Escape from adaptive conflict after duplication in an anthocyanin pathway gene

Gene duplications have been recognized as an important source of evolutionary innovation and adaptation since at least Haldane, and their varying fates may partly explain the vast disparity in observed genome sizes. The expected fates of most gene duplications involve primarily non-adaptive substitutions leading to either non-functionalization of one duplicate copy or subfunctionalization, neither of which yields novel function. A significant evolutionary problem is thus elucidating the mechanisms of adaptive evolutionary change leading to evolutionary novelty. Currently, the most widely recognized adaptive process involving gene duplication is neo-functionalization (NEO-F), in which one copy undergoes directional selection to perform a novel function after duplication. An alternative, but understudied, adaptive fate that has been proposed is escape from adaptive conflict (EAC), in which a single-copy gene is selected to perform a novel function while maintaining its ancestral function. This gene is constrained from improving either novel or ancestral function because of detrimental pleiotropic effects on the other function. After duplication, one copy is free to improve novel function, whereas the other is selected to improve ancestral function. Here we first present two criteria that can be used to distinguish NEO-F from EAC. Using both tests for positive selection and assays of enzyme function, we then demonstrate that adaptive evolutionary change in a duplicated gene of the anthocyanin biosynthetic pathway in morning glories (Ipomoea) is best interpreted as EAC. Finally, we argue that this phenomenon likely occurs more often than has been previously believed and may thus represent an important mechanism in generating evolutionary novelty.     

Strong atom-field coupling for Bose-Einstein condensates in an optical cavity on a chip

An optical cavity enhances the interaction between atoms and light, and the rate of coherent atom-photon coupling can be made larger than all decoherence rates of the system. For single atoms, this 'strong coupling regime' of cavity quantum electrodynamics has been the subject of many experimental advances. Efforts have been made to control the coupling rate by trapping the atom and cooling it towards the motional ground state; the latter has been achieved in one dimension so far. For systems of many atoms, the three-dimensional ground state of motion is routinely achieved in atomic Bose-Einstein condensates (BECs). Although experiments combining BECs and optical cavities have been reported recently, coupling BECs to cavities that are in the strong-coupling regime for single atoms has remained an elusive goal. Here we report such an experiment, made possible by combining a fibre-based cavity with atom-chip technology. This enables single-atom cavity quantum electrodynamics experiments with a simplified set-up and realizes the situation of many atoms in a cavity, each of which is identically and strongly coupled to the cavity mode. Moreover, the BEC can be positioned deterministically anywhere within the cavity and localized entirely within a single antinode of the standing-wave cavity field; we demonstrate that this gives rise to a controlled, tunable coupling rate. We study the heating rate caused by a cavity transmission measurement as a function of the coupling rate and find no measurable heating for strongly coupled BECs. The spectrum of the coupled atoms-cavity system, which we map out over a wide range of atom numbers and cavity-atom detunings, shows vacuum Rabi splittings exceeding 20 gigahertz, as well as an unpredicted additional splitting, which we attribute to the atomic hyperfine structure. We anticipate that the system will be suitable as a light-matter quantum interface for quantum information.