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Entanglement entropy quantifies the amount of uncertainty of a quantum state. For quantum fields in curved space, entanglement entropy of the quantum field theory degrees of freedom is well-defined for a fixed background geometry. In this paper, we propose a generalization of the quantum field theory entanglement entropy by including dynamical gravity. The generalized quantity named effective entropy, and its Renyi entropy generalizations, are defined by analytic continuation of a gravitational path integral on replica geometry with a co-dimension-$2$ brane at the boundary of region we are studying. We discuss different approaches to define the region in a gauge invariant way, and show that the effective entropy satisfies the quantum extremal surface formula. When the quantum fields carry a significant amount of entanglement, the quantum extremal surface can have a topology transition, after which an entanglement island region appears. Our result generalizes the Hubeny-Rangamani-Takayanagi formula of holographic entropy (with quantum corrections) to general geometries without asymptotic AdS boundary, and provides a more solid framework for addressing problems such as the Page curve of evaporating black holes in asymptotic flat spacetime. We apply the formula to two example systems, a closed two-dimensional universe and a four-dimensional maximally extended Schwarzchild black hole. We discuss the analog of the effective entropy in random tensor network models, which provides more concrete understanding of quantum information properties in general dynamical geometries. By introducing ancilla systems, we show how quantum information in the entanglement island can be reconstructed in a state-dependent and observer-dependent map. We study the closed universe (without spatial boundary) case and discuss how it is related to open universe.