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Aim  We address the unexplored question of whether the lack of information on intra‐specific diversity inherent in species‐level niche modelling might bias evaluation of the conservation requirements of species and phylogeographic lineages under changing climates. We test for directional biases that might arise due to these methodological differences in ways of assessing risks from climate change.

Location  The African continent.

Methods  We identified from peer‐reviewed studies that used both nuclear and plastid markers the distribution of deep phylogeographic divisions within nine species of African mammals and their phylogeographic lineages. We fitted ecological niche models to describe currently suitable, occupied climates and to project the shift of suitable climate to two future time slices. We applied gap analysis to reveal potential changes in the protection of phylogeographic diversity owing to …