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Our understanding of Amazonian biogeography is quickly increasing, catalyzed by the growing use of genomic datasets, improved knowledge of species distributions, and the accumulation of new data on the geological and climatic history of the region. The high number of species in Amazonia and their intricate patterns of geographic distribution triggered the development of many diversification hypotheses that shaped historical biogeography as a discipline. Here, we present a historical overview of avian biogeographic studies in Amazonia, their recent advances, outstanding questions, and future directions. We focus on how new approaches have led to novel understandings of the distribution patterns and diversification processes that underpin avian diversity. We show how genomic tools are being used to establish new hypotheses about the drivers of diversification and highlight the importance of recent studies of birds in previously overlooked environments, such as floodplains and open vegetation enclaves. We emphasize the importance of gene flow, species traits, and habitat affinities in studying diversification processes to fully acknowledge the complexity of Amazonian ecosystems and their history. We then discuss the current gaps in Amazonian taxonomic and biogeographic knowledge, with a focus on the issues that we believe hinder our understanding of the field. Amazonia has been facing increasing levels of forest loss due to agricultural expansion, infrastructure development, mining, climate change, and illegal activities catalyzed by weak governance. To halt biodiversity loss, it is crucial to increase our knowledge of the natural history and biogeography of Amazonian species. We suggest increasing incentives for research and training at institutions based in the region, as well as the establishment of partnerships with governments, local communities, NGOs, and international institutions to bring diverse communities together to address crucial questions. [ABSTRACT FROM AUTHOR]

Aim: Distribution maps for Amazonian birds are often limited to species‐level taxonomy even though many subspecies represent biological species. We provide digital maps depicting subspecies‐level distributions of Neotropical birds in the Amazonas River basin and adjoining areas. Location: Amazon region, which includes the entire Amazon basin, the east slope of the tropical Andes, French Guiana, Suriname, Guyana, south Venezuela (Bolivar and Amazonas departments), parts of the Brazilian Cerrado and the Araguaia‐Tocantins basin. Taxon: Birds (Class Aves). Methods: To build the distribution maps, we compiled a point‐locality database of 620,000 records, 90% of which represent specimens vouchered in research collections. After manually cleaning and optimising the quality of the point localities, we generated extent‐of‐occurrence polygons at the subspecies level using a concave hull function. We corrected each polygon based on the literature and expert knowledge. We used this data set to define zoogeographical regions based on multidimensional scaling and clustering analyses, and then compared subspecies‐defined regions to zoogeographic regions inferred from species‐level data. Results: We inferred range polygons for 3990 subspecies, representing 2043 species from 65 families. The average distribution size was 955,739 km2, with half of the taxa having range sizes smaller than 230,484 km2 (median value) and nearly one‐quarter of all subspecies having ranges smaller than 50,000 km2. We identified 10 zoogeographical regions from the subspecies data set in comparison with four areas based on a species‐level analysis of the same data. The 10 zoogeographical regions are largely congruent with previously identified areas of endemism. Main Conclusions: The new maps of Amazonian bird subspecies distributions allow biodiversity studies (e.g. macroecology, evolution, and conservation) to be conducted at the subspecies level, and facilitate biogeographic, ecological, evolutionary and conservation research on birds in the most biologically diverse region in the world. [ABSTRACT FROM AUTHOR]

Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops , whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.] [ABSTRACT FROM AUTHOR]

Secondary contact between species often results in the formation of a hybrid zone, with the eventual fates of the hybridizing species dependent on evolutionary and ecological forces. We examine this process in the Amazon Basin by conducting the first genomic and phenotypic characterization of the hybrid zone formed after secondary contact between two obligate army‐ant‐followers: the White‐breasted Antbird (Rhegmatorhina hoffmannsi) and the Harlequin Antbird (Rhegmatorhina berlepschi). We found a major geographic displacement (∼120 km) between the mitochondrial and nuclear clines, and we explore potential hypotheses for the displacement, including sampling error, genetic drift, and asymmetric cytonuclear incompatibilities. We cannot exclude roles for sampling error and genetic drift in contributing to the discordance; however, the data suggest expansion and unidirectional introgression of hoffmannsi into the distribution of berlepschi. [ABSTRACT FROM AUTHOR]

Secondary contact between species often results in the formation of a hybrid zone, with the eventual fates of the hybridizing species dependent on evolutionary and ecological forces. We examine this process in the Amazon Basin by conducting the first genomic and phenotypic characterization of the hybrid zone formed after secondary contact between two obligate army‐ant‐followers: the White‐breasted Antbird (Rhegmatorhina hoffmannsi) and the Harlequin Antbird (Rhegmatorhina berlepschi). We found a major geographic displacement (∼120 km) between the mitochondrial and nuclear clines, and we explore potential hypotheses for the displacement, including sampling error, genetic drift, and asymmetric cytonuclear incompatibilities. We cannot exclude roles for sampling error and genetic drift in contributing to the discordance; however, the data suggest expansion and unidirectional introgression of hoffmannsi into the distribution of berlepschi. [ABSTRACT FROM AUTHOR]

The São Paulo marsh antwren ( Formicivora paludicola) is a critically endangered bird endemic to marshes in the metropolitan region of São Paulo city, Brazil. The total population is estimated to be around 300 individuals, distributed among 15 small (<50 ha) fragments, suggesting that loss of genetic variability may affect the long-term viability of this species. To develop genetic tools for gaining information on effective population sizes, inbreeding and gene flow between populations, we describe nine polymorphic microsatellite loci isolated from a F. paludicola library using next-generation sequencing. We report on levels of variation in these novel microsatellites and eight additional heterologous loci in these birds. Expected ( H) and observed ( H) heterozygosities averaged 0.72 and 0.70, respectively, and the number of alleles per locus ranged from 3 to 10. These loci will permit evaluation of whether artificial translocations are necessary for long-term viability of this rare bird. [ABSTRACT FROM AUTHOR]

Secondary contact between species often results in the formation of a hybrid zone, with the eventual fates of the hybridizing species dependent on evolutionary and ecological forces. We examine this process in the Amazon Basin by conducting the first genomic and phenotypic characterization of the hybrid zone formed after secondary contact between two obligate army-ant-followers: the White-breasted Antbird (Rhegmatorhina hoffmannsi) and the Harlequin Antbird (Rhegmatorhina berlepschi). We found a major geographic displacement (∼120 km) between the mitochondrial and nuclear clines, and we explore potential hypotheses for the displacement, including sampling error, genetic drift, and asymmetric cytonuclear incompatibilities. We cannot exclude roles for sampling error and genetic drift in contributing to the discordance; however, the data suggest expansion and unidirectional introgression of hoffmannsi into the distribution of berlepschi., (© 2021 The Authors. Evolution © 2021 The Society for the Study of Evolution.)