Résumé
Aim: In highly mobile species, Migratory Connectivity (MC) has relevant consequences in population dynamics, genetic mixing, conservation and management. Additionally, in colonially breeding species, the maintenance of the breeding geographical structure during the non‐breeding period, that is, a strong MC, can promote isolation and population divergence, which ultimately can affect the process of lineage sorting. In geographically structured populations, studying the MC and differences in environmental preferences among colonies, populations, or taxa can improve our understanding of the ecological divergence among them.Location: Atlantic Ocean and Mediterranean Sea.Methods: We investigated the MC and non‐breeding ecological niche of three seabird taxa from the genus Calonectris ( n = 805 individuals). Using 1346 year‐round trips from 34 different breeding colonies, we assess the level (from taxa to colony) at which MC and non‐breeding spatial and environmental segregation emerge. Results At a taxon level, we found a clear difference in the non‐breeding distributions between Cory's ( C. borealis ) and Scopoli's ( C. diomedea ) shearwaters, and a clear ecological divergence between Cory's and Cape Verde ( C. edwardsii ) shearwaters. At an intermediate aggregation level, we found that birds breeding in proximity had similar non‐breeding habitat preferences, while birds breeding in very distant colonies (and therefore classified in different populations) had different non‐breeding habitat preferences. Furthermore, within each taxon, we found more structure (i.e. stronger MC) and non‐breeding divergence at an intermediate aggregation level than at the colony scale, where MC was weak.Main Conclusions: These results suggest that conspecifics from nearby colonies mix in common non‐breeding areas, but not with birds from more distant colonies or different taxa. These results support the need for management and conservation strategies that take into account this structure when dealing with migratory species with high connectivity.