Geographical variation in genetic structure of an Atlantic Coastal Forest frog reveals regional differences in habitat stability SARAH W. FITZPATRICK,* CINTHIA A. BRASILEIRO,† CE ´ LIO F. B. HADDAD† and KELLY R. ZAMUDIO* *Department of Ecology and Evolutionary Biology, Cornell University, E145 Corson Hall, Ithaca, NY 14853, USA, †Departamento de Zoologia, Instituto de Biocie ˆncias, Universidade Estadual Paulista, Caixa Postal 199, 13506-900 Rio Claro, SP, Brazil Abstract Climatic oscillations throughout the Pleistocene combined with geological and topo- graphic complexity resulted in extreme habitat heterogeneity along the Atlantic coast of Brazil. Inferring how these historic landscape patterns have structured the current diversity of the region’s biota is important both for our understanding of the factors promoting diversification, as well as the conservation of this biodiversity hotspot. Here we evaluate potential historical scenarios of diversification in the Atlantic Coastal Forest of Brazil by investigating the population genetic structure of a frog endemic to the region. Using mitochondrial and nuclear sequences, we generated a Bayesian popula- tion-level phylogeny of the Thoropa miliaris species complex. We found deep genetic divergences among five geographically distinct clades. Southern clades were monophy- letic and nested within paraphyletic northern clades. Analyses of historical demographic patterns suggest an overall north to south population expansion, likely associated with regional differences in habitat stability during the Pliocene and early Pleistocene. However, genetic structure among southern populations is less pronounced and likely represents more recent vicariant events resulting from Holocenic sea-level oscillations. Our analyses corroborate that the Atlantic Coastal Forest has been a biogeographically dynamic landscape and suggest that the high diversity of its fauna and flora resulted from a combination of climatic and geologic events from the Pliocene to the present. Keywords: glacial refugia, mitochondrial DNA, phylogeography, population expansion, Thoropa miliaris, Thoropa taophora Received 15 July 2008; revision received 20 March 2009; accepted 13 April 2009 Introduction The Atlantic Coastal Forest of Brazil is ranked among the top five biomes in priority for biodiversity conservation, primarily owing to its high levels of endemism, species richness, and high rates of habitat loss (Brown & Brown 1992; Morellato & Haddad 2000; Myers et al. 2000). Compared to other South American biomes, this region has the highest species diversity for its size; its degree of endemism, as high as 90% in some groups and averaging 50% overall, is surpassed only by the Amazon (Costa et al. 2000). The Atlantic Coastal Forest has experienced dra- matic habitat modification and fragmentation and remains under severe anthropogenic pressure, with only 7.3% of primary forest currently intact (Morellato & Haddad 2000). Despite these dramatic losses, researchers continue to discover new species, diverse plant–animal interactions, and novel features of natural history (Costa et al. 2000; Morellato & Haddad 2000; Pizo & Oliveira 2000; Haddad & Prado 2005; Brasileiro et al. 2007a, b, c). However, only a few studies of this megadiverse biome have addressed the evolutionary origins of its biodiversity (Moritz et al. 2000; Carnaval 2002; Pellegrino et al. 2005; Grazziotin et al . 2006; Cabanne et al . 2007; Carnaval & Bates 2007; Carnaval et al. 2009). Correspondence: Sarah W. Fitzpatrick, Fax: (607) 255-8088; E-mail: sf83@cornell.edu Ó 2009 Blackwell Publishing Ltd Molecular Ecology (2009) 18, 2877–2896 doi: 10.1111/j.1365-294X.2009.04245.x