Phylogeny and historical biogeography of the swallow family (Hirundinidae) inferred from comparisons of thousands of UCE loci.

Swallows (Hirundinidae) are a globally distributed family of passerine birds that exhibit remarkable similarity in body shape but tremendous variation in plumage, sociality, nesting behavior, and migratory strategies. As a result, swallow species have become models for empirical behavioral ecology and evolutionary studies, and variation across the Hirundinidae presents an excellent opportunity for comparative analyses of trait evolution. Exploiting this potential requires a comprehensive and well-resolved phylogenetic tree of the family. To address this need, we estimated swallow phylogeny using genetic data from thousands of ultraconserved element (UCE) loci sampled from nearly all recognized swallow species. Maximum likelihood, coalescent-based, and Bayesian approaches yielded a well-resolved phylogenetic tree to the generic level, with minor disagreement among inferences at the species level, which likely reflect ongoing population genetic processes. The UCE data were particularly useful in helping to resolve deep nodes, which previously confounded phylogenetic reconstruction efforts. Divergence time estimates from the improved swallow tree support a Miocene origin of the family, roughly 13 million years ago, with subsequent diversification of major groups in the late Miocene and Pliocene. Our estimates of historical biogeography support the hypothesis that swallows originated in the Afrotropics and have subsequently expanded across the globe, with major in situ diversification in Africa and a secondary major radiation following colonization of the Neotropics. Initial examination of nesting and sociality indicates that the origin of mud nesting - a relatively rare nest construction phenotype in birds - was a major innovation coincident with the origin of a clade giving rise to over 40% of extant swallow diversity. In contrast, transitions between social and solitary nesting appear less important for explaining patterns of diversification among swallows.

Passerine sister clade comparisons reveal variable macroevolutionary outcomes of interhemispheric dispersal.

Dispersal events offer a unique window into macroevolutionary processes, especially with respect to the effects of competition on diversification. Empirical studies testing alternative predictions of competitive effects are often limited in either geographic or phylogenetic scale. Here, we tested some of these hypotheses by comparing an assemblage of 16 oscine passerine clades, representing independent dispersal events into the Western Hemisphere, to their sister clades in the Eastern Hemisphere. We also compared the diversity of this assemblage of clades to an older, incumbent passerine clade in the Western Hemisphere, the suboscines. Specifically, we tested for ecological opportunity and incumbency-mediated constraints by analysis of clade-specific morphological disparities and rates of evolution relative to dispersal history. While there was no consistent outcome of oscine dispersal and macroevolution in the Western Hemisphere relative to their Eastern Hemisphere sister groups, most clades supported a role for ecological opportunity or incumbency effects, and such effects were better explained by differences in species accumulation than by differences in rates of trait evolution or colonization timing. This general pattern was not evident when comparing the entire oscine assemblage of the Western Hemisphere to the incumbent suboscine radiation; oscines and suboscines occupy comparable regions of functional trait diversity and, despite higher rates of trait evolution in oscines, these observations were consistent with simulated null expectations. This result suggests that oscine and suboscine assemblages may have evolved in relative isolation for a significant fraction of their history.

Chasing and surfing seasonal waves: Avian migration through the US tracks land surface phenology in fall, but not spring.

Climate change is altering the timing of seasonal events for many taxa. There is limited understanding of how northward/southward songbird migration follows or is limited by the latitudinal progression of seasonal transitions. Consistent environmental conditions that migrating birds encounter across latitudes likely represent or correlate with important resources or limiting factors for migration. We tested whether migratory passage-observed via radar-consistently tracked land surface variables and phenophases across latitudes in the US Central Flyway in both spring and fall. The daily temperatures, precipitation and vegetation greenness occurring on 10%, 50% and 90% cumulative passage dates changed substantially with latitude, indicating that most migrants experienced rapidly changing conditions as they headed north or south. Temperature did not limit the progression of migration in either season. Peak spring migration in the southern US occurred nearly 40 days after the spring green wave, the northward progression of vegetation growth, but nearly caught up to green-up at 48° N. Spring migration phenology may have evolved to prioritize earlier arrival for breeding. Across all latitudes, peak fall migration coincided with the same land surface phenophase, an interval of 26 days prior to dormancy onset. Migrants may rely on phenological events in vegetation during fall stopovers. Considering that (a) migratory passage tracked fall land surface phenology across latitudes at a continental scale, (b) previous studies at local scales have demonstrated the importance of fruit during fall migratory stopover and (c) fruiting phenology in North America is occurring later over time while fall migration is advancing, the potential for mismatch between fall fruiting and bird migration phenology urgently needs further investigation.

Verification of accuracy of qPCR method for intravital diagnostics of Macrorhabdus ornithogaster in avian droppings.

The objective of this study was to verify the accuracy of the quantitative PCR (qPCR) method for in vivo detection of Macrorhabdus ornithogaster. A total of 100 faecal and gastric mucosa samples from avian cadavers were investigated, using cytological and qPCR techniques (budgerigars, Fischer's lovebirds, red-crowned parakeets, scarlet-chested parrots, eastern rosellas, domestic canaries, zebra finches, white Java sparrow). Using qPCR, the probability of detecting positive samples of droppings was significantly higher than in the faecal smear microscopy (P < 0.01). Cytology detected the presence of Macrorhabdus ornithogaster in 34 faecal samples, whereas qPCR detected 54 positive samples. In all 46 qPCR negative faecal samples, gastric smear qPCR was performed and also yielded negative results. Gastric smear qPCR was also performed in 20 cadavers where faecal qPCR has detected the presence of Macrorhabdus ornithogaster and in all samples confirmed the positive result. This verifies the accuracy of faecal sample qPCR for intravital diagnostics. Overall, the faecal qPCR technique appears to be extremely reliable, as it made it possible to detect all infected individuals, including those with negative stool or gastric cytology.

Reactions of wintering passerines to male calls of the European cuckoo Cuculus canorus.

The reaction of birds to the nest parasite, the European cuckoo Cuculus canorus, has been the subject of extensive testing in various aspects. However, while the cuckoo is a long-distance migrant, some of its hosts are sedentary species. In this study, we aimed to investigate whether species, primarily hosts, react to the presence of the cuckoo also in the winter season. This behaviour may involve an attempt to drive the parasite away from locations that will subsequently become their breeding sites. During playback experiments conducted in the winter of 2021/2022 in Poland, we demonstrated that numerous bird species react to the male cuckoo calls in winter. These calls may be perceived as a source of danger, particularly by cuckoo hosts, who responded to this call more frequently than non-hosts and the control species (pigeon). Nonetheless, the birds' reactions were not strong, as they did not approach the source of the call. However, our results are constrained by the limited number of cuckoo host species wintering in Poland. To better evaluate the intensity of bird responses to the male cuckoo's call during the non-breeding season, further studies should be conducted in regions where a greater variety of species, especially those most susceptible to parasitism, overwinter.

Cutaneous Lesions in the Gular Region Caused by Feather Follicle Infestation with Harpirhynchidae sp. Mites in Great Crested Flycatchers (Myiarchus crinitus) in New York, USA 2016-23.

Great Crested Flycatchers (Myiarchus crinitus), migratory passerines with a breeding range throughout the northeastern, midwestern, and southern US, are banded annually at the Braddock Bay Bird Observatory located on the southern shore of Lake Ontario, New York, USA. In 2016, a Great Crested Flycatcher was observed with distinct lesions in the gular and ventral neck region, which prompted evaluation for similar lesions in subsequently trapped flycatchers and other passerine species. From 2016 to 2023, 62/102 banded Great Crested Flycatchers had their gular region examined, and seven were found to have lesions (11.3% incidence). Similar lesions were not found in any other species. Lesions were localized to the gular region and included extensive feather loss with thickened, corrugated, pale-yellow skin. Grossly visible 1- to 2-mm-diameter, raised, white-to-yellow foci throughout the affected region corresponded microscopically to feather follicles that were massively dilated with mites. Morphologic analysis of mites obtained from skin scrapes revealed that this mite species belongs to the family Harpirhynchidae. Mites in this family have restricted avian host ranges and cause varying clinical presentations in passerines, though many species remain unidentified. PCR efforts were unsuccessful in yielding a species-level identification. Further monitoring of Great Crested Flycatchers and other avian species is warranted, as the fitness implications of this ectoparasitism at the individual and population levels are not known.

Exploring the Prevalence and Resistance of Campylobacter in Urban Bird Populations.

The increasing urbanization of ecosystems has had a significant impact on wildlife over the last few years. Species that find an unlimited supply of food and shelter in urban areas have thrived under human presence. Wild birds have been identified as amplifying hosts and reservoirs of Campylobacter worldwide, but the information about its transmission and epidemiology is still limited. This study assessed the prevalence of Campylobacter in 137 urban birds admitted at a wildlife rescue center, with 18.8% of individuals showing positive. C. jejuni was the most frequent species (82.6%), followed by C. coli and C. lari (4.3% each). The order Passeriformes (33.3%) showed significant higher presence of Campylobacter when compared to orders Columbiformes (0%) and Ciconiiformes (17.6%), as well as in samples collected during the summer season (31.9%), from omnivorous species (36.8%) and young individuals (26.8%). Globally, Campylobacter displayed a remarkable resistance to ciprofloxacin (70.6%), tetracycline (64.7%), and nalidixic acid (52.9%). In contrast, resistance to streptomycin was low (5.8%), and all the isolates showed susceptibility to erythromycin and gentamycin. The results underline the importance of urban birds as reservoirs of thermophilic antimicrobial-resistant Campylobacter and contribute to enhancing the knowledge of its distribution in urban and peri-urban ecosystems.

Molecular diagnosis of avian viruses in grassland passerines and captive yellow cardinals Gubernatrix cristata in Brazil / Diagnóstico molecular de vírus aviários em passeriformes campestres e cardeais-amarelos Gubernatrix cristata cativos no Brasil

Avian influenza viruses (AIVs), Newcastle disease virus (NDV), West Nile virus (WNV), adenovirus (AV) and herpesvirus (HV) play an important role in the health of human and animal populations. However, knowledge of the prevalence of these viruses in wild birds is restricted to some groups (e.g. shorebirds) or regions worldwide. Information on grassland birds of South America, which is essential for their conservation, is scarce. The objectives of the present study were to evaluate occurrences of AIV, NDV, WNV, AV and HV for the first time in a bird community of a unique protected area in southern Brazil, which is home for the critically endangered yellow cardinal (Gubernatrix cristata), and captive yellow cardinals from fauna maintainers of the Brazilian Captive Program of the Yellow Cardinal. Passerine species of wild life were caught, identified and samples (swabs) were collected from the oropharynx and cloaca of 64 passerines of 26 species (including 3 yellow cardinals) and 30 yellow cardinals of captive, for molecular diagnosis. The samples were subjected to RNA and DNA extraction and the real-time polymerase chain reaction (RT-PCR) for AIV, NDV and WNV and nested PCR for AV and HV. One yellow cardinal of captive presented a positive result for AV, this result is important for planning, managing natural attributes and making decisions in relation to integrated conservation of threatened species. This is the first report of AV in yellow cardinal and epidemiological investigation of viruses in wild passerines of the Pampa biome, in Rio Grande do Sul, Brazil.(AU)

Os vírus da gripe aviária (VGA), vírus da doença de Newcastle (VDN), vírus do Nilo Ocidental (VNO), adenovírus (AV) e herpesvírus (HV) desempenham um papel importante na saúde das populações humana e animal. No entanto, o conhecimento da prevalência desses vírus em aves selvagens é restrito a alguns grupos (por exemplo, aves limícolas) ou regiões em todo o mundo. As informações sobre as aves campestres da América do Sul, essenciais para a sua conservação, são escassas. Os objetivos do presente estudo foram avaliar a ocorrência de VGA, VDN, VNO, AV e HV pela primeira vez em uma comunidade de aves de uma área única protegida no Sul do Brasil, que abriga o cardeal-amarelo (Gubernatrix cristata) criticamente ameaçado de extinção e em cardeais-amarelos de cativeiro dos mantenedores de fauna do Programa Brasileiro de Cativeiro do Cardeal-amarelo. Espécies de passeriformes silvestres foram capturadas, identificadas e amostras (swabs) foram coletadas da orofaringe e cloaca de 64 passeriformes de 26 espécies (incluindo 3 cardeais-amarelos) e 30 cardeais-amarelos de cativeiro, para diagnóstico molecular. As amostras foram submetidas à extração de RNA e DNA e à reação em cadeia da polimerase em tempo real (RT-PCR) para VGA, VDN e VNO e nested PCR para AV e HV. Um cardeal-amarelo de cativeiro apresentou resultado positivo para AV, este resultado é importante para o planejamento, manejo dos atributos naturais e tomada de decisões em relação à conservação integrada de espécies ameaçadas. Este é o primeiro relato de AV em cardeal-amarelo e de investigação epidemiológica de vírus em passeriformes silvestres do bioma Pampa, no Rio Grande do Sul, Brasil.(AU)

Molecular diagnosis of avian viruses in grassland passerines and captive yellow cardinals Gubernatrix cristata in Brazil

ABSTRACT: Avian influenza viruses (AIVs), Newcastle disease virus (NDV), West Nile virus (WNV), adenovirus (AV) and herpesvirus (HV) play an important role in the health of human and animal populations. However, knowledge of the prevalence of these viruses in wild birds is restricted to some groups (e.g. shorebirds) or regions worldwide. Information on grassland birds of South America, which is essential for their conservation, is scarce. The objectives of the present study were to evaluate occurrences of AIV, NDV, WNV, AV and HV for the first time in a bird community of a unique protected area in southern Brazil, which is home for the critically endangered yellow cardinal (Gubernatrix cristata), and captive yellow cardinals from fauna maintainers of the Brazilian Captive Program of the Yellow Cardinal. Passerine species of wild life were caught, identified and samples (swabs) were collected from the oropharynx and cloaca of 64 passerines of 26 species (including 3 yellow cardinals) and 30 yellow cardinals of captive, for molecular diagnosis. The samples were subjected to RNA and DNA extraction and the real-time polymerase chain reaction (RT-PCR) for AIV, NDV and WNV and nested PCR for AV and HV. One yellow cardinal of captive presented a positive result for AV, this result is important for planning, managing natural attributes and making decisions in relation to integrated conservation of threatened species. This is the first report of AV in yellow cardinal and epidemiological investigation of viruses in wild passerines of the Pampa biome, in Rio Grande do Sul, Brazil.

RESUMO: Os vírus da gripe aviária (VGA), vírus da doença de Newcastle (VDN), vírus do Nilo Ocidental (VNO), adenovírus (AV) e herpesvírus (HV) desempenham um papel importante na saúde das populações humana e animal. No entanto, o conhecimento da prevalência desses vírus em aves selvagens é restrito a alguns grupos (por exemplo, aves limícolas) ou regiões em todo o mundo. As informações sobre as aves campestres da América do Sul, essenciais para a sua conservação, são escassas. Os objetivos do presente estudo foram avaliar a ocorrência de VGA, VDN, VNO, AV e HV pela primeira vez em uma comunidade de aves de uma área única protegida no Sul do Brasil, que abriga o cardeal-amarelo (Gubernatrix cristata) criticamente ameaçado de extinção e em cardeais-amarelos de cativeiro dos mantenedores de fauna do Programa Brasileiro de Cativeiro do Cardeal-amarelo. Espécies de passeriformes silvestres foram capturadas, identificadas e amostras (swabs) foram coletadas da orofaringe e cloaca de 64 passeriformes de 26 espécies (incluindo 3 cardeais-amarelos) e 30 cardeais-amarelos de cativeiro, para diagnóstico molecular. As amostras foram submetidas à extração de RNA e DNA e à reação em cadeia da polimerase em tempo real (RT-PCR) para VGA, VDN e VNO e nested PCR para AV e HV. Um cardeal-amarelo de cativeiro apresentou resultado positivo para AV, este resultado é importante para o planejamento, manejo dos atributos naturais e tomada de decisões em relação à conservação integrada de espécies ameaçadas. Este é o primeiro relato de AV em cardeal-amarelo e de investigação epidemiológica de vírus em passeriformes silvestres do bioma Pampa, no Rio Grande do Sul, Brasil.

Population structuring of the endemic black-cheeked gnateater, Conopophaga melanops melanops (Vieillot, 1818) (Aves, Conopophagidae), in the Brazilian Atlantic Forest

Randomly amplified polymorphic DNA (RAPD) markers were used to analyze genetic differentiation among three populations of the endemic Black-cheeked Gnateater (Conopophaga melanops melanops) within a larger pristine reminiscent of the Brazilian Atlantic Forest. Analyses of molecular variance (AMOVA) (phiST = 0.13149, P < 0.0001) and the nonparametric test for homogeneity of the molecular variance (HOMOVA) (B = 0.32337; P = 0.0019) showed a statistically significant genetic divergence among the three Black-cheeked Gnateater populations in a continuous transect of 250 km. Some hypothetic explanations for these results are the sedentary nature of the species and the historical isolation of the populations in refuges during the Pleistocene. The present results suggest that the local populations were naturally differentiated along the entire original range before the recent process of massive deforestation.

Marcadores polimórficos de DNA amplificados ao acaso (RAPD) foram utilizados para analisar a diferenciação genética entre três populações do endêmico cuspidor-de-máscara preta (Conopophaga melanops melanops) de um amplo remanescente preservado da floresta Atlântica brasileira. Análises de Variância Molecular (AMOVA) (fiST = 0,13149, P < 0,0001) e o teste não paramétrico para a homogeneidade da variância molecular (HOMOVA) (B = 0,32337; P = 0,0019) comprovaram uma divergência genética significativa entre as três populações em um transecto contínuo de 250 km. Algumas explicações hipotéticas para estes resultados são a natureza sedentária da espécie e o isolamento histórico das populações em refúgios durante o Pleistoceno. Os presentes resultados sugerem que as populações locais foram diferenciadas naturalmente ao longo da distribuição original antes do recente processo de intenso desmatamento.

Terrestrial passerines in an Atlantic forest remnant of Southern Brazil

Microhabitats of four terrestrial passerines were studied in an Atlantic forest remnant of southern Brazil, in two areas (northern and southern) of the Mata dos Godoy State Park (PG). Grallaria varia and Hylopezus nattereri showed low abundance and occurred in only one PG area, while Chamaeza campanisona and Corythopis delalandi were recorded in two. The microhabitats of C. campanisona, G. varia, and H. nattereri had many large trees and a dense understory. Corythopis delalandi was in areas having few large trees.

Os microhábitats de quatro passeriformes de solo foram estudados no Parque Estadual Mata dos Godoy, um fragmento de floresta Atlântica no Sul do Brasil. Grallaria varia e Hylopezus nattereri apresentaram baixa abundância e ocorrência em apenas uma área do PG, enquanto Chamaeza campanisona e Corythopis delalandi foram registrados nas duas áreas. Os microhábitats de C. campanisona, G. varia e H. nattereri apresentaram muitas árvores de grande porte e um estrato inferior denso. O microhábitat de C. delalandi apresentou poucas árvores de grande porte.