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The Jurua River is the third largest white-water tributary of the Amazon River, yet, historically, it has not been considered an important barrier for bird communities. The upper region of the Jurua River was the focus of two ornithological collections in the early twentieth century, but the middle region, where the river and surrounding varzea flooded forest widen, has remained largely unexplored by ornithologists. Inspired by Dr. Emilie Snethlage, whose ornithological expeditions to Amazonian rivers during the early twentieth century were foundational in documenting the importance of river barriers, we undertook a month-long expedition to the middle Jurua River. We collected the first modern specimens, high-quality tissues, and sound recordings of birds from the middle Jurua region. Combining our data with those from previous collections, we present the first comprehensive inventory of bird species from the Jurua region, document several significant range extensions, and report the first evidence that the middle Jurua River acts as a barrier in at least four species complexes of terra firme upland forest birds. Our findings have important taxonomic and biogeographic implications for birds of the Jurua region and southwestern Amazon basin.

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.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species., A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

The Yellow-green Grosbeak Caryothraustes canadensis is a South American passerine occurring in Amazon and Atlantic Forests. Currently, it comprises four subspecies: Caryothraustes canadensis canadensis, Caryothraustes canadensis brasiliensis, Caryothraustes canadensis frontalis and Caryothraustes canadensis simulans. No study has ever revisited its taxonomy, hindering a complete understanding of the available diversity in Caryothraustes canadensis complex. We examined color and morphometric variation in 259 scientific specimens and sequenced the mitochondrial gene ND2 of 29 tissue samples. We also quantitatively and qualitatively analyzed 52 spectrograms of vocal recordings. Molecular analyzes demonstrated the existence of two divergent lineages in C. canadensis complex, one from Amazonia and the other in the Atlantic Forest, which can also be distinguished by morphometric and plumage characters. Here we propose that the C. canadensis complex is composed of two full species: C. canadensis and C. brasiliensis. Caryothraustes canadensis frontalis shows no reciprocal monophyly in the phylogenetic analyzes, despite having weak plumage diagnostic characters; therefore, we suggest it should be considered a synonym of C. brasilensis.

Clytoctantes atrogularis Lanyon, Stotz and Willard, 1990 (Thamnophilidae) is one of the most mysterious and poorly known birds of the Neotropics. Endemic to Amazonian Brazil, it was known only from the holotype and two sight records at the type locality in Rondonia, and a sighting of a pair with a recording on the Sucunduri River in Amazonas. Here we review the distribution and report five new records in the states of Mato Grosso, Amazonas, and Rondonia, considerably increasing the known range of the species. We present the first detailed descriptions of males, for which the plumage was previously unknown. The records presented herein were made in terra firme forest with understories dominated by Lepidocaryum palms and also with sparse Guadua spp. of bamboo, demonstrating that the bird species occurs in habitats other than those previously described. Stomach contents of six individuals included mostly ants and their eggs, possibly obtained by opening stems of Guadua spp. The high rate of deforestation that characterizes a large part of the range of C. atrogularis could be causing declines in local populations.

The Sao Paulo Marsh Antwren (Formicivora paludicola) is a recently discovered species in the family Thamnophilidae that inhabits marshes in the vicinity of the Sao Paulo metropolitan region, which is the most populous area of South America and within the Brazilian Southeastern Atlantic Forest. This species should be considered “Critically Endangered” following IUCN criteria, as it has a total area of occupancy of only 1.42 km2, a sparse and fragmented distribution, low dispersal capacity, and has lost ~300 km2 of habitat in the last 200 years. F. paludicola was discovered on the verge of extinction, and virtually nothing is known about its natural history, breeding biology, and life history, hence compromising any conservation effort. By capturing and banding individuals from the three largest populations of Sao Paulo Marsh Antwrens, we provide the first assessment of the breeding period and molt cycles of F. paludicola. Our observations indicate breeding season is from October to February, and t...

During the past 100 years in densely populated south-eastern Brazil, wetlands have been severely transformed due to urbanization, agriculture and mining. The recently discovered São Paulo Marsh Antwren (Formicivora paludicola) is endemic to these wetlands, and is listed as "Critically Endangered" by the IUCN. The species is only found in an area of 1.42 km2, it has a sparse and fragmented distribution, low dispersal capacity, and has probably lost around 300 km2 of habitat in the past 100 years. Furthermore, very little is known about F. paludicola natural history, and so it is difficult to construct a robust conservation plan. Using Kernel home range estimations and the Adjusted-SD/Torus Shift test (a novel tool for animal-habitat association studies), we showed that the species avoids patches of the alien invasive ginger lily (Hedychium coronarium). Given the high density of their population (3.6 mature individuals/ha), F. paludicola could thrive in relatively small areas of suitable wetlands protected from human occupation and water contamination, however special attention should be paid to biological invasions, which may represent a serious threat to the remaining populations. Protecting a few small wetlands used by F. paludicola would be an important step towards general conservation and restoration of Atlantic Forest wetlands and its endemic endangered species.