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Amazonian environments are being degraded by modern industrial and agricultural activities at a pace far above anything previously known, imperiling its vast biodiversity reserves and globally important ecosystem services. The most substantial threats come from regional deforestation, because of export market demands, and global climate change. The Amazon is currently perched to transition rapidly from a largely forested to a nonforested landscape. These changes are happening much too rapidly for Amazonian species, peoples, and ecosystems to respond adaptively. Policies to prevent the worst outcomes are known and must be enacted immediately. We now need political will and leadership to act on this information. To fail the Amazon is to fail the biosphere, and we fail to act at our peril.

Alpha taxonomy endeavours to propose a coherent vision of existing species and, simultaneously, to individualize the natural entities useful to understand evolutionary processes. This ideal is especially difficult when available data lack congruence. Here we address the polytypic species Synallaxis rutilans (ruddy spinetail), a suboscine passerine widely distributed in the Amazon Basin and whose taxonomy could, potentially, aid our understanding of processes shaping its biodiversity. Combining genetic [genomic ultraconserved elements (UCE) and mtDNA] and morphological data, we demonstrate that while delimitation of genetic lineages and their phylogenetic relationships are strongly associated with classic Amazonian geographic barriers, such as rivers, different coloration patterns appear to be more associated with local selection processes for phenotype. Employing an evolutionary approach, whereby the species is considered a taxonomic category, rather than a nomenclatural rank, we propose to recognize five species: S. amazonica, S. caquetensis, S. dissors, S. omissa and S. rutilans. The taxonomic arrangement proposed here permits better understanding of the similarities and differences among taxa from different areas of endemism, and represents patterns of genetic and morphological diversity resulting from distinct processes acting across certain time frames. This arrangement draws attention to the importance of understanding the evolutionary processes operating in the complex and constantly changing Amazonian landscape.

Aim Amazonian floodplains include distinct types of seasonally flooded habitats, determined by the flooding regime and sedimentation dynamics. Some bird species prefer specific habitat types within the floodplains. To investigate whether distinct habitats are differentially affected by geologic and climatic history, we compare population history in a sympatric and closely related pair of ovenbird species with different habitat associations. Location Amazonian floodplains. Taxa Synallaxis albigularis and Mazaria propinqua (Aves; Furnariidae). Methods Occurrence records were obtained from museums and public databases. Genomic data included nuclear loci (UCE) and the mitogenome for 49 samples. SNPs from UCE data were used to infer population genetic structure and effective migration. Mitogenomes were used to build phylogenetic trees and chronograms. Both datasets were used to infer historical demographic changes and test demographic scenarios. Results S. albigularis includes geographically structured mtDNA clades with a crown age of 250 ka, whereas M. propinqua includes a single clade with a crown age of 38 ka. Effective migration is lower at the base of the Andes for S. albigularis and at the lower Negro River for M. propinqua. Population expansion is detected for both species during the Quaternary, but was steeper and more recent in M. propinqua. Main conclusions The differences in population histories relate to distinct habitat associations along Amazonian floodplains. Preference of M. propinqua for more ephemeral island habitats may favour local extinctions, leading to demographic change, low genetic variability, no population structure and smaller effective population size. In contrast, more resilient habitats along the floodplains inhabited by S. albigularis may sustain local populations, generating and maintaining local diversity. Our results suggest that climatic variations of the late Pleistocene and Holocene caused changes in distribution and connectivity of the different types of habitats along the Amazonian floodplains, affecting gene flow and population sizes of associated bird populations.

Aim Ecological, climatic and palaeogeographical processes drive biological diversification. However, the evolutionary outcomes of those mechanisms are complex and difficult to discriminate. Here, we test how alternative drivers affected connectivity along the Amazonian floodplains generating current patterns of population structure and diversity within the Striped Woodcreeper, a widespread bird species tied to forests seasonally flooded by Amazonian rivers. Location Amazonian floodplains. Taxon Xiphorhynchus obsoletus (Aves, Furnariidae). Methods We sequenced 2213 loci of ultraconserved elements (UCEs) and 20 exons to investigate patterns of genetic structure and connectivity across the Striped Woodcreeper distribution, using a set of spatially explicit methods. Population genetics statistics were calculated for each sampled drainage and within each identified cluster. We tested alternative evolutionary scenarios and estimated past and current demographic parameters implementing a simulation-based framework. Results Three genetic clusters with high admixture proportions were identified. These clusters are distributed in the western, central and eastern parts of the Amazon Basin and are not correlated with different river water types representing ecological gradients along the floodplains. Instead, migration rates indicate two putative historical barriers along the main channel of the Amazonas-Solimoes River. Demographic model tests suggest a process of sequential differentiation, partitioned across the Amazon Basin, with stable population sizes and continuous gene flow. Main conclusion Our results support the hypothesis that late Quaternary changes in connectivity between the eastern and western Amazonian drainages were responsible for driving genetic differentiation in the Striped Woodcreeper. Genomic differentiation occurred in the presence of long-term gene flow throughout the X. obsoletus distribution, suggesting some degree of continuous historical connectivity across Amazonian floodplains. Compared to previous studies, our results suggest that although connectivity among populations of Amazonian bird species specialized in floodplain habitats varies in response to the same abiotic mechanisms, species-specific differences in habitat use may be a strong predictor of population divergence.

Context Amazonian white-sand ecosystems (campinas) are open vegetation patches which form a natural island-like system in a matrix of tropical rainforest. Due to a clear distinction from the surrounding matrix, the spatial characteristics of campina patches may affect the genetic diversity and composition of their specialized organisms, such as the small and endemic passerine Elaenia ruficeps. Objectives To estimate the relative contribution of the current extension, configuration and geographical context of campina patches to the patterns of genetic diversity and population structure of E. ruficeps. Methods We sampled individuals of E. ruficeps from three landscapes in central Amazonia with contrasting campina spatial distribution, from landscapes with large and connected patches to landscapes with small and isolated patches. We estimated population structure, genetic diversity, and contemporary and historical migration within and among the three landscapes and used landscape metrics as predictor variables. Furthermore, we estimated genetic isolation by distance and resistance within landscapes. Results We identified three genetically distinct populations with asymmetrical gene flow among landscapes and a decreasing migration rate with distance. Within each landscape, we found low differentiation without genetic isolation by distance nor by resistance. In contrast, we found differentiation and spatial correlation between landscapes. Conclusions Together with previous studies, the population dynamics of E. ruficeps suggests that both regional context and landscape structure shape the connectivity among populations of campina specialist birds. Also, the spatial distribution of Amazonian landscapes, together with their associated biota, has changed in response to climatic changes in the Late Pleistocene.

Aim Neotropical savanna birds occur north and south of, but mostly not in the Amazon Basin, except for a few isolated savanna patches. Here, we investigate the phylogeography of 23 taxa of Neotropical savanna birds co-distributed across multiple isolated savanna patches to assess to what extent these species have a shared history of spatial diversification. We explore the role of the forested Amazon Basin as a vicariant barrier separating northern and southern populations, particularly focusing on the role of the coastal savannas of Amapa as a potential corridor of gene flow between northern and southern populations. Location Neotropical savannas. Taxon Aves. Method We employ 775 mtDNA samples of 24 co-distributed savanna bird taxa from all major savanna patches in South America to infer phylogeographic patterns. For this purpose, we use 24 genomic samples (UCEs) of a subset of 12 taxa in addition to the mtDNA samples to estimate timing of divergence across the Amazon Basin. We use phylogeographic concordance factors (PCF) to assess the level of phylogeographic congruence across co-distributed taxa. Finally, we assess to which level physical distance drives genetic structuring by estimating isolation-by-distance (IBD) effects. Results We find that although the study taxa generally do not share similar diversification patterns geographically, many have at least two distinct genetic groups, one north and one south of the Amazon Basin, that have only recently diverged. The timing of divergence between both areas is generally centered in the late Pleistocene, but somewhat variable, indicating there is no single vicariant event responsible for driving diversification. Main conclusions Variability in divergence times indicates that landscape processes have not led to shared phylogeographic responses, which indicates a relatively minor role for vicariance. Shallow divergences suggest that Neotropical grassland habitats may have recently been more connected or that gene flow has played an important role. We did not find evidence of a single dominant corridor of dispersal between savannas north and south of the forested Amazon Basin.

The effect of large Amazonian rivers as barriers to distribution of species and gene flow has been the subject of debate for more than a century. The Madeira River is the largest tributary of the Amazon River, with the region comprising its basin undergoing complex changes from the Pliocene through the Holocene. Accordingly, the evolution of its drainage seems to have been an important factor in the biological diversification of different taxa. We characterize the phylogeographic pattern of Adelphobates quinquevittatus, focusing on the role of the Madeira River and the environmental changes in the region, as potential barriers to gene flow. For this, we used sequences of two mitochondrial genes from 65 individuals sampled in 15 locations. We identify population structure partially related to the current Madeira River configuration. However the most upstream session does not represent a historical barrier, suggesting that may have attained its current geomorphological configuration recently. Divergence among clades began in the last 1 million years, coinciding with documented changes in this landscape, and may be related to river dynamics associated with the presence of open vegetation areas. This phylogeographic pattern supports the dynamism of the drainage, and the historical complexity of the upper Madeira River.

La biota de la Amazonía se ha producido durante millones de años, a través de una combinación diná-mica de procesos geológicos, climáticos y evolutivos. Su singular historia produjo paisajes heterogé-neos en múltiples escalas geográficas, generó hábitats diversos, alteró las conexiones geográficas y genéticas entre las poblaciones e impactó las tasas de adaptación, especiación y extinción. Su biota ecológicamente diversa, a su vez, promovió una mayor diversificación, la coexistencia de especies y la coevolución, aumentando la biodiversidad con el tiempo.

A major barrier to advancing ornithology is the systemic exclusion of professionals from the Global South. A recent special feature, Advances in Neotropical Ornithology, and a shortfalls analysis therein, unintentionally followed a long-standing pattern of highlighting individuals, knowledge, and views from the Global North, while largely omitting the perspectives of people based within the Neotropics. Here, we review current strengths and opportunities in the practice of Neotropical ornithology. Further, we discuss problems with assessing the state of Neotropical ornithology through a northern lens, including discovery narratives, incomplete (and biased) understanding of history and advances, and the promotion of agendas that, while currently popular in the north, may not fit the needs and realities of Neotropical research. We argue that future advances in Neotropical ornithology will critically depend on identifying and addressing the systemic barriers that hold back ornithologists who live and work in the Neotropics: unreliable and limited funding, exclusion from international research leadership, restricted dissemination of knowledge (e.g., through language hegemony and citation bias), and logistical barriers. Moving forward, we must examine and acknowledge the colonial roots of our discipline, and explicitly promote anti-colonial agendas for research, training, and conservation. We invite our colleagues within and beyond the Neotropics to join us in creating new models of governance that establish research priorities with vigorous participation of ornithologists and communities within the Neotropical region. To include a diversity of perspectives, we must systemically address discrimination and bias rooted in the socioeconomic class system, anti-Blackness, anti-Brownness, anti-Indigeneity, misogyny, homophobia, tokenism, and ableism. Instead of seeking individual excellence and rewarding top-down leadership, institutions in the North and South can promote collective leadership. In adopting these approaches, we, ornithologists, will join a community of researchers across academia building new paradigms that can reconcile our relationships and transform science. Spanish and Portuguese translations are available in the Supplementary Material.

The extent and intensity of impacts of multiple new dams in the Amazon basin on specific biological groups are potentially large, but still uncertain and need to be better understood. It is known that river disruption and regulation by dams may affect sediment supplies, river channel migration, floodplain dynamics, and, as a major adverse consequence, are likely to decrease or even suppress ecological connectivity among populations of aquatic organisms and organisms dependent upon seasonally flooded environments. This article complements our previous results by assessing the relationships between dams, our Dam Environmental Vulnerability Index (DEVI), and the biotic environments threatened by the effects of dams. Because of the cartographic representation of DEVI, it is a useful tool to compare the potential hydrophysical impacts of proposed dams in the Amazon basin with the spatial distribution of biological diversity. As the impact of Amazonian dams on the biota of both rivers and periodically flooded riparian environments is severe, DEVIs from different Amazonian tributary basins are contrasted with patterns of diversity and distribution of fish, flooded forest trees and bird species. There is a consistent relationship between higher DEVI values and the patterns of higher species richness and endemism in all three biological groups. An assessment of vulnerability at the scale of tributary basins, the assessment of biodiversity patterns related to DEVI, and the analysis of teleconnections at basin scale, demonstrate that recent construction of dams is affecting the biota of the Amazon basin. The evidence presented here predicts that, if currently planned dams are built without considering the balance between energy production and environmental conservation, their cumulative effects will increase drastically and represent a major threat to Amazonian biodiversity. Nanyang Technological University Published version This research was supported partially by the Council for Scientific and Technological Development-CNPq, CAPES Foundation, and the Earth Observatory of Singapore.

Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally-dry forests. We use genomic, phenotypic and habitat heterogeneity data coupled with climatic niche modelling. Results suggest the evolutionary history of the species is mainly related to paleoclimatic changes, although changes in the strength of the Amazon river as a barrier to dispersal, current habitat heterogeneity and geographic distance were also relevant. We propose an ancestral distribution in the Guyana Shield, and recent colonization of areas south of the Amazon river at ~380 to 166 kya, and expansion of the distribution to southern Amazonia, Cerrado and the Atlantic Forest. Since then, populations south of the Amazon River have been subjected to cycles of isolation and possibly secondary contact due to climatic changes that affected habitat heterogeneity and population connectivity. Most Amazonian rivers are not associated with long lasting isolation of populations, but some might act as secondary barriers, susceptible to crossing under specific climatic conditions. Morphological variation, while stable in some parts of the distribution, is not a reliable indicator of genetic structure or phylogenetic relationships.

Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river-barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide markers to evaluate histories of divergence and introgression in six Amazonian avian species-complexes. We first tested the assumption that rivers are barriers for these taxa and found that even relatively small rivers facilitate divergence. We then tested whether species diverged with gene flow and recovered reticulate histories for all species, including one potential case of hybrid speciation. Our results support the hypothesis that river dynamics promote speciation and reveal that many rainforest taxa are micro-endemic, unrecognized and thus threatened with imminent extinction. We propose that Amazonian hyper-diversity originates in part from fine-scale barrier displacement processes –including river dynamics– which allow small populations to differentiate and disperse into secondary contact.

This chapter reviews the evolutionary history of the Amazon’s terrestrial and riverine ecosystems, involving geological and climatic events operating over millions of years and across the whole of continental South America. The chapter discusses the important roles of geographic barriers, habitat heterogeneity, climate change, and species interactions in generating and maintaining the most biodiverse ecosystems on Earth. This unique history produced heterogeneous environments and diverse habitats at multiple geographic scales, which altered the connections between populations and allowed for the accumulation of the most diverse biota on Earth.

AimWe tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene.LocationSolimoes River, Western Amazon, South AmericaTaxonMyrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilisMethods: We analyzed thousands of UltraConserved Elements to explore spatial patterns of genetic diversity and connectivity between individuals. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species in order to test if the occupation of dynamic habitats could predict spatial patterns of genetic diversity.ResultsOur study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space.Main conclusionsOur results suggest that demographic expansions along the Solimões River might be linked to geographic homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

We assessed population structure and the spatio‐temporal pattern of diversification in the Glossy Antshrike Sakesphorus luctuosus (Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. By targeting ultraconserved elements (UCEs) from 32 specimens of S. luctuosus, we identified independent lineages and estimated their differentiation, divergence times, and migration rates. We also estimated current and past demographic histories for each recovered lineage. We found evidence confirming that S. luctuosus consists of a single species, comprising at least four populations, with some highly admixed individuals and overall similar levels of migration between populations. We confirmed the differentiation of the Araguaia River basin population (S. l. araguayae) and gathered circumstantial evidence indicating that the taxon S. hagmanni may represent a highly introgressed population between three distinct phylogroups of S. luctuosus. Divergences between populations occurred during the last 1.2 mya. Signs of population expansions were detected for populations attributed to subspecies S. l. luctuosus, but not for the S. l. araguayae population. Our results support that S. luctuosus has had a complex population history, resulting from a high dependence on southeastern “clear water” seasonally flooded habitats and their availability through time. Spatial and demographic expansions toward the western “white water” flooded forests might be related to recent changes in connectivity and availability of these habitats. Our study reinforces the view that isolation due to absence of suitable habitat has been an important driver of population differentiation within Amazonian flooded forests, but also that differences between várzeas (“white water” floodplains, mostly in southwestern Amazonia) and igapós (“clear water” floodplains, especially located in the east) should be further explored as drivers of micro‐evolution for terrestrial species., We assessed population structure and the spatio‐temporal pattern of diversification in the Glossy Antshrike Sakesphorus luctuosus (Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. We found evidence confirming that S. luctuosus consists of a single species, comprising at least four populations, with some highly admixed individuals and similar levels of migration between populations. Our study reinforces the view that isolation due to absence of suitable habitat has been an important driver of population differentiation within Amazonian flooded forests, but also that differences between várzeas (“white water” floodplains, mostly in southwestern Amazonia) and igapós (“clear water” floodplains, especially located in the east) should be further explored as powerful drivers of micro‐evolution.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO’s virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.

Although the expansion of open vegetation within Amazonia was the basis for the Forest Refugia hypothesis, studies of Amazonian biota diversification have focussed mostly on forest taxa. Here we compare the phylogeographic patterns and population history of two sister species associated with Amazonian open-vegetation patches, Elaenia cristata and Elaenia ruficeps (Aves: Tyrannidae). We sampled individuals across Amazonia for both species, and in the central Brazilian savannas (Cerrado) for E. cristata. We sequenced one mitochondrial (ND2) and two nuclear (BFib7 and ACO) markers. We tested for population structure, estimated migration rates and elucidated the historical demography of each species. The Amazon River is the strongest barrier for E. ruficeps and the Branco River is a secondary barrier. For the more broadly distributed E. cristata, there was no discernible population structure. Both species attained their current genetic diversity recently and E. cristata has undergone demographic expansion since the Last Glacial Maximum, The results suggest distinct effects of recent landscape change on population history for the two species. E. ruficeps, which only occurs in Amazonian white sand habitats, has been more isolated in open-vegetation patches than E. cristata, which occupies Amazonian savannas, and extends into the Central Brazilian Cerrado.

Several bird taxa have been recently described or elevated to full species and almost twice as many bird species than are currently recognized may exist. Defining species is one of the most basic and important issues in biological science because unknown or poorly defined species hamper subsequent studies. Here, we evaluate the species limits and evolutionary history of Tunchiornis ochraceiceps-a widespread forest songbird that occurs in the lowlands of Central America, Choco and Amazonia-using an integrative approach that includes plumage coloration, morphometrics, vocalization and genomic data. The species has a relatively old crown age (~9 Ma) and comprises several lineages with little, if any, evidence of gene flow among them. We propose a taxonomic arrangement composed of four species, three with a plumage coloration diagnosis and one deeply divergent cryptic species. Most of the remaining lineages have variable but unfixed phenotypic characters despite their relatively old origin. This decoupling of genomic and phenotypic differentiation reveals a remarkable case of phenotypic conservatism, possibly due to strict habitat association. Lineages are geographically delimited by the main Amazonian rivers and the Andes, a pattern observed in studies of other understory upland forest Neotropical birds, although phylogenetic relationships and divergence times among populations are idiosyncratic.

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.

Amazonian rivers have been proposed to act as geographic barriers to species dispersal, either driving allopatric speciation or defining current distribution limits. The strength of the barrier varies according to the species’ ecological characteristics and the river's physical properties. Environmental heterogeneity may also drive compositional changes but has not been well assessed in Amazonia. Aiming to understand the contributions of riverine barriers and environmental heterogeneity in shaping compositional changes in Amazonian forest bird assemblages, we focus on the Tapajós River. We investigate how spatial variation in species composition is related to physical barriers (Tapajós and Jamanxim rivers), species’ ecological characteristics (distinct guilds), and environmental heterogeneity (canopy reflectance, soils, and elevation). We sampled birds through point-counts and mist nets on both banks of the Tapajós and Jamanxim rivers. To test for relationships between bird composition and environmental data, we used Mantel and partial Mantel tests, NMDS, and ANOVA + Tukey HSD. The Mantel tests showed that the clearest compositional changes occurred across the Tapajós River, which seems to act unequally as a significant barrier to the bird guilds. The Jamanxim River was not associated with differences in bird communities. Our results reinforce that the Tapajós River is a biogeographical boundary for birds, while environmental heterogeneity influences compositional variation within interfluves. We discuss the combined influence of geographical barriers, environmental heterogeneity, and ecological characteristics of species in shaping species distributions and community composition and the complexity of extrapolating the patterns found for birds to other Amazonian organisms. Abstract in Portuguese is available with online material.

The complex landscape history of the Neotropics has generated opportunities for population isolation and diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow reveals a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last ~2.5 Ma.

The Amazon basin region, which harbors the largest river system in the world, and which is drained by the Amazon River, has experienced several geomorphological and climatic changes over time. These shifts, as we know, led to distinct signatures in the abiotic variables and the diversification patterns of its native biota. One excellent and yet still understudied model system for biogeographic studies relating biotic diversification to landscape evolution in this region is the Tapajos River basin. Located in an ecotonal zone marked by the presence of geomorphological, climatic and biotic gradients, the basin is crossed by the geographical barrier determined by the Tapajos River, one of the large southern tributaries of the Amazon River. The basin is also marked by high diversity of amphibians and reptiles, with distinct assemblages across its extent and riverbanks. We compare the landscape dynamics within the middle Tapajos River region and the whole basin with a comparison of molecular diversification patterns across 16 taxa of amphibians and lizards. For that, we analyze spatial and temporal congruence in diversification through Bayesian gene trees, inter-bank genetic p-distances, and molecular dating based on novel mtDNA data. We find that most groups present spatial diversification patterns concordant with the current position of the Tapajos River, showing high genetic distance between banks. We recovered a continuous range of riverine-associated divergence times, which we group in three main time periods for discussion purposes: (1) ancient divergences, dating from the middle Miocene (ca. 10 Ma); (2) divergences in the late Miocene-Pliocene (ca. 5–3.5 Ma), and (3) more recent divergences, dating to Pleistocene (ca. 2–1 Ma). These results are consistent with a hypothesis of high landscape dynamism in the Tapajos River basin over time, leading to multiple vicariance or colonization events, but cannot be used to discard alternative hypotheses, such as that the river or basin represent areas of secondary contact only. Based on literature and new molecular data, we discuss the evolution of the landscape of the Tapajos River basin and its impact on the diversification of different taxonomic and functional groups.

We identify key interdisciplinary questions and approaches to understanding the paleogeographic and biotic history of Amazonia. We discuss the importance of comparing evolutionary taxonomic units across groups and considering their particular environmental affinities as a framework for a mechanistic understanding of how the diversity of Amazonia was assembled across space and time. Although lineage diversity of the Amazonian biota is often quite old, current evidence indicates that much of Amazonia’s observed “species-level” diversity, as exemplified by birds, mammals, and butterflies, is young, mostly dating to the Quaternary. Much of the modern Amazonian landscape, including in particular its hydrological and environmental systems, was shaped over the Pliocene and Quaternary (last 5 Ma), yet significant landscape change affecting the evolution of biotas is less than 2 million years old.

Jacamar species occur throughout Amazonia, with most species occupying forested habitats. One species-complex, Galbula leucogastra/chalcothorax, is associated to white sand ecosystems (WSE). Previous studies of WSE bird species recovered shallow genetic structure in mtDNA coupled with signs of gene flow among WSE patches. Here, we characterize diversification of the G. leucogastra/chalcothorax species-complex with dense sampling across its distribution using mitochondrial and genomic (Ultraconserved Elements, UCEs) DNA sequences. We performed concatenated likelihood and Bayesian analysis, as well as a species-tree analysis using ∗BEAST, to establish the phylogenetic relationships among populations. The mtDNA results recovered at least six geographically-structured lineages, with G. chalcothorax embedded within lineages of G. leucogastra. In contrast, both concatenated and species-tree analyses of UCE data recovered G. chalcothorax as sister to all G. leucogastra lineages. We hypothesize that the mitochondrial genome of one of the G. leucogastra lineage (Madeira) was captured into G. chalcothorax in the past. We discuss how WSE evolution and the coevolution of mtDNA and nuclear genes might have played a role in this apparently rare event.

Several biogeographic hypotheses have been proposed to explain connections between Amazonian and Atlantic forest biotas. These hypotheses are related to the timing of the connections and their geographic patterns. We performed a phylogeographic investigation of Tyrant-manakins (Aves: Pipridae, Neopelma/Tyranneutes) which include species inhabiting the Amazon and Atlantic forests, as well as gallery forests of the Cerrado. Using DNA sequence data, we determined phylogenetic relationships, temporal and geographic patterns of diversification, and recent intraspecific population genetic patterns, relative to the history of these biomes. We found Neopelma to be a paraphyletic genus, as N. chrysolophum is sister to Neopelma + Tyranneutes, with an estimated divergence of approximately 18 Myrs BP, within the oldest estimated divergence times of other Amazonian and Atlantic forest avian taxa. Subsequent divergences in the group occurred from Mid Miocene to Early Pliocene and involved mainly the Amazonian species, with an expansion into and subsequent speciation in the Cerrado gallery forests by N. pallescens. We found additional structure within N. chrysocephalum and N. sulphureiventer. Analysis of recent population dynamics in N. chrysocephalum, N. sulphureiventer, and N. pallescens revealed recent demographic fluctuations and restrictions to gene flow related to environmental changes since the last glacial cycle. No genetic structure was detected across the Amazon River in N. pallescens. The tyrant-manakins represent an old historical connection between the Amazon and Atlantic Forest.

The Pantepui region harbors one of the most distinctive endemic montane bird faunas in the Neotropics, and is located across the tepuis of northern South America. We made an extensive literature review to understand large-scale distribution patterns of birds in the Pantepui. The core avifauna of the tepuis is composed of 138 bird species, most forest-dwelling insectivores, of which 43 are endemic. In addition, 167 subspecies of birds are endemic to these mountains. The number of endemic species peaks between 1251 and 2000 m, whereas the diversity of non-endemic species is highest between 751 and 1000 m. A high proportion (28%) of endemic taxa (species plus subspecies) is restricted to a single mountain. Tepuis are distributed along a longitudinal gradient, and bird species compositions of mountains located in the eastern and western portion of this gradient are clearly differentiated. Maximum altitude of the mountains and their distance from the Andes are the best predictors of species richness and composition across the Pantepui. Also, bird species composition at site level exhibits significant nested patterns which are affected by maximum altitude, isolation and geographic position of the mountains. The unique bird assemblage of the Pantepui area of endemism is structured through a combination of the spatial distribution of the mountains, habitat diversity, and complex historical events.

Beginning in November 2018, Brazilian legislation regulating access to genetic heritage and associated traditional knowledge will cause a bureaucratic collapse of Biodiversity research in Brazil. Law number 13.123/2015 and Decree 8772/2016 impose severe barriers to basic and applied research, and to international cooperation by introducing mandatory registry of research access to native organisms in Brazil. This legal framework was meant to improve governmental control over systems of biotechnology research using genetic material and associated chemical compounds, which are central points of the Nagoya Protocol (CBD 2011) and the Convention on Biological Diversity (CBD 1992, 2012). However, the requirements imposed by the mandatory registry of research in the new National System for Governance of Genetic Heritage and Associated Traditional Knowledge (SisGen), the system of Material Transfer Agreements (MTAs), and the need to record access to organismal data prior to publication of scientific results or exportation of specimens for scientific research are technically impracticable and not part of the Nagoya Protocol or CBD ..

The ecological traits of organisms may predict their genetic diversity and population genetic structure and mediate the action of evolutionary processes important for speciation and adaptation. Making these ecological-evolutionary links is difficult because it requires comparable genetic estimates from many species with differing ecologies. In Amazonian birds, habitat association is an important component of ecological diversity. Here, we examine the link between habitat association and genetic parameters using 20 pairs of closely related Amazonian bird species in which one member of the pair occurs primarily in forest edge and floodplains and the other occurs in upland forest interior. We use standardized geographic sampling and data from 2,416 genomic markers to estimate genetic diversity, population genetic structure, and statistics reflecting demographic and evolutionary processes. We find that species of upland forest have greater genetic diversity and divergence across the landscape as well as signatures of older histories and less gene flow than floodplain species. Our results reveal that species ecology in the form of habitat association is an important predictor of genetic diversity and population divergence and suggest that differences in diversity between floodplain and upland avifaunas in the Amazon may be driven by differences in the demographic and evolutionary processes at work in the two habitats.

A revision of the avian Neotropical genus Automolus and the Furnariidae family points to the paraphyly of A. infuscatus and reveals a species complex comprising A. infuscatus, A. ochrolaemus, A. paraensis, A. leucophthalmus, A. lammi and A. subulatus, the latter historically classified in the genus Hyloctistes. Detailed knowledge of the taxonomy, geographic distribution, phylogenetic relationship and divergence times of a taxon allows exploration of its evolutionary history and the testing of different scenarios of diversification. In this context, we studied the A. infuscatus complex using molecular data in order to unveil its cryptic diversity and reveal its evolutionary history. For that we sequenced two mitochondrial (ND2 and cytb) and three nuclear markers (G3PDH, ACO, Fib7) for 302 individuals belonging to all species in the complex and most described subspecies. Our analysis supports the paraphyly of A. infuscatus, indicating the existence of at least two distinct clades not closely related. The remaining species were all recovered as monophyletic. Notwithstanding, a well-structured intraspecific diversity was found with 19 lineages suggesting substantial cryptic diversity within the described species. A. subulatus was recovered within the complex, corroborating its position inside the genus. In spite of the high congruence between distributions of different lineages, with several sister lineages currently separated by the same barriers, the temporal incongruence between divergences over the same barriers reveals a complex evolutionary history. While older events might be related to the emergence of barriers such as the Andes and major Amazonian rivers, younger events suggest dispersal after the consolidation of those barriers. Our analysis suggests that the complex had its origin around 6 million years (Ma) and inhabited Western Amazonia in Late Miocene-Early Pliocene. Considering the riparian habit of species in its sister clade, the rise and early diversifications of the complex may be related to the establishment of terra firme forests as it changed from a floodplain to a fluvial system. The late Amazonian colonization by A. subulatus and A. ochrolaemus lineages may have been hampered by the previous existence of well established A. infuscatus lineages in the region. © 2016 Elsevier Inc.

The complex landscape history of the Neotropics has generated opportunities for population isolation and diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow reveals a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last ∼2.5 Ma.

Diversification of Amazon birds led by climate stability: lineages originated in the wetter west and dispersed into the drier east., 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.

A biodiversidade aquática e a elevada produtividade pesqueira da Bacia Amazônica se devem principalmente à dinâmica anual dos pulsos de inundação e às extensas áreas alagáveis. Alguns dos principais impactos da construção de barragens para geração de hidroeletricidade incidem precisamente nesta dinâmica hidrológica. A construção da Usina Hidrelétrica (UHE) Belo Monte interfere na dinâmica hidrológica da Volta Grande do Xingu (VGX) ao desviar a maior parte da vazão para fora desse trecho do rio. Com base em uma análise crítica da literatura sobre o impacto de barragens e de monitoramentos em campo, que vêm sendo conduzidos tanto pelo empreendedor quanto por pesquisas independentes, verificamos que seriam necessários volumes de água substancialmente maiores do que o hidrograma proposto pela empresa e pela Agência Nacional de Águas (ANA), para não causar a total ruptura na conexão do rio com as planícies alagáveis, com efeitos negativos em cascata que comprometem, inclusive, a segurança alimentar em toda a VGX. A proposta de testar o hidrograma estabelecido pela empresa por seis anos, com uma drástica redução de vazão e perda da previsibilidade e regularidade do pulso anual de inundação, fere o Princípio Precaucionário, contraria o conhecimento ecológico acumulado sobre o tema e coloca em risco o ambiente, a biota e os modos de vida das populações humanas estabelecidas naquela região.Palavras-chave: Volta Grande do Xingu. Juruna (Yudjá). Hidrograma de Consenso. Regras de operação. Belo Monte.

The effects of climate changes on biotic expansion or divergence is a widely debated topic. This discussion is particularly relevant for northern Amazonia where patches of open vegetation environments that harbor high endemic and specialized species are present in a matrix of tall closed canopy forest. This paper presents the depositional chronology and evolution of an 8.7-m thick stabilized fluvial and eolian sediment profile in a sandy plain substrate that underpins the largest open vegetation enclave in northern Amazonia. Three depositional units were identified using optically stimulated luminescence and radiocarbon ages coupled with grain size, magnetic susceptibility, and reflectance analyses. A lower unit of coarse fluvial silt deposited between 53 and 28 ka is overlain unconformably by a 5-m thick middle unit of fine eolian sand deposited at high accumulation rates between the Last Glacial Maximum (23–19 ka) and Heinrich Stadial 1 (HS1; 18.1–14.7 ka) when persistent and long-lasting shifts of the Intertropical Convergence Zone (ITCZ) to the Southern Hemisphere promoted dry and windy conditions in northern South America. An upper ~2-m thick unit was deposited when the climate became wetter after HS1, promoting the formation of soils that support open vegetation habitats. This study indicates that abrupt millennial-scale climate events can induce significant changes in the Amazonian landscape, which in turn play an essential role in the distribution and diversification of specialized biota.