Reply to Raposo do Amaral et al.: the “Atlantis Forest hypothesis” adds a new dimension to Atlantic Forest biogeography

Abstract

One or two diversification models alone cannot explain biodiversity evolution in the Atlantic Forest, or any other megadiverse biome, as we (1, 2) pointed out long before Raposo do Amaral et al. (3). In our recent paper (4), we present the Atlantis Forest hypothesis (AFH), which is an additional perspective to the Atlantic Forest evolution, beyond the forest refuge hypothesis (FRH). The AFH incorporates irrefutable Quaternary sea-level changes, which had been overlooked in the literature, and this is the main point of our paper. Support for the AFH came from small mammal distribution modeling and coalescent simulations based on mitochondrial DNA (mtDNA) sequences, which have been successfully used in thousands of biogeographical studies for over 30 y, forming the basis of the booming field of phylogeography (5) and providing support for the FRH (6). We agree that analyses based on a single locus might be subject to stochastic error, and a recent review found mito-nuclear discordance in 18% of biogeographical studies (7). This is not a negligible number, but most mtDNA results can be taken as reliable indicators of geographical population structure and phylogeographical patterns (8).