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The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.

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The primary (PSR), secondary (SSR) and adult (ASR) sex ratios of sexually reproducing organisms influence their life histories. Species exhibiting reversed sexual size dimorphism (RSD) may imply a higher cost of female production or lower female survival, thus generating biases in PSR, SSR and/or ASR towards males. The Harpy Eagle is the world's largest eagle exhibiting RSD. This species is found in the Neotropical region and is currently threatened with extinction. We used molecular markers to determine the sex of 309 Harpy Eagles spanning different life stages-eaglets, subadults and adults-from 1904 to 2021 within the Amazon Rainforest and Atlantic Forest. Sex ratios for all life stages revealed a female-biased deviation across all periods and regions. Our results suggest that the population bias towards females is an evolutionary ecological pattern of this species, and SSR and ASR likely emerged from the PSR. This natural bias towards females may be compensated by an earlier sexual maturation age of males, implying a longer reproductive lifespan and a higher proportion of sexually active males. A better understanding of the Harpy Eagle's life history can contribute to understanding sex-role evolution and enable more appropriate conservation strategies for the species.

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The Harpy Eagle (Harpia harpyja) is threatened with extinction throughout its distribution in the neotropical forests. In the Atlantic Forest, deforestation has reduced the number of suitable habitats, with only a few remnant forest fragments hosting active nests; currently, the only known nests in this region are in the Central Atlantic Forest Ecological Corridor (CAFEC), in Brazil. Little is known about Harpy Eagle diets in this region, despite this information being essential for developing effective conservation strategies. We classified the composition, frequency, richness, ecological attributes, and conservation status of the species that make up the Harpy Eagle's diet in its last refuges in the CAFEC. Between 2017 and 2021, we collected and analyzed 152 prey remains and 285 camera trap photographs from seven active nests. We identified at least 16 mammal species (96.7%), one parrot and other bird remains (3.3%). The Harpy Eagle's diet consisted mainly of medium-sized arboreal, folivorous, frugivorous, and diurnal mammals. Five prey species are currently threatened with extinction at global, six at national and seven at regional levels. The majority of the diet consists of Sapajus robustus, which is threatened, and Bradypus variegatus, which is not threatened. In addition to the effects of habitat loss and hunting, the Harpy Eagle may also suffer from the decline in the populations of their prey in the Atlantic Forest.

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Morphnus guianensis is a species belonging to the Accipitridae family classified as almost threatened by the International Union for Conservation of Nature (IUCN). Trypanosomes are flagellated protozoa that carry out their life cycle in the circulatory system of vertebrate hosts and within the digestive tract of invertebrate hosts. This study recorded Trypanosoma sp. parasitizing M. guianensis in the Brazilian Amazon, providing data related to the morphology and morphometry of the trypomastigote forms of peripheral blood of this bird. The mean values of the measured morphological regions were used to compare morphometric similarity with morphotypes described for Trypanosoma sp. through the Bray-Curtis method and, after statistical analysis, the dendrogram was generated from the morphological similarities with a similarity greater than 95% with T. paddae described for different hosts in different geographical regions.

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Habitat loss and fragmentation intensify the effects of genetic drift and endogamy, reducing genetic variability of populations with serious consequences for wildlife conservation. The Harpy Eagle (Harpia harpyja) is a forest dwelling species that is considered near threatened and suffers from habitat loss in the forests of the Neotropical region. In this study, 72 historical and current samples were assessed using eight autosomal microsatellite markers to investigate the distribution of genetic diversity of the Harpy Eagle of the Amazonian and Atlantic forests in Brazil. The results showed that the genetic diversity of Harpy Eagle decreased in the regions where deforestation is intense in the southern Amazon and Atlantic Forest.

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This study evaluated the potential of lowland tapirs as seed dispersers in the northern Brazilian Amazon. The study analyzed the viability of seeds after passage through the gut. Fecal samples were collected from 6 different vegetation physiognomies in Viruá National Park during the dry season. The samples were then kept in a greenhouse for 16 months to allow the seeds to germinate. The seedling species were identified and classified according to the type of fruit, plant habit, seed size and type of ingestion. Of the 111 fecal samples, 94 (84.7%) had viable seeds of 75 species. Melastomataceae was the most frequent family with viable seeds in the fecal samples (69.1% of samples, N= 18 species). The data suggest that the importance of the lowland tapirs as dispersers is not restricted to the species consumed actively by frugivory but also extends to species accidentally consumed during browsing. The occurrence of both large and small viable seeds in the fecal samples as well as a number of large drupes, which probably cannot be transported via endozoochory by any other animal species, provide evidence of the ecological importance of lowland tapirs to the dynamics of the forest-campinarana vegetation mosaic in the region.

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Riparian habitats are important for the maintenance of regional biodiversity. Many studies have compared bird distributions between riparian and non-riparian habitats but have not established how wide riparian habitats used by birds are, as measured by distance from the nearest stream. We investigated the distribution of understory birds along gradients of distance from streams, soil clay content, and slope in a central Amazonian forest, by mist-netting birds three times in 45 plots. We used nonmetric multidimensional scaling (NMDS) to reduce the dimensionality of species quantitative (abundance) and qualitative (presence-absence) composition to one multivariate axis. Estimates of the width of riparian habitats as indicated by understory birds depended on the community attribute considered, measuring 90 m for species quantitative composition and 140 m for species qualitative composition. Species distributions were correlated with clay content but were independent of slope, while distance from streams was positively correlated with clay content but independent of slope. Clay content affects plant species composition, which in turn, may influence bird species composition. However, distribution patterns of birds in relation to distance from streams are consistent among studies carried out in many different temperate and tropical regions, indicating an effect of distance from streams itself. Protection of riparian habitats is one of the most widely used conservation strategies, and Brazilian environmental legislation mandates the protection of a 30 m wide strip of riparian vegetation on either side of small streams. We show that the protected strip should be much wider and recommend strategies to place other forms of land protection contiguous with riparian areas so that Brazilian environmental legislation better fulfills its role of protecting biodiversity associated with riparian habitats.

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Nós capturamos pequenos mamíferos em oito fragmentos florestais (43 a 1.411 ha) nos períodos seco e chuvoso, no sudoeste de Mato Grosso, Brasil, e investigamos a variação na riqueza e na abundância de pequenos mamíferos e em variáveis relacionadas à estrutura da floresta (volume da liteira e abertura do dossel) e à disponibilidade de artrópodes, entre os dois períodos do ano. As amostragens foram realizadas durante o período chuvoso entre 2002 e 2003 e durante período seco de 2003. Em cada fragmento, foram utilizadas armadilhas Sherman, Tomahawk, Snap trap e Pitfall durante 10 dias consecutivos em cada época do ano, totalizando 17.600 armadilhas x noites. Foram obtidas no total 379 capturas de 20 espécies, sendo sete de marsupiais e 13 de roedores, com sucesso de captura de 2,2 por cento (1,6 por cento para o período chuvoso e 2,7 por cento para o período seco). Não houve diferenças significativas na riqueza total, riqueza de roedores, riqueza de marsupiais, abundância total e abundância de roedores entre os períodos seco e chuvoso. Já a abundância de marsupiais foi significativamente maior na época da seca, quando a quantidade de chuvas é menor. O volume da liteira foi significativamente maior durante a seca, enquanto a disponibilidade de artrópodes foi significativamente maior durante o período chuvoso. Sendo assim, a grande disponibilidade de alimento no ambiente durante a estação chuvosa pode ter tornado as iscas das armadilhas menos atrativas. De maneira geral, as variações entre períodos seco e chuvoso observados estão de acordo com padrões descritos em outros estudos.

We captured small mammals in eight forest fragments (43 a 1.411 ha.) during the dry and wet seasons, in southwest Mato Grosso, Brazil, and investigated the variation in small mammal richness and abundance, as well as in forest structure variables (litter volume and canopy openness) and arthropod availability, between the two seasons. Sampling was carried out during the wet season between 2002 and 2003 and in the dry season of 2003. In each fragment, we used Sherman, Tomahawk, snap, and pitfall traps during 10 consecutive days per season, totaling 17,600 trap x nights. In total, we obtained 379 captures of 20 species, seven of marsupials and 13 of rodents. Overall capture success was 2.2 percent (1.6 percent during the wet season and 2.7 percent during the dry season). Total richness, richness of rodents, richness of marsupials, total abundance and abundance of rodents did not varied significantly between seasons. However, marsupial abundance was significantly lower in the dry season, when rainfall is high. Litter volume was significantly higher during the dry season, while arthropod availability was significantly higher during the wet season. Therefore, higher food availability during the wet season may have made trap baits less attractive. In general, the observed variations between dry and wet seasons are in accordance with patterns described in other studies.

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We report the characterization and optimization of 45 heterologous microsatellite loci, and the development of a new set of molecular sex markers for the conservation and management of the Neotropical harpy eagle (Harpia harpyja L. 1758). Of the 45 microsatellites tested, 24 were polymorphic, six monomorphic, 10 uncharacterizable due to multiple bands and five did not amplify. The observed gene diversity of the analyzed sample of H. harpyja was low and similar to that of other threatened Falconiformes. While a high proportion of the microsatellite markers were highly variable, individuals of H. harpyja could be differentiated by a joint analysis of just three (p = 2.79 x 10-4) or four markers (p = 2.89 x 10-5). Paternity could be rejected with 95.23 percent and 97.83 percent probabilities using the same three and four markers, respectively. The sex determination markers easily and consistently differentiated males from females even with highly degraded DNA extracted from naturally shed feathers. The markers reported in this study potentially provide an excellent set of molecular tools for the conservation and management of wild and captive H. harpyja and they may also prove useful for the enigmatic Neotropical crested eagle (Morphnus guianensis Daudin 1800).

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We studied the energy flow from C3 and C4 plants to higher trophic levels in a central Amazonian savanna by comparing the carbon stable-isotope ratios of potential food plants to the isotope ratios of species of different consumer groups. All C4 plants encountered in our study area were grasses and all C3 plants were bushes, shrubs or vines. Differences in δ13C ratios among bushes (x¯ = -30.8, SD = 1.2), vines (x¯ = -30.7, SD = 0.46) and trees (x¯ = -29.7, SD = 1.5) were small. However the mean δ13C ratio of dicotyledonous plants (x¯ = -30.4, SD = 1.3) was much more negative than that of the most common grasses (x¯ = -13.4, SD = 0.27). The insect primary consumers had δ13C ratios which ranged from a mean of -29.5 (SD = 0.47) for the grasshopper Tropidacris collaris to a mean of -14.7 (SD = 0.56) for a termite (Nasutitermes sp.), a range similar to that of the vegetation. However, the common insectivorous and omnivorous vertebrates had intermediate values for δ13C, indicating that carbon from different autotrophic sources mixes rapidly as it moves up the food chain. Despite this mixing, the frogs and lizards generally had higher values of δ13C (x¯ = -21.7, SD = 1.6; x¯ = -21.9, SD = 1.8, respectively) than the birds (x¯ = -24.8, SD = 1.8) and the only species of mammal resident in the savanna (x¯ = -25.4), indicating that they are generally more dependent on, or more able to utilise, food chains based on C4 grasses.