multiple species. Substantial levels of cryptic diversity are discovered among the three widely distributed freshwater fish species analyzed with a total of 21 evolutionary independent mitochondrial lineages (BINs) observed in Barbodes binotatus, Channa gachua and Glyptothorax platypogon. The maximum genetic distance for each coalescent tree ranges from 6.78 to 7.76 K2P genetic distances for C. gachua and G. platypogon, respectively. Diversification and population genetic analyses support a scenario of allopatric differentiation. The analysis of the BINs spatial distribution indicates concordant distribution patterns among the three species that allow identifying 18 ESUs. Implications for the conservation genetics of these species are discussed at the light of the history of the region.
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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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| 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".