Table 1. Summary of the predictions of each hypothesis and overview of the methods used to test them (*Diversification any time subsequent to the formation of the Amazon river (5–12 mya) would be consistent with the riverine barrier hypothesis, therefore only diversification prior to 12 mya would falsify this prediction; we chose not to use this as a test of the riverine barrier hypothesis because it is nearly impossible to reject for these species, which originated no more than 14 mya [81].).

Predictions	Pleistocene refugia	Marine incursion	Riverine barrier	Methods used
Reciprocal monophyly of populations:	in different refugia	in Eastern base of Andes, Brazilian Shield, and/or Guiana Shield	on opposite banks of Amazon River	Parametric bootstrap, Bayesian hypothesis tests
Basal populations are located:	in refugia	in Eastern base of Andes, Brazilian Shield, and/or Guiana Shield	N/A	ML and Bayesian gene tree reconstruction
Derived populations are located:	outside refugia	in Amazonian lowlands	N/A	ML and Bayesian gene tree reconstruction
Barrier to gene flow:	areas between refugia	Amazonian lowlands	Amazon River	AMOVA, Mantel tests
Population history includes:	bottlenecks and expansion	bottlenecks and expansion	N/A	Mismatch distributions, Tajima's D
Population structure formed:	during Pleistocene (10 kya–1.8 mya)	during Miocene (10–15 mya)	N/A*	IM