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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.

Long-term studies from undisturbed forests provide a baseline by which to assess impacts of human activities, including climate change, on vertebrate population dynamics in lowland tropical forests. We use camera-trap data from January to March, 2005 to 2015, to examine patterns of variation in numbers of images and occupancy (proportion of cameras where images of a species were obtained), variables that may reflect changes in abundance or activity patterns of terrestrial mammals and birds in an undisturbed lowland forest of eastern Ecuador. We accumulated 1,961 independent records of 31 mammal species and 427 images of 17 bird species during 5,547 trap-days. Number of mammal species ranged from 15 to 25 per year (107 to 466 images), whereas birds ranged from 3 to 11 species per year (10 to 122 images). Capture rates varied both among species and among years but showed no evidence of declines; populations of several species appeared to increase (Priodontes maximus, Dasypus novemcinctus, Pecari tajacu, and Dasyprocta fuliginosa). Similarly, occupancy rates provided no indication of consistent declines; occupancy rates increased significantly for D. fuliginosa, D. novemcinctus, and P. maximus. There was no indication that variation in either capture rates or occupancy was related to variation in large-scale climate trends as represented by the Southern Oscillation Index. Results suggest that populations of most species that are well sampled by camera traps have remained relatively stable over 11 years. Long-term studies from other regions in the tropics are needed to evaluate the generality of this pattern.Estudios a largo plazo en bosques no alterados por humanos son necesarios para determinar los impactos actuales y futuros de las actividades humanas, incluyendo el cambio climático, en la dinámica de las poblaciones de vertebrados en los bosques bajos tropicales. Utilizamos datos de cámaras trampa de enero a marzo desde 2005 hasta 2015 para examinar patrones de variación en número de imágenes y ocupación (proporción de cámaras en las cuales se obtuvo la imagen de una especie), variables que pueden reflejar cambios en la abundancia o patrones de actividad de mamíferos y aves terrestres grandes en un bosque tropical de tierras bajas no alterado del oriente de Ecuador. Se obtuvieron 1,961 registros independientes de 31 especies de mamíferos y 427 imágenes de 17 especies de aves durante 5,547 días-trampa. El número de especies de mamíferos osciló entre 15 a 25 por año (107 a 466 imágenes), mientras que el de aves osciló entre 3 a 11 especies por año (10 a 122 imágenes). Las tasas de captura variaron tanto entre especies como entre años, pero no mostraron evidencia de descenso en las poblaciones; las poblaciones de varias especies parecieron incrementarse (Priodontes maximus, Dasypus novemcinctus, Pecari tajacu, Dasyprocta fuliginosa). De igual manera, las tasas de ocupación no mostraron indicios de declinaciones consistentes; las tasas de ocupación se incrementaron significativamente para D. fuliginosa, D. novemcinctusy P. maximus. No hubo indicios de que la variación en cualquiera de los índices (tasas de captura, ocupación) estuviera relacionada con la variación en las tendencias climáticas a gran escala, representado por el Índice de Oscilación del Sur (Southern Oscillation Index). Los resultados sugieren que las poblaciones de la mayoría de especies que son bien monitoreadas por cámaras trampa han permanecido relativamente estables en los últimos 11 años. Se necesitan estudios adicionales a largo plazo de otras regiones de los trópicos para evaluar la generalidad de este patrón.

Parasites of the genera Plasmodium and Haemoproteus (Apicomplexa: Haemosporida) are a diverse group of pathogens that infect birds nearly worldwide. Despite their ubiquity, the ecological and evolutionary factors that shape the diversity and distribution of these protozoan parasites among avian communities and geographic regions are poorly understood. Based on a survey throughout the Neotropics of the haemosporidian parasites infecting manakins (Pipridae), a family of Passerine birds endemic to this region, we asked whether host relatedness, ecological similarity and geographic proximity structure parasite turnover between manakin species and local manakin assemblages. We used molecular methods to screen 1343 individuals of 30 manakin species for the presence of parasites. We found no significant correlations between manakin parasite lineage turnover and both manakin species turnover and geographic distance. Climate differences, species turnover in the larger bird community and parasite lineage turnover in non-manakin hosts did not correlate with manakin parasite lineage turnover. We also found no evidence that manakin parasite lineage turnover among host species correlates with range overlap and genetic divergence among hosts. Our analyses indicate that host switching (turnover among host species) and dispersal (turnover among locations) of haemosporidian parasites in manakins are not constrained at this scale. [ABSTRACT FROM AUTHOR]

Ocelots (Leopardus pardalis) are common in lowland forests of Amazonia. We used camera traps to document the occurrence and activity of ocelots at a site in eastern Ecuador during 2005–2012 (15,058 trap-days). We accumulated 384 independent images of 16 males (147 images), 19 females (234 images), and 3 not assigned to individual or sex. Individuals varied in number of images (1 to > 50), number of camera locations (1–8), and number of months from first to last image (1–85). Photographic rate varied across years, from 15.3 to 29.9/1,000 trap-days in 2006 and 2010, respectively. Males and females were primarily active at night and showed similar hourly patterns of activity. Up to 3 individual males and 4 individual females were recorded at different camera locations each year. Resident males typically were photographed at more locations (mean of 4.1) than females (mean of 3.2). Results indicate that multiple ocelots, of both sexes, may be found within a relatively small (~650 ha) area of lowland forest in eastern Ecuador and emphasize the importance of the region for conservation of ocelots and other species.Los ocelotes (Leopardus pardalis) son felinos comunes en los bosques de tierras bajas de la Amazonía. Utilizamos cámaras trampa para documentar la ocurrencia y actividad de ocelotes en un sitio en el Este de Ecuador durante 2005–2012 (15.058 días-trampa). Acumulamos 384 imágenes independientes de 16 machos (147 fotografías), 19 hembras (234 fotografías), y tres a los que no se les asignó individuo o sexo. Los individuos variaron en número de imágenes (1 a > 50), número de locaciones de las cámaras (1 a 8) y en el número de meses desde la primera hasta la última imagen (1 a 85). La tasa de captura fotográfica varió a través de los años, de 15,3 a 29,9 / 1.000 días-trampa en 2006 y 2010, respectivamente. Machos y hembras fueron activos principalmente durante la noche y mostraron patrones similares de actividad por hora. Hasta tres individuos machos y cuatro individuos hembras fueron registrados en diferentes locaciones cada año. Machos residentes fueron fotografiados en más lugares (media de 4,1) que hembras (media de 3,2). Los resultados indican que varios ocelotes, de ambos sexos, pueden encontrarse dentro de un área relativamente pequeña (~ 650 ha) de bosques de tierras bajas en el Este de Ecuador y enfatizan en la importancia de la región para la conservación de ocelotes y otras especies.

Spatial distribution of fruit-eating birds and fruiting shrubs of the Melastomataceae and Rubiaceae were examined on a 10 ha plot in tropical lowland wet forest of Costa Rica. Many plant species and most birds exhibited considerable spatial variation in their occurrence on the plot, as indicated by the distribution patterns of shrubs with ripe fruits and captures in mist nets, respectively. In many cases, captures of fruit-eating birds were correlated with abundance of fruiting plants, particularly for species that rely heavily on fruits. In general, fruit-eating birds concentrated their use of the plot to areas rich in fruiting shrubs. This differential use of certain areas likely results in differential visitation to fruiting plants located in these areas and in a heterogeneous dissemination of seeds into the habitat.

The probability of interspecific seedling competition from bird droppings is high because fruit-eating birds, on average, deposit more than two species in a single dropping. Moreover, birds vary both in the number of plant species they deposit in a given dropping and in the seed composition of those droppings. In a preliminary experiment, I examined effects of interspecific seedling competition from seeds found in bird droppings. Certain plant species were competitively superior in pairwise growth experiments using six common second-growth species. The survival of certain shrubs depended on which species it was disseminated with in bird droppings. Rapid germination time may promote competitive superiority in some cases. Birds affect plant fitness not only because of their behavior following dispersal, but also because they deposit seeds in different densities and combinations.

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.

We investigated species composition of the bat assemblage in continuous forest and natural forest islands in a savanna ecosystem in northern Bolivia. We captured 396 bats of 24 species. Five species accounted for almost 70% of the captures: Sturnira lilium, Artibeus obscurus, Carollia brevicauda, Carollia perspicillata, and Artibeus lituratus. Species composition of the bat assemblage differed between continuous forest and forest islands; Artibeus jamaicensis and S. lilium were captured more often in islands, whereas Platyrrhinus helleri and Mesophylla macconnelli were more common in the continuous forest. The distribution of species over the forest islands and the continuous forest revealed a nested distribution pattern, with the continuous forest having the highest number of species, and the smallest island having the fewest species. However, bats were almost 5-fold more abundant in forest islands than in continuous forest. Examination of recapture data indicated movements of bats among forest islands and between islands and continuous forest. Our results suggest that bat populations, especially in the fruit-eating guild, can persist in a naturally fragmented landscape.