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Leite et al. (1) conclude that isolation according to the forest refuge hypothesis (FRH) may have had a minor, if any, role on Atlantic Forest (AF) biotic evolution based on genetic data from five mammal species. Their evidence comes from signatures of population expansion during both glacial and interglacial periods, and fragmentation of reconstructed distributions during interglacial periods. Despite its novelty (i.e., the influence of sea-level changes in AF phylogeography), Leite et al.’s study presents many issues that need a critical appraisal. First, analyses based on a single locus are prone to stochastic error and often lack sufficient variation for detecting historical processes, such as bottlenecks and shallow population structure, which are key in contrasting refugium vs. nonrefugium hypotheses. Leite et al.’s (1 …

The “Atlantis Forest hypothesis” does not explain Atlantic Forest phylogeography