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The lack of synthesized information regarding biodiversity is a major problem among researchers, leading to a pervasive cycle where ecologists make field campaigns to collect information that already exists and yet has not been made available for a broader audience. This problem leads to long-lasting effects in public policies such as spending money multiple times to conduct similar studies in the same area. We aim to identify this knowledge gap by synthesizing information available regarding two Brazilian long-term biodiversity programs and the metadata generated by them. Using a unique dataset containing 1904 metadata, we identified patterns of metadata distribution and intensity of research conducted in Brazil, as well as where we should concentrate research efforts in the next decades. We found that the majority of metadata were about vertebrates, followed by plants, invertebrates, and fungi. Caatinga was the biome with least metadata, and that there's still a lack of information regarding all biomes in Brazil, with none of them being sufficiently sampled. We hope that these results will have implications for broader conservation and management guiding, as well as to funding allocation programs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The general assumption that the survival patterns of tropical and southern temperate birds are similar lacks empirical data from higher latitudes. Regional comparisons of New World species are rare, and this assumption has been based on data from African studies. Here, we estimate the survival rates of 88 tropical and southern temperate bird populations (69 species) from eight localities in South America to evaluate the hypothesis that the survival of these populations is homogeneous at the regional scale. We estimated survival based on the Cormack-Jolly-Seber model and compared values from different environments. The survival estimates ranged from 0.30 to 0.80 (0.56 ± 0.12). Apparent survival did not differ significantly between low-latitude tropical environments (03°S) and the other sites from high-latitudes (between 22° and 34°S). Despite a predicted positive trend, body size was not significantly related to survival among passerines. On the other hand, phylogenetic relationships explained more than a third of the variation in bird survival. Based on the largest available database on South American bird species, our findings support the hypothesis that bird survival is homogeneous, at the regional scale, along the southern hemisphere. In particular, we reinforce the hypothesis that climatic variation has a limited influence on bird survival in the southern hemisphere., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The escape behaviour, measured as flight initiation distance (FID; the distance at which individuals take flight when approached by a potential predator, usually a human in the study systems), is a measure widely used to study fearfulness and risk-taking in animals. Previous studies have shown significant differences in the escape behaviour of birds inhabiting cemeteries and urban parks in European cities, where birds seem to be shyer in the latter. We collected a regional dataset of the FID of birds inhabiting cemeteries and parks across Latin America in peri-urban, suburban and urban parks and cemeteries. FIDs were recorded for eighty-one bird species. Mean species-specific FIDs ranged from 1.9 to 19.7 m for species with at least two observations (fifty-seven species). Using Bayesian regression modelling and controlling for the phylogenetic relatedness of the FID among bird species and city and country, we found that, in contrast to a recent publication from Europe, birds escape earlier in cemeteries than parks in the studied Latin American cities. FIDs were also significantly shorter in urban areas than in peri-urban areas and in areas with higher human density. Our results indicate that some idiosyncratic patterns in animal fearfulness towards humans may emerge among different geographic regions, highlighting difficulties with scaling up and application of regional findings to other ecosystems and world regions. Such differences could be associated with intrinsic differences between the pool of bird species from temperate European and mostly tropical Latin American cities, characterized by different evolutionary histories, but also with differences in the historical process of urbanization., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Espinilho savanna ("seasonal steppe savanna") is a unique vegetation formation of the Pampas biome that is found near the tri-border of Brazil, Uruguay, and Argentina. The Yellow Cardinal (Gubernatrix cristata) is a flagship species of this ecosystem, but it is classified as "critically endangered" in Brazil due to habitat loss and poaching for the illegal trade. Population supplementation through the release of individuals that were captive-bred or apprehended by authorities from the illegal trade has been considered as a conservation strategy for this species; however, the risk of pathogen introduction is a critical concern. We used microscopy and molecular methods to investigate the occurrence of blood parasites in wild passerines (n = 64, including three Yellow Cardinals) at Espinilho State Park, Rio Grande do Sul, Brazil, and in captive Yellow Cardinals (n = 30) at three facilities in Brazil. Haemosporidian parasites were detected in the blood smears of 10.9% of the wild passerines, comprising the morphospecies Haemoproteus erythrogravidus in Rufous-collared Sparrow (Zonotrichia capensis), H. quiscalus in Grayish Baywing (Agelaioides badius), and H. tyranni in Great Kiskadee (Pitangus sulphuratus); these are the southernmost records for these morphospecies and their first record for the Pampas biome. No haemosporidian parasites were detected in the blood smears of the Yellow Cardinals, wild or captive. Microfilariae were detected in the blood smears of 14.1% of the wild passerines, including all wild Yellow Cardinals, and in 43.3% of captive Yellow Cardinals. Trypanosoma sp. was detected in the blood smear of one captive Yellow Cardinal. Nested PCR and gene sequencing of the cyt-b gene of Haemoproteus/Plasmodium was used to test a subset of wild passerines and captive Yellow Cardinals, allowing for the molecular barcoding of H. quiscalus lineage AGEBAD04 and H. tyranni lineage PITSUL01; additionally, DNA identical to that of lineage PITSUL01 was detected in the blood of one captive Yellow Cardinal. This study provides valuable data to support the conservation management of the Yellow Cardinal and other threatened passerines from the Pampas and highlights the need for further studies on the epidemiology and pathology of filarioid worms and trypanosomes in passerines from this biome., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Tawny-bellied Seedeater (Sporophila hypoxantha) is an endangered (in Brazil) grassland dependent species, whose breeding success remains poorly known hampering conservation measures on its breeding grounds. Here we analyze the nest survival of the species in relation to temporal and environmental variables over three breeding seasons in hilly dry grasslands in southern Brazil. The apparent nest success was 40%, and MARK survival 20%. Predation was the main cause of failure, affecting 55% of the unsuccessful nests, followed by desertion, infestation by Philornis fly larvae, cattle trampling and burning. The productivity was 1.77 young per pair. Best models include time-specific factors (nest age and time of breeding season), reflected by a gradual reduction in nest survival over the nesting cycle, accompanied by an increase in temperature, subcutaneous larvae infestation, and predation. Nest site characteristics did not influence nest survival. Predation is more prevalent in the nestling rearing period than during incubation. This tendency may be caused by an increase in the activity in the nests, as is predicted by the Skutch hypothesis. The conclusion that time-specific factors influence nest survival more than ecological variables is important to plan on seasonally dependent conservation and management measures.

Host phylogenetic relatedness and ecological similarity are thought to contribute to parasite community assembly and infection rates. However, recent landscape level anthropogenic changes may disrupt host-parasite systems by impacting functional and phylogenetic diversity of host communities. We examined whether changes in host functional and phylogenetic diversity, forest cover, and minimum temperature influence the prevalence, diversity, and distributions of avian haemosporidian parasites (genera Haemoproteus and Plasmodium) across 18 avian communities in the Atlantic Forest. To explore spatial patterns in avian haemosporidian prevalence and taxonomic and phylogenetic diversity, we surveyed 2241 individuals belonging to 233 avian species across a deforestation gradient. Mean prevalence and parasite diversity varied considerably across avian communities and parasites responded differently to host attributes and anthropogenic changes. Avian malaria prevalence (termed herein as an infection caused by Plasmodium parasites) was higher in deforested sites, and both Plasmodium prevalence and taxonomic diversity were negatively related to host functional diversity. Increased diversity of avian hosts increased local taxonomic diversity of Plasmodium lineages but decreased phylogenetic diversity of this parasite genus. Temperature and host phylogenetic diversity did not influence prevalence and diversity of haemosporidian parasites. Variation in the diversity of avian host traits that promote parasite encounter and vector exposure (host functional diversity) partially explained the variation in avian malaria prevalence and diversity. Recent anthropogenic landscape transformation (reduced proportion of native forest cover) had a major influence on avian malaria occurrence across the Atlantic Forest. This suggests that, for Plasmodium, host phylogenetic diversity was not a biotic filter to parasite transmission as prevalence was largely explained by host ecological attributes and recent anthropogenic factors. Our results demonstrate that, similar to human malaria and other vector-transmitted pathogens, prevalence of avian malaria parasites will likely increase with deforestation., (Copyright © 2021 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.)

The Program for Biodiversity Research (PPBio) is an innovative program designed to integrate all biodiversity research stakeholders. Operating since 2004, it has installed long-term ecological research sites throughout Brazil and its logic has been applied in some other southern-hemisphere countries. The program supports all aspects of research necessary to understand biodiversity and the processes that affect it. There are presently 161 sampling sites (see some of them at Supplementary Appendix), most of which use a standardized methodology that allows comparisons across biomes and through time. To date, there are about 1200 publications associated with PPBio that cover topics ranging from natural history to genetics and species distributions. Most of the field data and metadata are available through PPBio web sites or DataONE. Metadata is available for researchers that intend to explore the different faces of Brazilian biodiversity spatio-temporal variation, as well as for managers intending to improve conservation strategies. The Program also fostered, directly and indirectly, local technical capacity building, and supported the training of hundreds of undergraduate and graduate students. The main challenge is maintaining the long-term funding necessary to understand biodiversity patterns and processes under pressure from global environmental changes.

Despite the importance and ubiquity of grasslands, the degradation and the loss of these habitats have negatively affected bird populations throughout the world. The use of fire to manage grassland areas in some regions of southern Brazil can help to maintain these areas but can also influence the bird community in different ways. We assessed temporal changes in richness, abundance, and composition of bird communities in areas with different histories of fire disturbance in highland grasslands of southern Brazil, the most extensive remnant of grassland of the Atlantic Forest domain. We censused birds during four breeding seasons (2015-2018), through point counts in areas burned only once in the last ten years (OF, n = 3), areas burned annually (AF, n = 2), and areas without fire in the last ten years (WF, n = 2). In OF the richness, abundance, and species composition changed in the year of the fire, compared to the previous year, and returned to the initial values two years later. In AF and WF we found some differences among the years, but not with an equally clear pattern. Three of the six grassland associated species assessed individually for density responded significantly to temporal habitat modification since the fire. Our results show that two years without fire were enough time for the bird community to recover after a fire, but some responses are species-specific. Therefore, fire can be used as a management tool for grasslands and may help in the conservation of birds of southern Brazil, as long as with a minimum interval between fires in an area is guaranteed., Competing Interests: The authors have declared that no competing interests exist.

Grassland ecosystems are evolutionarily linked to disturbances such as grazing and fire. These disturbances define grassland plant communities and habitat heterogeneity, which influence animal communities. We evaluated the influence of fire disturbance on plant and bird communities and on habitat structure by sampling grassland fragments with different time elapsed since the last fire event. Habitat structure was sampled using plant life forms and abiotic variables and birds were sampled through point counts. We recorded 862 bird individuals from 70 species. Intermediately-burnt sites harbor higher habitat heterogeneity and plant species richness in comparison with recently or long-burnt sites. Bird abundance and taxonomic diversity decreased linearly as time since fire increased. Finally, time since fire influenced the relative distribution of plant life forms and bird food guilds. Our results indicate that fire management should be included in the framework for conservation and sustainable use of grasslands, because it promotes habitat heterogeneity and diversity. To maintain habitat heterogeneity and the related habitat-specific bird species and functional groups, conservation efforts should maintain grassland patches under different management intensities and frequencies on a landscape level. However, studies focused on determining the periodicity with which fire management should be used are still lacking.

Geographic variation in environmental conditions as well as host traits that promote parasite transmission may impact infection rates and community assembly of vector-transmitted parasites. Identifying the ecological, environmental and historical determinants of parasite distributions and diversity is therefore necessary to understand disease outbreaks under changing environments. Here, we identified the predictors and contributions of infection probability and phylogenetic diversity of Leucocytozoon (an avian blood parasite) at site and species levels across the New World. To explore spatial patterns in infection probability and lineage diversity for Leucocytozoon parasites, we surveyed 69 bird communities from Alaska to Patagonia. Using phylogenetic Bayesian hierarchical models and high-resolution satellite remote-sensing data, we determined the relative influence of climate, landscape, geography and host phylogeny on regional parasite community assembly. Infection rates and parasite diversity exhibited considerable variation across regions in the Americas. In opposition to the latitudinal gradient hypothesis, both the diversity and prevalence of Leucocytozoon parasites decreased towards the equator. Host relatedness and traits known to promote vector exposure neither predicted infection probability nor parasite diversity. Instead, the probability of a bird being infected with Leucocytozoon increased with increasing vegetation cover (NDVI) and moisture levels (NDWI), whereas the diversity of parasite lineages decreased with increasing NDVI. Infection rates and parasite diversity also tended to be higher in cooler regions and higher latitudes. Whereas temperature partially constrains Leucocytozoon diversity and infection rates, landscape features, such as vegetation cover and water body availability, play a significant role in modulating the probability of a bird being infected. This suggests that, for Leucocytozoon, the barriers to host shifting and parasite host range expansion are jointly determined by environmental filtering and landscape, but not by host phylogeny. Our results show that integrating host traits, host ancestry, bioclimatic data and microhabitat characteristics that are important for vector reproduction are imperative to understand and predict infection prevalence and diversity of vector-transmitted parasites. Unlike other vector-transmitted diseases, our results show that Leucocytozoon diversity and prevalence will likely decrease with warming temperatures., (© 2019 The Authors. Journal of Animal Ecology © 2019 British Ecological Society.)

Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we are limited in our understanding of intra- and interspecies spatial morphological variation. Here, we present the ATLANTIC BIRD TRAITS, a data set that includes measurements of up to 44 morphological traits in 67,197 bird records from 2,790 populations distributed throughout the Atlantic forests of South America. This data set comprises information, compiled over two centuries (1820-2018), for 711 bird species, which represent 80% of all known bird diversity in the Atlantic Forest. Among the most commonly reported traits are sex (n = 65,717), age (n = 63,852), body mass (n = 58,768), flight molt presence (n = 44,941), molt presence (n = 44,847), body molt presence (n = 44,606), tail length (n = 43,005), reproductive stage (n = 42,588), bill length (n = 37,409), body length (n = 28,394), right wing length (n = 21,950), tarsus length (n = 20,342), and wing length (n = 18,071). The most frequently recorded species are Chiroxiphia caudata (n = 1,837), Turdus albicollis (n = 1,658), Trichothraupis melanops (n = 1,468), Turdus leucomelas (n = 1,436), and Basileuterus culicivorus (n = 1,384). The species recorded in the greatest number of sampling localities are Basileuterus culicivorus (n = 243), Trichothraupis melanops (n = 242), Chiroxiphia caudata (n = 210), Platyrinchus mystaceus (n = 208), and Turdus rufiventris (n = 191). ATLANTIC BIRD TRAITS (ABT) is the most comprehensive data set on measurements of bird morphological traits found in a biodiversity hotspot; it provides data for basic and applied research at multiple scales, from individual to community, and from the local to the macroecological perspectives. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or teaching and educational activities., (© 2019 The Authors. Ecology © 2019 The Ecological Society of America.)

Identifying the ecological factors that shape parasite distributions remains a central goal in disease ecology. These factors include dispersal capability, environmental filters and geographic distance. Using 520 haemosporidian parasite genetic lineages recovered from 7,534 birds sampled across tropical and temperate South America, we tested (a) the latitudinal diversity gradient hypothesis and (b) the distance-decay relationship (decreasing proportion of shared species between communities with increasing geographic distance) for this host-parasite system. We then inferred the biogeographic processes influencing the diversity and distributions of this cosmopolitan group of parasites across South America. We found support for a latitudinal gradient in diversity for avian haemosporidian parasites, potentially mediated through higher avian host diversity towards the equator. Parasite similarity was correlated with climate similarity, geographic distance and host composition. Local diversification in Amazonian lineages followed by dispersal was the most frequent biogeographic events reconstructed for haemosporidian parasites. Combining macroecological patterns and biogeographic processes, our study reveals that haemosporidian parasites are capable of circumventing geographic barriers and dispersing across biomes, although constrained by environmental filtering. The contemporary diversity and distributions of haemosporidian parasites are mainly driven by historical (speciation) and ecological (dispersal) processes, whereas the parasite community assembly is largely governed by host composition and to a lesser extent by environmental conditions., (© 2019 John Wiley & Sons Ltd.)

In vocal learning birds, memorization and song production rely on a set of telencephalic nuclei referred to as the song control system. Seasonal changes in song production are correlated with changes in the volume of the song control nuclei and are influenced by photoperiodic conditions and hormonal cues. The seasonal volume changes in the avian brain that controls singing are thought to involve regulation of neuronal replacement, which is a striking example of neuronal plasticity. The Rufous-bellied Thrush (Turdus rufiventris) is a seasonally breeding bird that actively sings during the spring and summer (breeding season) and is relatively silent in the fall, yet possible mechanisms behind the periodic changes in song production remain unknown. Here, we have examined two song control nuclei: High vocal center (HVC) and robust nucleus of arcopallium (RA) in fall males, spring males, and fall females of Rufous-bellied Thrush. The cytoarchitectonic organization was analyzed and quantified from Nissl-stained sections, and gene expression of song nuclei markers was examined by in situ hybridization during breeding and nonbreeding seasons. We observed a reduction in HVC volume and reductions in parvalbumin, and RGS4 expression in HVC and RA in males during the nonbreeding season. These findings provide evidence of seasonal changes in the song system of a representative tropical-breeding Turdidae species that does not maintain territories or mate bonding, setting the histological and molecular groundwork for future studies aimed at better understanding of song nuclei changes in seasonally breeding songbirds., (© 2019 Wiley Periodicals, Inc.)

Instances of recent and rapid speciation are suitable for associating phenotypes with their causal genotypes, especially if gene flow homogenizes areas of the genome that are not under divergent selection. We study a rapid radiation of nine sympatric bird species known as capuchino seedeaters, which are differentiated in sexually selected characters of male plumage and song. We sequenced the genomes of a phenotypically diverse set of species to search for differentiated genomic regions. Capuchinos show differences in a small proportion of their genomes, yet selection has acted independently on the same targets in different members of this radiation. Many divergent regions contain genes involved in the melanogenesis pathway, with the strongest signal originating from putative regulatory regions. Selection has acted on these same genomic regions in different lineages, likely shaping the evolution of cis-regulatory elements, which control how more conserved genes are expressed and thereby generate diversity in classically sexually selected traits.

Among known bird species, oscines are one of the few groups that produce complex vocalizations due to vocal learning. One of the most conspicuous oscine passerines in southeastern South America is the Rufous-bellied Thrush, Turdus rufiventris. The complete mitochondrial genome of this species was sequenced with the Illumina HiSeq platform (Illumina Inc., San Diego, CA), assembled using MITObim software and annotated by MITOS web server and Artemis software. This mitogenome contained 16 669 bases, organized as 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (d-loop). The sequencing of the Rufous-bellied Thrush mitochondrial genome is of particular interest for better understanding of population genetics and phylogeography of the Turdidae family.

Scytalopus and the recently erected Eleoscytalopus are among the Neotropical groups of birds whose taxonomy is most difficult to resolve given their very conservative morphology. We investigated the phylogeny and species limits of Eleoscytalopus and the eastern Scytalopus using two mitochondrial genes and two nuclear introns of multiple individuals from all species of these groups. The eastern Scytalopus are separated in three well defined clades also supported by morphological or vocal characteristics, although the relationships between these clades could not be resolved. We found several allopatric and very divergent lineages in these genera whose characteristics are consistent with species-level divergence, especially in S.speluncae. The great divergence between E. psychopompus and its sister species supports the former as a valid species. Our results corroborate the importance of the Bahia refuge as an avian center of endemism.