Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic diversity of Honey Bees (Apis mellifera)
Bibliographic record
Abstract
Abstract Previous morpho-molecular studies of evolutionary relationships within the economically important genus of honey bees (Apis), including the Western Honey Bee (A. mellifera L.), have suggested Out of Africa or Asia origins and subsequent spread to Europe. I test these hypotheses by a meta-analysis of complete mitochondrial DNA coding regions (11.0 Kbp) of 22 nominal subspecies represented by 74 individual sequences of A. mellifera. Parsimony, distance, and likelihood analyses identify six nested clades: Things Fall Apart with Out of Africa or Asia hypotheses. Phylogeographic analysis shows instead a basal origin of A. m. mellifera in Europe ~780 Kya, and extension to Southeast Europe and Asia Minor ~720 Kya. European bees spread southward via a Levantine / Nilotic / Arabian corridor into Africa ~540 Kya. A circum- Mediterranean clade was re-established in Iberia ~100 Kya, and thence back through the Mediterranean islands into North Africa. Paraphyletic anomalies are artefacts of mis-referral in GenBank of sequences to the wrong subspecies, which are clarified by inclusion of multiple individuals from each subspecies. Further errors arise from reliance on faulty sequences and (or) methods of inference. Nominal subspecies within the Asia Minor and Mediterranean clades are less differentiated than are individuals within other subspecies.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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".