Despite the widespread recognition of adaptive radiation as a driver of speciation, the mechanisms by which natural selection generates new species are incompletely understood. The evolutionary radiation of endemic East Asian cyprinids has been proposed as evolving through a change in spawning habits, involving a transition from semibuoyant eggs to adhesive eggs in response to crosslinked river-lake system formation. Here, we investigated the molecular mechanisms that underpin this radiation, associated with egg hydration and adhesiveness. We demonstrated that semibuoyant eggs enhance hydration by increasing the degradation of yolk protein and accumulation of Ca2+ and Mg2+ ions, while adhesive eggs improve adhesiveness and hardness of the egg envelope by producing an adhesive layer and a unique 4th layer to the egg envelope. Based on multiomics analyses and verification tests, we showed that during the process of adaptive radiation, adhesive eggs downregulated the “vitellogenin degradation pathway,” “zinc metalloprotease pathway,” and “ubiquitin-proteasome pathway” and the pathways of Ca2+ and Mg2+ active transport to reduce their hydration. At the same time, adhesive eggs upregulated the crosslinks of microfilament-associated proteins and adhesive-related proteins, the hardening-related proteins of the egg envelope, and the biosynthesis of glycosaminoglycan in the ovary to generate adhesiveness. These findings illustrate the novel molecular mechanisms associated with hydration and adhesiveness of freshwater fish eggs and identify critical molecular mechanisms involved in the adaptive radiation of endemic East Asian cyprinids. We propose that these key egg attributes may function as “magic traits” in this adaptive radiation.

The Yangtze River is the largest river in Asia, but its evolutionary history has long been debated. Diverse groups of endemic freshwater fishes have evolved in this river. Here we represent the historical spatiotemporal pattern of the endemic East Asian cyprinid clade based on the largest molecular phylogeny of Cyprinidae, including 1420 species and fossil records. Based on the evolution of egg types adapting to different hydrological conditions, we show that the ancestors of this endemic clade (laying adhesive eggs) were distributed in southern East Asia before ~24 Ma and subsequently dispersed to the Yangtze River basin to spawn semi-buoyant eggs at ~19 Ma. These results indicate that the Yangtze River reversed its flow direction from southward to eastward to form the present river system within the Oligocene-Miocene boundary (~24-19 Ma). Some East Asian cyprinids evolved into fishes producing adhesive eggs again at ~13 Ma, together with an increased net diversification rate, indicating that the river began to form a potamo-lacustrine system during the Mid-Miocene. The new sketch of the formation history of the Yangtze River system through Cyprinidae phylogeny, together with the evolution of egg types in endemic East Asia cyprinids, has better spatiotemporal integrity than traditional geological studies.