The Amazon is the primary source of Neotropical diversity and a nexus for discussions on processes that drive biotic diversification. Biogeographers have focused on the roles of rivers and Pleistocene climate change in explaining high rates of speciation. We combine phylogeographic and niche-based paleodistributional projections for 23 upland terra firme forest bird lineages from across the Amazon to derive a new model of regional biological diversification. We found that climate-driven refugial dynamics interact with dynamic riverine barriers to produce a dominant pattern: Older lineages in the wetter western and northern parts of the Amazon gave rise to lineages in the drier southern and eastern parts. This climate/drainage basin evolution interaction links landscape dynamics with biotic diversification and explains the east-west diversity gradients across the Amazon.

Aim  We examined patterns of spatial and temporal diversification of the Amazonian endemic chestnut‐tailed antbird, Mymeciza hemimelaena (Thamnophilidae), to evaluate the diversification of a widespread avian taxon across rivers that potentially represent major natural barriers. Location  Lowland Amazonia. Methods  Sequences of the mitochondrial ND2 and cytochrome b genes were investigated from 65 individuals distributed throughout the entire range of M. hemimelaena, and including the two currently valid subspecies M. h. hemimelaena and M. h. pallens. Based on a combination of phylogeographic tools, molecular dating, and population genetic methods, we reconstructed a spatio‐temporal scenario of diversification of M. hemimelaena in the Amazon. Results  The data revealed three genetically divergent and monophyletic groups in M. hemimelaena, which can also be distinguished by a combination of morphological and vocal characters. Two of these clades correspond to the previously described taxa M. h. hemimelaena and M. h. pallens, which are separated by the upper Madeira River, a main Amazonian tributary. The third clade is distributed between the middle reaches of the Madeira River and the much smaller tributaries Jiparaná and Aripuanã, and, although currently treated as M. h. pallens, clearly constitutes an independent evolutionary lineage probably deserving separate species status. Molecular clock and population genetic analyses indicate that diversification in this group occurred throughout the Pleistocene, with demographic fluctuations assumed for M. h. hemimelaena and M. h. pallens. Main  conclusions  The findings implicate rivers as barriers driving diversification in the M. hemimelaena complex. Levels of mitochondrial DNA divergence and associated morphological and vocal traits support its division into at least three separate species with comparatively small ranges. The existence of a previously unrecognized lineage in the M. hemimelaena complex, and the high degree of population structuring found in M. h. hemimelaena underscore the pervasiveness of cryptic endemism throughout Amazonia and the importance of DNA‐based taxonomic and phylogeographic studies in providing the accurate estimates of diversity that are essential for conservation planning.

Aim To investigate the role of historical processes in the evolution of the spotbacked antbird species complex Hylophylax naevius/Hylophylax naevioides (Aves, Thamnophilidae).Location Throughout the Amazon Basin and across the Andes in Central and northern South America.Methods We investigated the evolutionary history of the H. naevius/H. naevioides complex based on a total of 100 individuals from opposite banks of the major Amazonian rivers and both sides of the Andes. Nucleotide sequences from two mitochondrial DNA genes [1015 bp of cytochrome b (cyt b) and 1023 bp of NADH dehydrogenase subunit 2 (ND2)] and one nuclear marker [539 bp of intron 5 of the b-fibrinogen (BF5)] were obtained. Phylogenetic relationships were inferred using Bayesian and maximum likelihood methods. We used Bayesian coalescent-based approaches to evaluate demographic changes through time, and to estimate the timing of the diversification events.Results Well-supported allopatric and parapatric lineages were recovered within the H. naevius/H. naevioides complex, with high levels of genetic differentiation, both on opposite sides of rivers (0.6-7.1%) and across the Andes (6.9%). Molecular dating and population demography suggest cladogenesis in various periods, associated with distinct vicariance and dispersal events.Main conclusions Our data support the hypothesis that the uplift of the northern Andes and the consolidation of the modern Amazon drainage system were key to promoting the diversification of forest-dwelling bird lineages in the northern Neotropics.