Two models of ancestral area reconstruction were tested using BioGeoBEARS implemented in R 3.1 (51, 55), one considering distributions among nine areas of endemism/interfluvia, following Borges and Silva (8), and another considering four geological areas (33, 34) (Fig. 1). These two models were chosen because distribution of most of the reciprocally monophyletic lineages analyzed can be allocated to areas of endemism previously described for the Amazon region (table S1) (8). However, in some cases, more than one lineage is present within the same area (e.g., H. naevius/Hylophylax naevioides complex) or a single lineage occurs in distinct areas (e.g., X. guttatus), occasionally with a distribution more coincident with the geological division of the AB (33, 34) (e.g., P. carnifex/P. nigricollis). Yet, because estimates based on the interfluvia include a much higher number of possible ancestral areas, they might be more informative (as also demonstrated for other BioGeoBEARS estimates) (55, 56).

For each model of areas, we performed a total of six different analyses including the Dispersal-Extinction Cladogenesis (DEC) model, a likelihood version of the Dispersal-Vicariance Analysis (DIVALIKE), and a version of the Bayesian inference of historical biogeography for discrete areas (BAYAREALIKE), as well as “+J” versions of these three models, which include founder-event speciation, an important process left out of most inference methods (56). These biogeographic processes were implemented in a maximum likelihood (DEC, DEC+J, DIVALIKE, and DIVALIKE+J) or Bayesian (BAYAREALIKE and BAYAREALIKE+J) framework, as free parameters estimated from the data. Our multilocus species trees were used to infer the ancestral area probabilities to each lineage, which were computed for each node and subsequently plotted on the majority-rule chronograms. Outgroups were excluded from analyses to avoid insufficient representation of its diversity in our sampling, which could mislead biogeographic estimates. Last, we compared the six different models for statistical fit via comparison of Log-Likelihood (ln L) and AIC values. Dispersal (d), extinction (e), founder (J), ln L, and AIC values were directly obtained from BioGeoBEARS (results are summarized in table S2).

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