Density-dependent processes often play a key role in the spatial structuring of genetic variation. In particular, related processes such as gene surfing and high-density blocking can generate striking geographic contrasts in the distributions of genes. Well-characterised phylogeographic patterns associated with postglacial recolonization, progressive island colonization, microbial sectoring, and the ‘Out of Africa’ pattern of human expansion, are fundamentally similar, and arguably underpinned by a ‘founder takes all’ density-dependent principle. In the current study, comparisons of ancient DNA and modern DNA from New Zealand’s pinniped and penguin assemblages reveal sudden spatio-temporal genetic shifts, apparently in response to human-mediated extirpation events. These rapid phylogeographic transitions underscore the role of ‘founder takes all’ processes in constraining the distributions of genes and species.