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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.

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.

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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.

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

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...

Regional, intratropical avian migrations have rarely been studied. Here, we employ an occurrence records review and ecological niche modeling tools to test the hypothesis that an understudied Neotropical bird, the Little Wood-Rail (Aramides mangle, Rallidae), seasonally migrates between the humid Atlantic coast and the dry Caatinga biome of interior northeastern Brazil. We divided records geographically between coastal and inland, and temporally between wet/breeding and dry/non-breeding seasons. Coastal records peak when inland records are fewest and vice-versa, and independence between season and region in which records were made was statistically rejected. However, ecological niche modeling shows that coastal regions are suitable habitats for A. mangle year-round, and models built with records from each season were considered statistically equivalent. It seems that this species neither performs erratic, unpredictable movements nor typical avian “to-and-fro” migration. Instead, it undergoes peri...

The Picumnus exilis complex is composed of 6–7 subspecies distributed from eastern Colombia, through Venezuela, the Guianas, to northern and northeastern Brazil. They are characterized by a greenish back, whitish or yellowish belly (barred or tainted with black), and males with a red and/or orange forehead. Here we review the taxonomy of this complex based on morphometric and plumage characters from a total of 487 specimens that were analyzed. Eighteen plumage characters were found, of which 12 proved to be informative. The results suggest the existence of five valid taxa: Picumnus exilis (Lichtenstein 1823), a Brazilian endemic found near the coasts of Bahia and Sergipe States; Picumnus pernambucensis Zimmer (1947) another Brazilian endemic occurring north of the Sao Francisco River in the “Pernambuco” Area of Endemism; Picumnus buffonii Lafresnaye (1845) found in the Guiana Shield, east of the Rio Branco and east of the Rio Tocantins on the southern side of the Amazon River; Picumnus undulatus Hargitt (1889) occurring between the Rio Branco, Rio Negro, and Orinoco Rivers, and Picumnus obsoletus Allen (1892) which ranges from the Orinoco Delta north to far northeastern Venezuela. Furthermore, both P. e. salvini Hargitt (1893) and P. nigropunctatus Zimmer and Phelps (1950) proved to be junior synonyms of Picumnus obsoletus Allen (1892). Similarities between the species considered here and other representatives of this genus strongly suggest that the Picumnus exilis complex could also be related to groups of other complexes. This highlights the need for taxonomic reviews to understand the cryptic diversity within the Picumnus genus.

Made available in DSpace on 2018-11-26T15:28:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-10-08 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Small populations of endangered species can be impacted by genetic processes such as drift and inbreeding that reduce population viability. As such, conservation genetic analyses that assess population levels of genetic variation and levels of gene flow can provide important information for managing threatened species. The Sao Paulo Marsh Antwren (Formicivora paludicola) is a recently-described and critically endangered bird from Sao Paulo State (Brazil) whose total estimated population is around 250-300 individuals, distributed in only 15 isolated marshes around Sao Paulo metropolitan region. We used microsatellite DNA markers to estimate the population genetic characteristics of the three largest remaining populations of this species all within 60 km of each other. We detected a high and significant genetic structure between all populations (overall F-ST = 0.103) which is comparable to the highest levels of differentiation ever documented for birds, (e.g., endangered birds found in isolated populations on the tops of African mountains), but also evidence for first-generation immigrants, likely from small local unsampled populations. Effective population sizes were small (between 28.8-99.9 individuals) yet there are high levels of genetic variability within populations and no evidence for inbreeding. Conservation implications of this work are that the high levels of genetic structure suggests that translocations between populations need to be carefully considered in light of possible local adaptation and that remaining populations of these birds should be managed as conservation units that contain both main populations studied here but also small outlying populations which may be a source of immigrants. Univ Estadual Paulista, Inst Biociencias, Dept Genet, BR-18618970 Sao Paulo, Brazil Ohio State Univ, Dept Evolut Ecol & Organismal Biol, Columbus, OH 43210 USA Univ Fed Sao Carlos, Dept Ciencias Ambientais, BR-18052 Sao Paulo, Brazil Louisiana State Univ, Museum Nat Sci, Baton Rouge, LA 70803 USA Univ Sao Paulo, Secao Aves, Museu Zool, BR-04218970 Sao Paulo, Brazil Univ Estadual Paulista, Inst Biociencias, Dept Genet, BR-18618970 Sao Paulo, Brazil FAPESP: 2012/09105-7 FAPESP: 2013/01604-2

Piculus chrysochloros (Vieillot 1818) is a species of woodpecker that ranges from Argentina to Panama, occurring in lowland forests as well as Cerrado, Caatinga and Chaco vegetation. Currently, nine subspecies are accepted, but no study has evaluated individual variation within populations, so the status of these taxa remains uncertain. Here we review the taxonomy and distribution of this species, based on morphological and morphometric data from 267 specimens deposited in ornithological collections. Our results suggest the existence of six unambiguous taxonomic units that can be treated as phylogenetic species: Piculus xanthochloros (SclaterSalvin 1875), from northwestern South America; Piculus capistratus (Malherbe 1862), from northern Amazonia west to the Branco River; Piculus laemostictus Todd 1937, from southern Amazonia; Piculus chrysochloros (Vieillot 1818), from the Cerrado, Caatinga and Chaco; Piculus paraensis (Snethlage 1907) from the Belém Center of Endemism; and Piculus polyzonus (Valenciennes 1826) from the Atlantic Forest. Both Brazilian endemics (P. polyzonus and P. paraensis) are threatened due to habitat loss. In addition, we found one undescribed form from the Tapajós-Tocantins interfluve, now under study, that may prove to be a valid species once more specimens and other data become available.