Tropical deforestation and forest fragmentation are among the most important biodiversity conservation issues worldwide, yet local extinctions of millions of animal and plant populations stranded in unprotected forest remnants remain poorly explained. Here, we report unprecedented rates of local extinctions of medium to large-bodied mammals in one of the world's most important tropical biodiversity hotspots. We scrutinized 8,846 person-years of local knowledge to derive patch occupancy data for 18 mammal species within 196 forest patches across a 252,669-km2 study region of the Brazilian Atlantic Forest. We uncovered a staggering rate of local extinctions in the mammal fauna, with only 767 from a possible 3,528 populations still persisting. On average, forest patches retained 3.9 out of 18 potential species occupancies, and geographic ranges had contracted to 0–14.4% of their former distributions, including five large-bodied species that had been extirpated at a regional scale. Forest fragments were highly accessible to hunters and exposed to edge effects and fires, thereby severely diminishing the predictive power of species-area relationships, with the power model explaining only ∼9% of the variation in species richness per patch. Hence, conventional species-area curves provided over-optimistic estimates of species persistence in that most forest fragments had lost species at a much faster rate than predicted by habitat loss alone.

Reports on use of stones as hammers and anvils to open hard nuts by wild capuchin monkeys are scarce and limited to Cebus libidinosus. Here, we report for the first time data on tool use-stones as hammer and anvils to open nuts-in wild C. xanthosternos and a description of new tool using sites for C. libidinosus. Our records were made by visiting anvil sites and by information obtained from local residents. We surveyed three different biomes: Caatinga (dry forest and thorn scrub), Cerrado (Brazilian bush savannah), and Atlantic forest (wet forest), all records of tool use were from Caatinga or transitional areas between habitats. The behavior is suggested to be routinely performed and widespread among several populations. The fruits of six plant species in different localities were opened with hammer stones by C. xanthosternos. Hammer stones were of similar weigh as those described in other studies of C. libidinosus. Conditions found in Caatinga, such as a more frequent use of the ground by the monkeys and/or food scarcity, may play an important role in the acquisition of nut-cracking behavior. The absence of more reports of nut cracking and other forms of tool use in other species of wild Cebus is likely to result from a lack of surveys in very dry and food-limited habitats or intrinsic characteristics of other Cebus species.

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We provide data on wild Callithrix kuhlii, a little studied species. We describe their ecology, focusing on demography, diet, and ranging patterns in 8 groups studied from 1995 to 1999. The groups averaged 4.3 individuals, with 1 breeding female and 1-2 adult males, and reproduction was seasonal. Evidence from nonstudy groups indicated the possibility of polygynous group structure. We observed group formation and the transfer of adults between groups. The marmosets ate 20 species of fruit and nectar and 5 exudate species. Home ranges were 34-39 ha, and daily path lengths averaged 1498 m. We include our data in a comprehensive review of eastern Brazilian marmosets to characterize their ecology. Callithrix kuhlii ate more fruit species and less gum species, and had larger home ranges and daily path lengths versus those of most congeners. There was also a tradeoff between travel time and other behaviors. Species with smaller home ranges spent more time foraging and resting and less time traveling than the ones with larger ranges. Attributes consistent with all species included their reliance on gum during fruit scarcity and preference for disturbed habitat. We explored factors relating to the variation in diet and ranging patterns within the eastern Brazilian marmosets, in particular by considering the species in relation to elevation and the extent and proximity of their distribution to the sea. However, large intraspecific variation resulting in part from variable levels of anthropogenic disturbance across Int sites confounded our ability to verify trends corresponding to the geographic characteristics.

Metabarcoding of environmental DNA (eDNA) is now widely used to build diversity profiles from DNA that has been shed by species into the environment. There is substantial interest in the expansion of eDNA approaches for improved detection of terrestrial vertebrates using invertebrate‐derived DNA (iDNA) in which hematophagous, sarcophagous, and coprophagous invertebrates sample vertebrate blood, carrion, or faeces. Here, we used metabarcoding and multiple iDNA samplers (carrion flies, sandflies, and mosquitos) collected from 39 forested sites in the southern Amazon to profile gamma and alpha diversity. Our main objectives were to (1) compare diversity found with iDNA to camera trapping, which is the conventional method of vertebrate diversity surveillance; and (2) compare each of the iDNA samplers to assess the effectiveness, efficiency, and potential biases associated with each sampler. In total, we collected and analysed 1759 carrion flies, 48,686 sandflies, and 4776 mosquitos. Carrion flies revealed the greatest total vertebrate species richness at the landscape level, despite the least amount of sampling effort and the fewest number of individuals captured for metabarcoding, followed by sandflies. Camera traps had the highest median species richness at the site‐level but showed strong bias towards carnivore and ungulate species and missed much of the diversity described by iDNA methods. Mosquitos showed a strong feeding preference for humans as did sandflies for armadillos, thus presenting potential utility to further study related to host‐vector interactions.

From 2006 through 2014, we conducted seroepidemiological surveys on non-human primates and sloths to investigate the possible circulation of arboviruses in Bahia Atlantic Forest, Brazil. We collected a total of 196 samples from 103 Leontopithecus chrysomelas, 7 Sapajus xanthosternos, 22 Bradypus torquatus and 7 Bradypus variegatus. Serum samples were tested using neutralization test and hemagglutination inhibition test to detect total antibodies against 26 different arboviruses. The overall prevalence of arboviruses was 36.6% (51/139), with the genus Flavivirus having the highest prevalence (33.1%; 46/139), followed by Phlebovirus (5.0%; 7/139), Orthobunyavirus (4.3%; 6/139) and Alphavirus (0.7%; 1/139). Monotypic reactions suggest that the wild animals were exposed naturally to at least twelve arboviruses. Added results from the neutralization test, animals were exposed to thirteen arboviruses. Most of these viruses are maintained in transmission cycles independent of human hosts, although antibodies against dengue virus serotypes 1, 2 and 3 were found in this study. To our knowledge, this is the first study reporting exposure to arboviruses in L. chrysomelas, S. xanthosternos and B. torquatus. Our results also highlight that the Southern Bahia Atlantic Forest has a variety of vertebrate hosts and potential vectors, which may support the emergence or re-emergence of arboviruses, including those pathogenic to humans.

Primates play an important role in ecosystem functioning and offer critical insights into human evolution, biology, behavior, and emerging infectious diseases. There are 26 primate species in the Atlantic Forests of South America, 19 of them endemic. We compiled a dataset of 5,472 georeferenced locations of 26 native and 1 introduced primate species, as hybrids in the genera Callithrix and Alouatta. The dataset includes 700 primate communities, 8,121 single species occurrences and 714 estimates of primate population sizes, covering most natural forest types of the tropical and subtropical Atlantic Forest of Brazil, Paraguay and Argentina and some other biomes. On average, primate communities of the Atlantic Forest harbor 2 ± 1 species (range = 1–6). However, about 40% of primate communities contain only one species. Alouatta guariba (N = 2,188 records) and Sapajus nigritus (N = 1,127) were the species with the most records. Callicebus barbarabrownae (N = 35), Leontopithecus caissara (N = 38), and Sapajus libidinosus (N = 41) were the species with the least records. Recorded primate densities varied from 0.004 individuals/km2 (Alouatta guariba at Fragmento do Bugre, Paraná, Brazil) to 400 individuals/km2 (Alouatta caraya in Santiago, Rio Grande do Sul, Brazil). Our dataset reflects disparity between the numerous primate census conducted in the Atlantic Forest, in contrast to the scarcity of estimates of population sizes and densities. With these data, researchers can develop different macroecological and regional level studies, focusing on communities, populations, species co‐occurrence and distribution patterns. Moreover, the data can also be used to assess the consequences of fragmentation, defaunation, and disease outbreaks on different ecological processes, such as trophic cascades, species invasion or extinction, and community dynamics. There are no copyright restrictions. Please cite this Data Paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.

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