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Background  The tropical Andes and Amazon are among the richest regions of endemism for mammals, and each has given rise to extensive  in situ  radiations. Various animal lineages have radiated  ex situ  after colonizing one of these regions from the other: Amazonian clades of dendrobatid frogs and passerine birds may have Andean ancestry, and transitions from the Amazon to Andes may be even more common. To examine biogeographic transitions between these regions, we investigated the evolutionary history of three clades of rodents in the family Echimyidae: bamboo rats ( Dactylomys-Olallamys-Kannabateomys ), spiny tree-rats ( Mesomys-Lonchothrix ), and brush-tailed rats ( Isothrix ). Each clade is distributed in both the Andes and Amazonia, and is more diverse in the lowlands. We used two mitochondrial (cyt -  b  and 12S) and three nuclear (GHR, vWF, and RAG1) markers to reconstruct their phylogenetic relationships. Tree topologies and ancestral geographic ranges were then used to determine whether Andean forms were basal to or derived from lowland radiations.    Results  Four biogeographic transitions are identified among the generic radiations. The bamboo rat clade unambiguously originated in the Amazon  ca.  9 Ma, followed by either one early transition to the Andes ( Olallamys ) and a later move to the Amazon ( Dactylomys ), or two later shifts to the Andes (one in each genus). The Andean species of both  Dactylomys  and  Isothrix  are sister to their lowland species, raising the possibility that highland forms colonized the Amazon Basin. However, uncertainty in their reconstructed ancestral ranges obscures the origin of these transitions. The lone Andean species of  Mesomys  is confidently nested within the lowland radiation, thereby indicating an Amazon-to-Andes transition  ca.  2 Ma.    Conclusions  Differences in the timing of these biogeographic transitions do not appear to explain the different polarities of these trees. Instead, even within the radiation of a single family, both Andean and Amazonian centers of endemism appear enriched by lineages that originated in the other region. Our survey of other South American lineages suggests a pattern of reciprocal exchange between these regions—among mammals, birds, amphibians, and insects we found no fewer than 87 transitions between the Andes and Amazon from Miocene-Pleistocene. Because no clear trend emerges between the timing and polarity of transitions, or in their relative frequency, we suggest that reciprocal exchange between tropical highland and lowland faunas in South America has been a continual process since  ca.  12 Ma.

Transitions between Andean and Amazonian centers of endemism in the radiation of some arboreal rodents