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Recent discussion about the increase in international research collaboration suggests a comprehensive global network centred around a group of core countries and driven by generic socio-economic factors where the global system influences all national and institutional outcomes. In counterpoint, we demonstrate that the collaboration pattern for countries in Africa is far from universal. Instead, it exhibits layers of internal clusters and external links that are explained not by monotypic global influences but by regional geography and, perhaps even more strongly, by history, culture and language. Analysis of these bottom-up, subjective, human factors is required in order to provide the fuller explanation useful for policy and management purposes.