Title: Tracking the emergence of cooperation in complex networked populations Abstract: Social networks affect in such a fundamental way the dynamics of the population they support that the global, population-wide behavior that one observes often bears no relation to the individ- ual processes it stems from. Up to now, linking the global networked dynamics to such individual mechanisms has remained elusive. Here we define a dynamic observable and use it to track the self- organization of cooperators when co-evolving with defectors in networked populations interacting via a Prisoner s Dilemma. We find that homogeneous networks promote the coexistence between cooperators and defectors, while heterogeneous networks favor the coordination between them. Using the same observable, we show how the global dynamics co-evolves with the motifs of cooperators in the population, the overall emergence of cooperation depending sensitively on this co-evolution.