Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they have diversified rapidly. Here, we compare signals from DNA sequences with morphological signals using pictures of skulls and computational simulations. Phylogenetic analyses reveal step-wise geographic divergence across the Northern Hemisphere. In Central and South America, tree squirrels form two separate clades, which split from a common ancestor. Simulations of ancestral distributions show western Amazonia as the epicenter of speciation in South America. This finding suggests that wet tropical forests on the foothills of Andes possibly served as refugia of squirrel diversification during Pleistocene climatic oscillations. Comparison of phylogeny and morphology reveals one major discrepancy: Microsciurus species are a single clade morphologically but are polyphyletic genetically. Modeling of morphology-diet relationships shows that the only group of species with a direct link between skull shape and diet are the bark-gleaning insectivorous species of Microsciurus. This finding suggests that the current designation of Microsciurus as a genus is based on convergent ecologically driven changes in morphology.

Department of Botany and Zoology Masaryk University Kotlářská 2 602 00 Brno Czech Republic; Institute of Vertebrate Biology Academy of Sciences of the Czech Republic v v i Květná 8 603 65 Brno Czech Republic; Department of Zoology Stockholm University 10691 Stockholm Sweden; Department of Bioinformatics and Genetics Swedish Museum of Natural History PO Box 50007 10405 Stockholm Sweden;

Institute of Vertebrate Biology Academy of Sciences of the Czech Republic v v i Květná 8 603 65 Brno Czech Republic; Institute of Biostatistics and Analyses Masaryk University Kamenice 3 625 00 Brno Czech Republic

Institute of Vertebrate Biology Academy of Sciences of the Czech Republic v v i Květná 8 603 65 Brno Czech Republic; Institute of Fundamental Sciences Massey University Private Bag 11 222 Palmerston North New Zealand; and

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