An integrative approach to studying speciation in a recent adaptive radiation

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.