Stenotrophomonas maltophilia Belonging to Novel Sequence Types ST473 and ST474 in Wild Birds Inhabiting the Brazilian Amazonia.

Stenotrophomonas maltophilia is an opportunistic human pathogen associated with nosocomial and community-acquired infections. We have conducted a microbiological and genomic surveillance study of broad-spectrum cephalosporin- and carbapenem-resistant Gram-negative bacteria colonizing wild birds inhabiting the Brazilian Amazonia. Strikingly, two S. maltophilia strains (SM79 and SM115) were identified in Plain-throated antwren (Isleria hauxwelli) passerines affected by Amazonian fragmentation and degradation. Noteworthy, SM79 and SM115 strains belonged to new sequence types (STs) ST474 and ST473, respectively, displaying resistance to broad-spectrum ß-lactams, aminoglycosides and/or fluoroquinolones. In this regard, resistome analysis confirmed efflux pumps (smeABC, smeDEF, emrAB-tolC and macB), blaL1 and blaL2, aph(3')-IIc and aac(6')-Iak, and Smqnr resistance genes. Comparative phylogenomic analysis with publicly available S. maltophilia genomes clustered ST473 and ST474 with human strains, whereas the ST474 was also grouped with S. maltophilia strains isolated from water and poultry samples. In summary, we report two novel sequence types of S. maltophilia colonizing wild Amazonian birds. The presence of opportunistic multidrug-resistant pathogens in wild birds, from remotes areas, could represent an ecological problem since these animals could easily promote long-distance dispersal of medically important antimicrobial-resistant bacteria. Therefore, while our results could provide a baseline for future epidemiological genomic studies, considering the limited information regarding S. maltophilia circulating among wild animals, additional studies are necessary to evaluate the clinical impact and degree of pathogenicity of this human opportunistic pathogen in wild birds.

Spatiotemporal dynamics reveals forest rejuvenation, fragmentation, and edge effects in an Atlantic Forest hotspot, the Pernambuco Endemism Center, northeastern Brazil.

Large forested tracts are increasingly rare in the tropics, where conservation managers are often presented with the challenge of preserving biodiversity in small and isolated fragments. The Atlantic Forest is one of the world's most important biodiversity hotspots, jeopardized by habitat loss and fragmentation. The Pernambuco Endemism Center (PEC) is the most degraded of the Atlantic Forest regions and because of the dramatic levels of deforestation, fragmentation, and ongoing species losses, studies on the distribution and configuration of the PEC's forest cover are necessary. However, across dynamic tropical landscapes, investigating changes over time is essential because it may reveal trends in forest quality attributes. Here, we used Google Earth Engine to assess land use and land cover data from MapBiomas ranging from 1985 to 2020 to calculate current landscape metrics and to reveal for the first time the spatiotemporal dynamics of the PEC's forests. We identified a forest cover area that ranged from 571,661 ha in 1985 to 539,877 ha in 2020, and about 90% of the fragments were smaller than 10 ha. The average fragment size was about 11 ha, and only four fragments had more than 5,000 ha. Deforestation was mostly concentrated in northern Alagoas, southern Pernambuco, and non-coastal Paraíba and Rio Grande do Norte. On average, borders represented 53.6% of the forests from 1985 to 2020, and younger forests covered 52.3% of the area in 2017, revealing a vegetation rejuvenation process 2.5 times higher than in total Atlantic Forest. In 2017, older forest cores in fragments larger than 1000 ha (i.e., higher-quality habitats) represented only 12% of the remaining forests. We recommend that the amount of forest cover alone may poorly assist conservation managers, and our results indicate that ensuring legal protection and increasing surveillance of the PEC's few last higher-quality habitats is urgently needed.

Systematics of Thraupis (Aves, Passeriformes) reveals an extensive hybrid zone between T. episcopus (Blue-gray Tanager) and T. sayaca (Sayaca Tanager).

The Neotropical avian genus Thraupis (Passeriformes, Thraupidae) currently comprises seven species that are widespread and abundant throughout their ranges. However, no phylogenetic hypothesis with comprehensive intraspecific sampling is available for the group and, therefore, currently accepted species limits remain untested. We obtained sequence data for two mitochondrial (ND2, cyt-b) and three non-coding nuclear (TGFB2, MUSK, and ßF5) markers from 118 vouchered museum specimens. We conducted population structure and coalescent-based species-tree analyses using a molecular clock calibration. We integrated these results with morphometric and coloration analyses of 1,003 museum specimens to assess species limits within Thraupis. Our results confirm that Thraupis is a monophyletic group and support its origin in the late Miocene and subsequent diversification during the Pleistocene. However, we found conflicts with previous phylogenies. We recovered Thraupis glaucocolpa to be sister to all other species in the genus, and T. cyanoptera to the remaining five species. Our phylogenetic trees and population structure analyses uncovered phylogeographic structure within Thraupis episcopus that is congruent with geographic patterns of phenotypic variation and distributions of some named taxa. The first genetic and phenotypic cluster in T. episcopus occurs east of the Andes and is diagnosed by the white patch on the lesser and median wing coverts, whereas the second group has a blue patch on the wing and distributes to the west of Colombia's eastern Andes. Finally, we present evidence of hybridization and ongoing gene flow between several taxa at different taxonomic levels and discuss its taxonomic implications.

Concerted variation in melanogenesis genes underlies emergent patterning of plumage in capuchino seedeaters.

Coloration traits are central to animal communication; they often govern mate choice, promote reproductive isolation and catalyse speciation. Specific genetic changes can cause variation in coloration, yet far less is known about how overall coloration patterns-which involve combinations of multiple colour patches across the body-can arise and are genomically controlled. We performed genome-wide association analyses to link genomic changes to variation in melanin (eumelanin and pheomelanin) concentration in feathers from different body parts in the capuchino seedeaters, an avian radiation with diverse colour patterns despite remarkably low genetic differentiation across species. Cross-species colour variation in each plumage patch is associated with unique combinations of variants at a few genomic regions, which include mostly non-coding (presumably regulatory) areas close to known pigmentation genes. Genotype-phenotype associations can vary depending on patch colour and are stronger for eumelanin pigmentation, suggesting eumelanin production is tightly regulated. Although some genes are involved in colour variation in multiple patches, in some cases, the SNPs associated with colour changes in different patches segregate spatially. These results suggest that coloration patterning in capuchinos is generated by the modular combination of variants that regulate multiple melanogenesis genes, a mechanism that may have promoted this rapid radiation.

Avian Assemblages in Forest Fragments do not Sum to the Expected Regional Community in the Brazilian Atlantic Forest.

While bird diversity in the Atlantic Forest can be considered well-known, how the communities have been affected by deforestation and habitat fragmentation is not. We studied birds in 10 forest fragments of distinct sizes (all originally within the Atlantic Forest) in southern Bahia. In 5,391 bird encounters, we found 251 species, with 46 endemics and eight considered globally vulnerable or endangered. We also compiled a list of the 380 species that should comprise the expected regional assemblage, and found that only 66% of these species were present in all the fragments combined. Only 9% of all observed species were found in all fragments. The largest fragment (700 ha) had the greatest number of endemic species (40), and seven threatened species. All fragments had some conservation-important species (some were found in one or a few fragments), but no fragment included them all. Fragments shared 10% of endemic species, but overall, the contingent of endemics was unique in each fragment. Finally, most functional traits of bird assemblages decreased with increasing fragment size. Neither species richness nor similarity correlated with fragment size or distance between fragments, and unknown, non-random factors probably influence the likelihood of species survival in each fragment. Thus, to ensure the persistence of threatened species, as well as maintain the most common species, conservation management decisions should include all fragments together because no single fragment is most representative of the local community.

Natural history museums and zoological collections of São Paulo State / Museus de história natural e coleções zoológicas do Estado de São Paulo

Abstract Scientific collections constitute a valuable source for contributions to scientific research and the training of human resources in systematics, but also other areas of biological knowledge. In this contribution, we intend to discuss these advancements in collections and the role played by FAPESP in sponsoring them, as well as a general overview of the zoological collections in São Paulo state. We also aim to stress the importance of zoological collections and the need for continuous logistic and financial support from institutions and research agencies to maintain and develop these unique repositories of biodiversity. From 1980 to the present, FAPESP supported 118 research projects focused on several areas of zoology that are directly or indirectly associated with collections. There is a constant growth in the number of projects, and the financial support provided by FAPESP through the Biota Program was paramount for the advancement of our knowledge of biodiversity in Brazil. Parallel to the scientific advances, but not less important, this support allowed curators to increase the number of specimens, and to organize, maintain and digitize them in these valuable and irreplaceable collections. Regarding the lack of new taxonomists, it is essential that FAPESP and universities in São Paulo encourage the formation of new academics in zoological groups where specialists are rare. Considering the investment provided by FAPESP, it is quite important that the institutions that benefited from these resources took greater responsibility to safeguard these collections, and they should consider including resources on their budgets to obtain safety certificates, ensuring their permanence for many generations to come. Zoological collections are a heritage of humanity and are essential not only for the improvement of our knowledge of biodiversity but also with direct applications, among other services provided by these biological resources. It is important that research and teaching institutions in São Paulo that house specimens under their care start to value more this important patrimony and this heritage, as these collections represent the most valuable testimony of our impressive biodiversity, records of our past, and windows to our future, essential to our academic, scientific, cultural and social sovereignty.

Resumo As coleções científicas constituem uma fonte valiosa para contribuições à pesquisa científica e para a formação de recursos humanos em sistemática, mas também em outras áreas do conhecimento biológico. Nesta contribuição, pretendemos discutir esses avanços nas coleções e o papel desempenhado pela FAPESP no seu patrocínio, bem como um panorama geral das coleções zoológicas do estado de São Paulo. Também pretendemos enfatizar a importância das coleções zoológicas e a necessidade de apoio logístico e financeiro contínuo de instituições e agências de pesquisa para manter e desenvolver esses repositórios únicos de biodiversidade. Ao longo de 1980 até os dias atuais, a FAPESP apoiou 118 projetos de pesquisa focados em diversas áreas da zoologia, direta ou indiretamente associados a coleções. Há um crescimento constante no número de projetos, e o apoio financeiro da FAPESP por meio do Programa Biota foi fundamental para o avanço do nosso conhecimento sobre a biodiversidade no Brasil. Paralelamente aos avanços científicos, mas não menos importante, este apoio permitiu aos curadores aumentar o número de exemplares, e organizá-los, mantê-los e digitalizá-los nestas valiosas e insubstituíveis coleções. Em relação à falta de novos taxonomistas, é fundamental que a FAPESP e as universidades paulistas estimulem a formação de novos acadêmicos em grupos zoológicos onde os especialistas são raros. Considerando o investimento realizado pela FAPESP, é de suma importância que as instituições beneficiadas com esses recursos tenham maior responsabilidade na salvaguarda desses acervos, devendo considerar a inclusão de recursos em seus orçamentos para obtenção de certificados de segurança, garantindo sua permanência por muitas gerações. As coleções zoológicas são patrimônio da humanidade, e são essenciais não apenas para o aprimoramento do nosso conhecimento sobre a biodiversidade, mas também com aplicações diretas, entre outros serviços prestados por esses recursos biológicos. É importante que as instituições de pesquisa e ensino paulistas que abrigam exemplares sob seus cuidados passem a valorizar mais esse importante patrimônio e essa herança, pois essas coleções representam o testemunho mais valioso de nossa impressionante biodiversidade, registros do nosso passado e janelas para o nosso futuro, essenciais à nossa soberania acadêmica, científica, cultural e social.

Are publications on zoological taxonomy under attack?

Taxonomy is essential to biological sciences and the priority field in face of the biodiversity crisis. The industry of scientific publications has made extensive promotion and display of bibliometric indexes, resulting in side effects such as the Journal Impact Factor™ (JIF) mania. Inadequacies of the widely used indexes to assess taxonomic publications are among the impediments for the progress of this field. Based on an unusually high proportion of self-citations, the mega-journal Zootaxa, focused on zoological taxonomy, was suppressed from the Journal Citation Reports (JCR, Clarivate™). A prompt reaction from the scientific community against this decision took place exposing myths and misuses of bibliometrics. Our goal is to shed light on the impact of misuse of bibliometrics to the production in taxonomy. We explored JCR's metrics for 2010-2018 of 123 zoological journals publishing taxonomic studies. Zootaxa, with around 15 000 citations, received 311% more citations than the second most cited journal, and shows higher levels of self-citations than similar journals. We consider Zootaxa's scope and the fact that it is a mega-journal are insufficient to explain its high level of self-citation. Instead, this result is related to the 'Zootaxa phenomenon', a sociological bias that includes visibility and potentially harmful misconceptions that portray the journal as the only one that publishes taxonomic studies. Menaces to taxonomy come from many sources and the low bibliometric indexes, including JIF, are only one factor among a range of threats. Instead of being focused on statistically illiterate journal metrics endorsing the villainy of policies imposed by profit-motivated companies, taxonomists should be engaged with renewed strength in actions directly connected to the promotion and practice of this science without regard for citation analysis.

Human-modified landscapes narrow the isotopic niche of neotropical birds.

Deforestation and habitat loss resulting from land use changes are some of the utmost anthropogenic impacts that threaten tropical birds in human-modified landscapes (HMLs). The degree of these impacts on birds' diet, habitat use, and ecological niche can be measured by isotopic analysis. We investigated whether the isotopic niche width, food resources, and habitat use of bird trophic guilds differed between HMLs and natural landscapes (NLs) using stable carbon (δ13C) and nitrogen isotopes (δ15N). We analyzed feathers of 851 bird individuals from 28 landscapes in the Brazilian Atlantic Forest. We classified landscapes into two groups according to the percentage of forest cover (HMLs ≤ 30%; NLs ≥ 47%), and compared the isotopic niche width and mean values of δ13C and δ15N for each guild between landscape types. The niches of frugivores, insectivores, nectarivores, and omnivores were narrower in HMLs, whereas granivores showed the opposite pattern. In HMLs, nectarivores showed a reduction of 44% in niche width, while granivores presented an expansion of 26%. Individuals in HMLs consumed more resources from agricultural areas (C4 plants), but almost all guilds showed a preference for forest resources (C3 plants) in both landscape types, except granivores. Degraded and fragmented landscapes typically present a lower availability of habitat and food resources for many species, which was reflected by the reduction in niche width of birds in HMLs. Therefore, to protect the diversity of guilds in HMLs, landscape management strategies that offer birds more diverse habitats must be implemented in tropical regions.

On the validity and taxonomic status of emCrypturellus/em emobsoletus/em emgriseiventris/em (Salvadori, 1895) and emC. o. hypochraceus/em (Miranda-Ribeiro, 1938) (Aves, Tinamidae).

The nine currently recognized subspecies in the Brown Tinamou (Crypturellus obsoletus) complex are disjunctly widespread in South America, and at least three of them occur in Brazil. Morphological diagnosis of most of these taxa is imprecise, in contrast with consistent vocal differences described in the literature. We conducted a taxonomic review of two Amazonian taxa, C. o. griseiventris and C. o. hypochraceus, using morphological, morphometric, and vocal characters. Our results indicate that C. o. hypochraceus (Miranda-Ribeiro, 1938) is a junior synonym of C. o. griseiventris (Salvadori, 1895), and that Crypturellus griseiventris (Salvadori, 1895) must be treated as a full species, based on unique and fully diagnosable plumage and vocal patterns.

Rapid speciation via the evolution of pre-mating isolation in the Iberá Seedeater.

Behavioral isolation can catalyze speciation and permit the slow accumulation of additional reproductive barriers between co-occurring organisms. We illustrate how this process occurs by examining the genomic and behavioral bases of pre-mating isolation between two bird species (Sporophila hypoxantha and the recently discovered S. iberaensis) that belong to the southern capuchino seedeaters, a recent, rapid radiation characterized by variation in male plumage coloration and song. Although these two species co-occur without obvious ecological barriers to reproduction, we document behaviors indicating species recognition by song and plumage traits and strong assortative mating associated with genomic regions underlying male plumage patterning. Plumage differentiation likely originated through the reassembly of standing genetic variation, indicating how novel sexual signals may quickly arise and maintain species boundaries.

The evolution of a tropical biodiversity hotspot.

The tropics are the source of most biodiversity yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leveraged samples assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, the suboscine passerines. Our phylogeny, estimated using data from 2389 genomic regions in 1940 individuals of 1283 species, reveals that peak suboscine species diversity in the Neotropics is not associated with high recent speciation rates but rather with the gradual accumulation of species over time. Paradoxically, the highest speciation rates are in lineages from regions with low species diversity, which are generally cold, dry, unstable environments. Our results reveal a model in which species are forming faster in environmental extremes but have accumulated in moderate environments to form tropical biodiversity hotspots.

Life history and ecology might explain incongruent population structure in two co-distributed montane bird species of the Atlantic Forest.

Comparative phylogeography is a powerful approach to investigate the role of historical and environmental processes in the evolution of biodiversity within a region. In this regard, comparative studies of species with similar habitat preferences are valuable to reduce the confounding influence of habitat association when interpreting phylogeographic patterns. In the Atlantic Forest of South America, phylogeographic studies of highland and lowland species have shown distinct population structure patterns so far, suggesting that such species have responded differently to Pleistocene glacial cycles. Herein, we performed a comparative analysis using molecular data and paleodistribution models of two Montane Atlantic Forest (MAF) co-distributed passerine birds with similar habitat requirements but with distinct life-history traits and ecologies: the frugivore lek-breeding Blue Manakin (Chiroxiphia caudata) and the insectivore and socially monogamous Drab-Breasted Bamboo Tyrant (Hemitriccus diops). We aimed to shed light on the role of contrasting life histories and ecologies onto the demography and population structure of MAF species. We sampled both species throughout most of their distribution range, sequenced a mitochondrial and a nuclear molecular marker, and used standard phylogeographic methods to investigate population structure and ecological niche modeling (ENM) to infer the species' paleodistributions. Our analyses recovered a phylogeographic break in H. diops in the region of the Doce River, but no genetic structure in C. caudata. We also found higher differentiation among subpopulations within each lineage of H. diops than among subpopulations of C. caudata. We suggest that these discrepancies in population structure might be due to distinct life-history traits and their impact on gene flow and generation time. For example, while H. diops is an insectivore species, C. caudata is a frugivore and the latter ecological aspect likely selects for a higher dispersion distance. Additionally, because C. caudata is a lek-breeding species, it has a longer generation time than H. diops. These traits could hinder genetic differentiation when populations become geographically isolated. Nonetheless, both species showed some common biological features, such as signatures of synchronous population expansion and larger distribution ranges during the Last Glacial Maximum, possibly due to similar cold tolerance.

Are publications on zoological taxonomy under attack?

Taxonomy is essential to biological sciences and the priority field to be supported in face of the biodiversity crisis. The industry of scientific publications has made extensive use of bibliometric indexes, resulting in distortions to institutions, organizations, and researchers, such as the side effect known as Journal Impact Factor (JIF) mania. Inadequacies of the most widely used bibliometric indexes from giant companies Clarivate™ (InCites™) and RELX™ Elsevier B.V. (Scopus®) to assessment of the relevance of taxonomic publications were considered as one of the impediments for the progress of this field. Recently, Clarivate suppressed the mega-journal Zootaxa, focused on taxonomy, from Journal Citation Reports (JCR), a database with 12,000 periodicals. Zootaxa suppression, together with other 32 journals, was based on an unusual high proportion of self-citations. Suppressed journals would thus not receive a value of JIF for 2020. A prompt reaction from the scientific community against the suppression of Zootaxa took place and, accordingly, Clarivate announced its reinstatement. This situation exposed many persistent myths and misuses of bibliometric indexes. The goal of this study is to shed light on the impacts of bibliometric indexes to the taxonomic field and on underlying aspects of the suppression of Zootaxa. Our major question is whether the suppression of any journal from JIF can really affect the production in the taxonomic field. We explored data metrics from the JCR (Web of Science Core Collection™) for 2010­2018 of the top ten zoological journals (eight are included in JCR) in the number of new taxa and journals focused on or regularly publishing taxonomic studies, totaling 123 journals. Zootaxa shows higher levels of self-citations than similar journals. We consider that two possible explanations provided for the high number of self-citations, i.e., Zootaxa's scope on taxonomy and the fact that it is a mega-journal, are inadequate. Instead, putative explanations are related to the "Zootaxa phenomenon," a sociological bias that includes visibility, and potential harmful myths that portray Zootaxa as the unique journal that publishes taxonomic studies with an inviting JIF value. Menaces to taxonomy as a science come from many sources and the low bibliometric values of its journals are only one of the factors that contribute for establishing the so-called taxonomic impediment. We suggest rejection of bibliometric indexes, including JIF, instead of considering them when convenient. Taxonomists as a community, instead of being deeply focused on journal metrics endorsing the villainy of bibliometric policies imposed by dominant companies, should be engaged with renewed strength in actions directly connected to the development and promotion of this science.

The Fossil Birds of Peter Lund.

The Danish naturalist Peter Wilhelm Lund (1801-1880), regarded as the father of Brazilian palaeontology and archaeology, is known mainly for his work with fossil mammals of Quaternary age from the limestone caves of the Lagoa Santa region in the state of Minas Gerais, southeastern Brazil. However, during one decade of fieldwork (1835-1844), he also collected a large number of remains of other animal groups from these caves. Birds were well represented and, following assessment by the Danish ornithologist Oluf Winge (1855-1889), most of the specimens collected by Lund belong to species still living in the area. Here we present an overview of the bird remains (fossil and recent), found by Lund and others in the region, we update their taxonomic attributions, and comment on the history of the material, making information previously published only in Danish available in English.

Earth history and the passerine superradiation.

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.

Taxonomy, natural history, and conservation of the Great-billed Seed-Finch Sporophila maximiliani (Cabanis, 1851) (Thraupidae, Sporophilinae).

Seed-finches are small-sized Neotropical granivorous birds characterized by extremely strong and thick beaks. Among these birds, the Great-billed Seed-Finch Sporophila maximiliani has been selectively and intensively trapped to the extent that has become one of the most endangered bird species in South America, yet its taxonomy remains complex and controversial. Two subspecies have been recognized: S. m. maximiliani (Cabanis, 1851), mainly from the Cerrado of central South America, and S. m. parkesi Olson (= Oryzoborus m. magnirostris), from northeastern South America. Originally, S. m. parkesi was diagnosed as being larger than the Large-billed Seed-Finch, S. c. crassirostris (Gmelin, 1789), but proper comparisons with S. m. maximiliani, which is larger than S. c. crassirostris, were never performed. Here we provide a review of the taxonomic and nomenclatural history of S. maximiliani, reevaluate the validity and taxonomic status of the subspecies based on morphological characters, and significantly revise its geographic distribution. Analyses based on plumage patterns and a Principal Component Analysis of morphometric characters indicated that S. m. parkesi is most appropriately treated as a synonym of the nominate taxon, which results in a monotypic S. maximiliani comprising two disjunct populations. Further, we conducted systematic searches for S. maximiliani in Brazil, in an attempt to obtain natural history information. After more than 6,000 hours of fieldwork in 45 areas of potential and historical occurrence, S. maximiliani was located only in two sites, in marshy environments called veredas, confirming the critical conservation status of this species, at least in Brazil. We discuss the conservation potential for, and the problems involved with, captive breeding of S. maximiliani for reintroduction into the wild.

ATLANTIC BIRDS: a data set of bird species from the Brazilian Atlantic Forest.

South America holds 30% of the world's avifauna, with the Atlantic Forest representing one of the richest regions of the Neotropics. Here we have compiled a data set on Brazilian Atlantic Forest bird occurrence (150,423) and abundance samples (N = 832 bird species; 33,119 bird individuals) using multiple methods, including qualitative surveys, mist nets, point counts, and line transects). We used four main sources of data: museum collections, on-line databases, literature sources, and unpublished reports. The data set comprises 4,122 localities and data from 1815 to 2017. Most studies were conducted in the Florestas de Interior (1,510 localities) and Serra do Mar (1,280 localities) biogeographic sub-regions. Considering the three main quantitative methods (mist net, point count, and line transect), we compiled abundance data for 745 species in 576 communities. In the data set, the most frequent species were Basileuterus culicivorus, Cyclaris gujanensis, and Conophaga lineata. There were 71 singletons, such as Lipaugus conditus and Calyptura cristata. We suggest that this small number of records reinforces the critical situation of these taxa in the Atlantic Forest. The information provided in this data set can be used for macroecological studies and to foster conservation strategies in this biodiversity hotspot. No copyright restrictions are associated with the data set. Please cite this Data Paper if data are used in publications and teaching events.

Plant invasion: Another threat to the São Paulo Marsh Antwren (Formicivora paludicola), a species on the verge of extinction.

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.