An integrative approach to studying speciation in a recent adaptive radiation
Bibliographic record
Abstract
Alcolapia cichlid fishes are a small and exceptionally young species flock native to extreme soda lakes Natron (3 species) and Magadi (1 species) in East Africa. Previous research discovered narrow genomic divergence, overlapping niches and widespread interspecific gene flow, indicating that Alcolapia are at the nascent stages of speciation. We employed an integrative approach to study different mechanisms underlying their speciation. To investigate premating isolation, we characterised the strength of assortative mate choice between species using laboratory mating trials. Mating was similarly partially assortative between sympatric and allopatric species, suggesting that reproductive barriers can emerge or be maintained without recent gene flow. Next, to dissect the extent of dietary specialization among sympatric species, we characterised the cryptic diversity in the Alcolapia diet and gut microbiota using a metabarcoding approach. Alcolapia were found to lack some core microbial taxa found in other cichlids, but were enriched in extremophile taxa, suggesting that the hostile conditions may influence gut microbe communities. Sympatric species substantially overlap in their diet and gut microbial communities, and the small but significant differences indicated that while species differentially target certain trophic resources, they predominantly feed on the same sources using alternative foraging modes. Finally, we used genomic datasets to highlight extensive historical and ongoing gene flow between the species. Demographic models supported the paraphyly of the Natron species, with the Alcolapia common ancestor occurring before the Magadi-Natron split, suggesting a complex pattern of population structuring and hybridization even in this small radiation of fishes. Taken together, our findings indicate that a combination of ecological, sexual, and historical processes are involved in Alcolapia speciation. These results support a growing literature finding that reproductive isolation between sympatric species is driven by multiple mechanisms acting in concert.
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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 | 0.002 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.004 | 0.004 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.001 | 0.003 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
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".