Although cooperative communication has been proposed at the physical layer to address multi-path fading e®ects, how physical layer gains with cooperative communication can translate to tangible perfor- mance bene¯ts in end-to-end °ows remains to be an open problem. This paper represents one step forward towards a deeper understanding of the interplay between end-to-end throughput and physical layer cooperative communication, in the general context of multi-hop multi-channel wire- less networks. Based on a decode-and-forward physical layer design with rateless codes, we reformulate the problem of routing and channel assign- ment to account for physical layer cooperation. We design a distributed protocol to solve the new problem. Our simulation results have validated the e®ectiveness of our protocol to o®er a substantial gain with respect to stabilizing the o®ered aggregate throughput in the network.