Timetree and biogeographic reconstruction for species of arboreal spiny rats. Geographic ranges are coded as Amazon (green tree), Andes (brown mountain), or Atlantic Forest (blue tree). Divergence time estimates at nodes are means (black) with error bars (light gray; 95% HPD) above posterior probabilities for given relationships (dark gray), and were pruned from the Bayesian relaxed clock analyses of all taxa and 5 genes (cyt-b + 12S rRNA + GHR + vWF + RAG1). Ancestral geographic ranges are estimated using maximum likelihood in Lagrange. Pie chart(s) represent the relative probability that the ancestors of each daughter branch occupied a given region immediately after speciation. Branches are colored to correspond with ancestral ranges of > 75% probability; gray branches are uncertain ancestral ranges, and dashed branches indicate inferred dispersal along a branch. Andes-Amazon transitions (T1–T4) are marked along the branches preceding a transition, and represent instances of either dispersal or vicariance from stem ancestors to descendant taxa (see Table 4 for additional details). Transitions T2a and T3a should be compared to the alternative topologies in Figure 5. Some transitions might have occurred along the branch of the [i] stem ancestor, [ii] two branches back, or [iii] three branches back. The timing of all geological epochs is from Gradstein et al. .
Upham et al. BMC Evolutionary Biology 2013 13:191 doi:10.1186/1471-2148-13-191