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Cooperative communications can significantly enhance transmission reliability and bandwidth efficiency in wireless networks. However, many upper layer aspects of cooperative communications merit further research. In this paper, we investigate its impacts on network topology and network capacity, which is determined by considerable aspects, such as physical layer capacity, interference, path length, etc. Since cooperative communications enhance physical layer capacity and relay selection impacts network topology directly, we present a Capacity-Optimized COoperative (COCO) topology control scheme for mobile ad hoc networks (MANETs) with cooperative communications. We consider both upper layer network capacity and physical layer relay selections in the proposed scheme. In addition, only the channel estimate, not the perfect channel status, is assumed to be known in our scheme. The topology control problem in MANETs is then formulated as a discrete stochastic optimization problem, which can be solved using a stochastic approximation approach. Further, an improved COCO is presented to reconfigure network topology to track the changing mobile environment dynamically. Simulation results are presented to show the effectiveness of the proposed scheme.