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More than a hundred hydropower dams have already been built in the Amazon basin and numerous proposals for further dam constructions are under consideration. The accumulated negative environmental effects of existing dams and proposed dams, if constructed, will trigger massive hydrophysical and biotic disturbances that will affect the Amazon basin’s floodplains, estuary and sediment plume. We introduce a Dam Environmental Vulnerability Index to quantify the current and potential impacts of dams in the basin. The scale of foreseeable environmental degradation indicates the need for collective action among nations and states to avoid cumulative, far-reaching impacts. We suggest institutional innovations to assess and avoid the likely impoverishment of Amazon rivers. The current and expected environmental consequences of built dams and proposed dam constructions in the Amazon basin are explored with the help of a Dam Environmental Vulnerability Index. Damming in the Amazon There are already more than 100 hydropower dams in place across the Amazon basin. They are not just a source of energy, but also of on-going contention between developers, government officials, locals and environmentalists. This Perspective explores the current and expected environmental consequences of existing and proposed dams in the Amazon basin, with the help of a Dam Environmental Vulnerability Index (DEVI). The authors quantitatively assess the vulnerability of different regions of the basin, and propose that an integrative legal framework is required to guide all nine stakeholder countries towards minimizing the negative socio-economic and environmental impacts of present and future dams.

Precise characterization of hydroclimate variability in Amazonia on various timescales is critical to understanding the link between climate change and biodiversity. Here we present absolute-dated speleothem oxygen isotope records that characterize hydroclimate variation in western and eastern Amazonia over the past 250 and 20 ka, respectively. Although our records demonstrate the coherent millennial-scale precipitation variability across tropical–subtropical South America, the orbital-scale precipitation variability between western and eastern Amazonia exhibits a quasi-dipole pattern. During the last glacial period, our records imply a modest increase in precipitation amount in western Amazonia but a significant drying in eastern Amazonia, suggesting that higher biodiversity in western Amazonia, contrary to ‘Refugia Hypothesis’, is maintained under relatively stable climatic conditions. In contrast, the glacial–interglacial climatic perturbations might have been instances of loss rather than gain in biodiversity in eastern Amazonia, where forests may have been more susceptible to fragmentation in response to larger swings in hydroclimate. The long-term hydroclimate variability in Amazonia and its influence on biodiversity remain poorly understood. Here, new speleothem oxygen isotope records characterize spatial–temporal changes in precipitation and provide new insights to understanding the west–east contrasting pattern of biodiversity in Amazonia.

Aim: To evaluate the role of historical processes in the evolution of Sclerurus leaftossers by integrating phylogenetic and phylogeographical approaches. Location: Humid forests of the Neotropical region. Methods: We reconstructed the evolutionary history of Sclerurus based on DNA sequences representing all species and 20 of the 26 recognized subspecies using one autosomal nuclear locus and three protein-coding mitochondrial gene sequences. 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 diversification events. Based on these results, we examined the temporal accumulation of divergence events using lineage-through-time plots. Results: The monophyly of all Sclerurus species was strongly supported except for Sclerurus mexicanus, which was paraphyletic in relation to Sclerurus rufigularis, and for the sister pair Sclerurus scansor—Sclerurus albigularis, which were not reciprocally monophyletic in the nuclear tree. We found remarkably deep phylogeographical structure within all Sclerurus species, and overall this structure was congruent with currently recognized subspecies and Neotropical areas of endemism. Diversification within Sclerurus has occurred at a relatively constant rate since the Middle Miocene. Main conclusions: Our results strongly support the relevance of physiographical (e.g. Nicaragua Depression, Isthmus of Panama, Andean Cordillera, great rivers of Amazonia) and ecological barriers (open vegetation corridor) and ecological gradients (elevational zonation) to the diversification of Neotropical forest-dwelling organisms. Despite the high congruence among the spatial patterns identified, the variance in divergence times suggests multiple speciation events occurring independently across the same barrier, and a role for dispersal. The phylogenetic patterns and cryptic diversity uncovered in this study demonstrate that the current taxonomy of Sclerurus underestimates the number of species.

White‐sand vegetation (WSV) harbors a unique avifauna within Amazonia, including species with patchy distributions. The history of these species' populations is likely related to variation in the availability and connectivity among WSV patches though time. By investigating the phylogeographic history of WSV bird species, we aim to better understand the dynamic evolution of forested and open habitats in Amazonia. Here, we perform a phylogeographic analysis of two WSV specialist bird species, a tanager, Tachyphonus phoenicius, and a hummingbird, Polytmus theresiae. We obtained and analyzed sequences of one mitochondrial and one nuclear gene region from 152 individuals. Results indicate that the two species have different histories. Tachyphonus phoenicius split from its Atlantic Forest/Cerrado sister clade at about 11 Ma and includes two divergent lineages, north and south of the Amazon River. Polytmus theresiae split from its Tepuian sister group at about 2.5 Ma and shows no genetic structure within Amazonia. Both lineages of T. phoenicius and P. theresiae show signs of recent population expansion. Although the two WSV species originated at different moments, and show distinct patterns of population structure, both seem to have expanded their population sizes recently, indicating that availability of white‐sand habitats may have been increasing historically and the connectivity among different white‐sand patches may have been higher in the recent past.

Aim: To test the importance of alternative diversification drivers and biogeographical processes for the evolution of Amazonian upland forest birds through a densely sampled analysis of diversification of the endemic Amazonian genus Rhegmatorhina at multiple taxonomic and temporal scales. Location: Amazonia. Taxon: Antbirds (Thamnophilidae). Methods: We sequenced four mtDNA and nuclear gene regions of 120 individuals from 50 localities representing all recognized species and subspecies of the genus. We performed molecular phylogenetic analyses using both gene tree and species tree methods, molecular dating analysis and estimated population demographic history and gene flow. Results: Dense sampling throughout the distribution of Rhegmatorhina revealed that the main Amazonian rivers delimit the geographic distribution of taxa as inferred from mtDNA lineages. Molecular phylogenetic analyses resulted in a strongly supported phylogenetic hypothesis for the genus, with two main clades currently separated by the Madeira River. Molecular dating analysis indicated diversification during the Quaternary. Reconstruction of recent demographic history of populations revealed a trend for population expansion in eastern Amazonia and stability in the west. Estimates of gene flow corroborate the possibility that migration after divergence had some influence on the current patterns of diversity. Main Conclusions: Based on broad-scale sampling, a clarification of taxonomic boundaries, and strongly supported phylogenetic relationships, we confirm that, first, mitochondrial lineages within this upland forest Amazonian bird genus agree with spatial patterns known for decades based on phenotypes, and second, that most lineages are geographically delimited by the large Amazonian rivers. The association between past demographic changes related to palaeoclimatic cycles and the historically varying strength and size of rivers as barriers to dispersal may be the path to the answer to the long-standing question of identifying the main drivers of Amazonian diversification.

Avian malaria is a vector transmitted disease caused by Plasmodium and recent studies suggest that variation in its prevalence across avian hosts is correlated with a variety of ecological traits. Here we examine the relationship between prevalence and diversity of Plasmodium lineages in southeastern Amazonia and: (1) host ecological traits (nest location, nest type, flocking behaviour and diet); (2) density and diversity of avian hosts; (3) abundance and diversity of mosquitoes; and (4) season. We used molecular methods to detect Plasmodium in blood samples from 675 individual birds of 120 species. Based on cytochrome b sequences, we recovered 89 lineages of Plasmodium from 136 infected individuals sampled across seven localities. Plasmodium prevalence was homogeneous over time (dry season and flooding season) and space, but heterogeneous among 51 avian host species. Variation in prevalence among bird species was not explained by avian ecological traits, density of avian hosts, or mosquito abundance. However, Plasmodium lineage diversity was positively correlated with mosquito abundance. Interestingly, our results suggest that avian host traits are less important determinants of Plasmodium prevalence and diversity in southeastern Amazonia than in other regions in which they have been investigated.

To determine the effect of rivers, environmental conditions, and isolation by distance on the distribution of species in Amazonia. Location: Brazilian Amazonia. Time period: Current. Major taxa studied: Birds, fishes, bats, ants, termites, butterflies, ferns + lycophytes, gingers and palms. We compiled a unique dataset of biotic and abiotic information from 822 plots spread over the Brazilian Amazon. We evaluated the effects of environment, geographic distance and dispersal barriers (rivers) on assemblage composition of animal and plant taxa using multivariate techniques and distance- and raw-data-based regression approaches. Environmental variables (soil/water), geographic distance, and rivers were associated with the distribution of most taxa. The wide and relatively old Amazon River tended to determine differences in community composition for most biological groups. Despite this association, environment and geographic distance were generally more important than rivers in explaining the changes in species composition. The results from multi-taxa comparisons suggest that variation in community composition in Amazonia reflects both dispersal limitation (isolation by distance or by large rivers) and the adaptation of species to local environmental conditions. Larger and older river barriers influenced the distribution of species. However, in general this effect is weaker than the effects of environmental gradients or geographical distance at broad scales in Amazonia, but the relative importance of each of these processes varies among biological groups.