Shohat, H.; Ciren, D.; Arrones, A.; Gentile, I.; Ramakrishnan, S.; Hendelman, A.; Jenike, K. M.; Brown, N. L.; Luna-Ramos, J.; Passalacqua, M. J.; Satterlee, J. W.; Fitzgerald, B.; Baraja-Fonseca, V.; Robitaille, G. M.; Seman, B. M.; Gillis, J.; Van Eck, J.; Prohens, J.; Schatz, M. C.; Lippman, Z. B.

Neofunctionalization is a rare fate of gene duplication, classically defined as the acquisition of novel functions that potentiate the emergence of new traits. Rather than evolving to function autonomously, neofunctionalized genes may also remain embedded within their ancestral regulatory networks, potentially reshaping the genetic trajectories through which phenotypic change occurs. Testing this hypothesis, we leveraged a pan-genetic platform comprising ten Solanaceae species and show that a paralog of the flowering hormone florigen neofunctionalized into a flowering antagonist and was repeatedly selected during crop domestication and adaptation of wild plants across 50 million years of evolution. Independent selection of cis-regulatory and coding mutations in SELF-PRUNING 5G (SP5G) enabled rapid flowering in the wild ancestor of domesticated tomato from Central America as well as major and indigenous eggplant crop lineages domesticated in Asia and Africa. We further found that cis-regulatory sequence changes reduced SP5G expression and flowering time in wild species native to distinct environments in the Americas and Australia, relationships that we validated by genome editing. Together with similar patterns observed across diverse species and developmental networks, we propose that antagonistic neofunctionalized paralogs create evolutionary contingencies that channel adaptive trajectories across plant lineages.