Singh, P.

While the contribution of gene expression (GE) to adaptive evolution is widely accepted, the role of alternative splicing (AS) remains less understood. Here, we investigate AS and GE across three iconic adaptive radiations of African cichlid fishes that evolved within <16,000 to 3.8 million years. We show that AS evolves faster than GE, with both sources of variation being \'fine-tuned\' over evolutionary time to become species-specific and clade-specific, respectively. Ecologically divergent species from younger radiations exhibit greater differences in splicing than those from older radiations. Most of these differentially spliced isoforms arose from standing variation, which was also present at low levels in non-radiating species, and increased in frequency during the adaptive radiation process. We identified several novel isoforms of craniofacial remodelling genes that emerged within each lake radiation and were differentially incorporated in the jaws of herbivorous vs. carnivorous species. Our findings indicate that a complex temporal interplay of GE and AS underlies adaptive radiation, with ancestral splice variation enabling rapid ecological diversification at early stages of speciation.