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 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.

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Geographic isolation and reduced population sizes can lead to local extinction, low efficacy of selection and decreased speciation. However, population differentiation is an essential step of biological diversification. In allopatric speciation, geographically isolated populations differentiate and persist until the evolution of reproductive isolation and ecological divergence completes the speciation process. Pitcairnia flammea allows us to study the evolutionary consequences of habitat fragmentation on naturally disjoint rock-outcrop species from the Brazilian Atlantic Rainforest (BAF). Our main results showed low-to-moderate genetic diversity within populations, and deep population structuring caused by limited gene flow, low connectivity, genetic drift and inbreeding of long-term isolation and persistence of rock-outcrop populations throughout Quaternary climatic oscillations. Bayesian phylogenetic and model-based clustering analyses found no clear northern and southern phylogeographic structure commonly reported for many BAF organisms. Although we found two main lineages diverging by ~2 Mya during the early Pleistocene, species' delimitation analysis assigned most of the populations as independent evolving entities, suggesting an important role of disjoint rock outcrops in promoting high endemism in this rich biome. Lastly, we detected limited gene flow in sympatric populations although some hybridization and introgression were observed, suggesting a continuous speciation process in this species complex. Our data not only inform us about the extensive differentiation and limited gene flow found among Pitcairnia flammea species complex, but they also contain information about the mechanisms that shape the genetic architecture of small and fragmented populations of isolated rock outcrop of recently radiated plants.

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