Camera trap surveys of Atlantic Forest mammals: A data set for analyses considering imperfect detection (2004-2020)

Camera traps became the main observational method of a myriad of species over large areas. Data sets from camera traps can be used to describe the patterns and monitor the occupancy, abundance, and richness of wildlife, essential information for conservation in times of rapid climate and land-cover changes. Habitat loss and poaching are responsible for historical population losses of mammals in the Atlantic Forest biodiversity hotspot, especially for medium to large-sized species. Here we present a data set from camera trap surveys of medium to large-sized native mammals (>1 kg) across the Atlantic Forest. We compiled data from 5380 ground-level camera trap deployments in 3046 locations, from 2004 to 2020, resulting in 43,068 records of 58 species. These data add to existing data sets of mammals in the Atlantic Forest by including dates of camera operation needed for analyses dealing with imperfect detection. We also included, when available, information on important predictors of detection, namely the camera brand and model, use of bait, and obstruction of camera viewshed that can be measured from example pictures at each camera location. Besides its application in studies on the patterns and mechanisms behind occupancy, relative abundance, richness, and detection, the data set presented here can be used to study species' daily activity patterns, activity levels, and spatiotemporal interactions between species. Moreover, data can be used combined with other data sources in the multiple and expanding uses of integrated population modeling. An R script is available to view summaries of the data set. We expect that this data set will be used to advance the knowledge of mammal assemblages and to inform evidence-based solutions for the conservation of the Atlantic Forest. The data are not copyright restricted; please cite this paper when using the data.

Hitting the Road: Haplotype Diversity of Fire Ants Nesting on Disturbed Atlantic Forest Habitats

Ants of the genus Solenopsis are globally distributed, presenting high diversity and many generalist species. In South America, the dominant species is Solenopsis saevissima (Smith, 1855), commonly found nesting in grassy fields surrounding humanized areas. In spite of being so common, there has been no research evaluating the effect of human disturbances on the mitochondrial DNA (mtDNA) haplotype diversity in this species. In this context, we here characterized the mtDNA haplotype diversity in S. saevissima nests by highway roadsides, dust roads, and forest borders of Atlantic Forest, based on partial sequences of cytochrome c oxidase subunit I (COI). Based on the facts that the species is a rapid colonizer of disturbed habitats, we specifically probed how the genetic diversity of native S. saevissima is impacted by highways and roads infrastructure expanding around the rainforest. Species diagnosis was established both by morphological characters and obtained mtDNA COI sequences. Overall, the species exhibited high haplotypes and nucleotide diversity, particularly around forest borders; though all haplotypes seemed closely related across the different habitats. We identified seven mitochondrial haplotypes (H1 to H7), where haplotype H1 was exclusively found in highway roadside nests, and H7 on dust roads; the remaining haplotypes were recorded from all habitats. Haplotype H1 was geographically isolated to the south of the Atlantic Forest, supporting previous suggestions that it acts as a biogeographical barrier. The pattern is suggestive of a recent species expansion, probably resulting from extensive habitat fragmentation. Taken together, our data demonstrates fire ant haplotypes prevailing in some anthropized habitats, characterizing how a native species lining the remnants of the Brazilian Atlantic Forest might be a concern for environmental conservation.

Occurrence of Pheidole tijucana Borgmeier, 1927 (Hymenoptera, Formicidae) in the state of São Paulo, Brazil

Pheidole Westwood, 1839 is a hyperdiverse ant genus that is widely distributed in a variety of terrestrial ecosystems, especially in the tropics. The identification of Pheidole species is challenging, thus contributing to the description of several questionable morphospecies in the literature and making the geographic distribution of most species uncertain. In this work, we present the first records of Pheidole tijucana Borgmeier, 1927 from the state of São Paulo, Brazil. The specimens were recorded at Parque Ibirapuera Conservação, an urban green area located in the southern part of the city of São Paulo. The sampling was performed in 2015, 2016, and 2017 using pitfall traps. In total, 224 specimens (one major worker and 223 minor workers) of P. tijucana were recorded. Our new data help fill a distribution gap and highlights the importance of reporting species that are a challenge to identify.

Natural regeneration in Atlantic Forest Fragments: using ants (Hymenoptera: Formicidae) for monitoring a conservation unit

The Brazilian Atlantic Forest is considered one of the most threatened tropical forests in the world due to the extensive environmental impact it has endured throughout history. Only 12.4% of its original vegetation is estimated to remain. Even though reduced and highly fragmented, it houses enormous biodiversity, and its preservation is paramount to the maintenance of the country’s fauna, flora, funga and microbiota. One of the most efficient measures adopted by public agencies aimed at protecting biodiversity has been the creation of conservation units. To evaluate the preservation state of protected areas, several environmental studies have been performed; species inventories are one among them. Ants are excellent bioindicators, for they are not only sensitive to environmental changes, but they also have a history of being used in impact assessment (i.e., fragmentation). In this study we assessed the ant communities inhabiting the leaf litter in areas with different regeneration states at the RPPN Botujuru – Serra do Itapety (Mogi das Cruzes, São Paulo – Brazil). Mini-Winkler traps were used in the ant survey, and diversity analyses were performed. In total, we recorded 86 species of ants, with a highlight to Camponotus cillae Forel, 1912, a species that remained unrecorded for the state of São Paulo for over 100 years, and a possible new species of Octostruma Forel, 1912. Overall, the species found show that the areas are in the process of natural regeneration. Our data on RPPN Botujuru is unprecedented, and our species list has the potential of being used as an effective monitoring tool for this conservation unit.

NEOTROPICAL ALIEN MAMMALS: a data set of occurrence and abundance of alien mammals in the Neotropics

Biological invasion is one of the main threats to native biodiversity. For a species to become invasive, it must be voluntarily or involuntarily introduced by humans into a nonnative habitat. Mammals were among first taxa to be introduced worldwide for game, meat, and labor, yet the number of species introduced in the Neotropics remains unknown. In this data set, we make available occurrence and abundance data on mammal species that (1) transposed a geographical barrier and (2) were voluntarily or involuntarily introduced by humans into the Neotropics. Our data set is composed of 73,738 historical and current georeferenced records on alien mammal species of which around 96% correspond to occurrence data on 77 species belonging to eight orders and 26 families. Data cover 26 continental countries in the Neotropics, ranging from Mexico and its frontier regions (southern Florida and coastal-central Florida in the southeast United States) to Argentina, Paraguay, Chile, and Uruguay, and the 13 countries of Caribbean islands. Our data set also includes neotropical species (e.g., Callithrix sp., Myocastor coypus, Nasua nasua) considered alien in particular areas of Neotropics. The most numerous species in terms of records are from Bos sp. (n = 37,782), Sus scrofa (n = 6,730), and Canis familiaris (n = 10,084); 17 species were represented by only one record (e.g., Syncerus caffer, Cervus timorensis, Cervus unicolor, Canis latrans). Primates have the highest number of species in the data set (n = 20 species), partly because of uncertainties regarding taxonomic identification of the genera Callithrix, which includes the species Callithrix aurita, Callithrix flaviceps, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Callithrix penicillata, and their hybrids. This unique data set will be a valuable source of information on invasion risk assessments, biodiversity redistribution and conservation-related research. There are no copyright restrictions. Please cite this data paper when using the data in publications. We also request that researchers and teachers inform us on how they are using the data.

What do different landscapes of the Atlantic Forest reveal about the occurrence of Discothyrea Roger, 1863 (Formicidae: Proceratiinae)?

Abstract: Discothyrea is a genus composed of specialist predatory species rarely recorded and with little known biology. Specimen collection is usually associated with preserved native vegetation. In this work, we explore the landscape of sites with occurrence of Discothyrea seeking to improve knowledge about the natural history of this genus. Species of Discothyrea were recorded in ten Atlantic Forest sites. We analyzed the landscape around the place of occurrence of each species using a 500-m buffer. We classified the landscape as heterogeneous and homogeneous according to the percentage of natural (native vegetation), urban, and rural areas. We found 67 specimens of Discothyrea; 59 of them were D. sexarticulata, occurring in 88% of the fragments. There were also eight specimens of D. neotropica occurring in 12% of the fragments. The results show that D. sexarticulata can be found in homogeneous landscapes with anthropic influence (0-51% of rural area and 0-68% of urban area). Discothyrea neotropica is found in heterogeneous landscapes with a dominant presence of native vegetation (between 74-95%). The results improve knowledge on the biology of Discothyrea mainly in relation to the vicinity of occurrence sites. In addition, the results indicate that regional studies are important to understand species ecology.

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics

Xenarthrans-anteaters, sloths, and armadillos-have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data.

Winged ants (Hymenoptera: Formicidae) presence in twigs on the leaf litter of Atlantic Forest

Abstract: In the leaf litter, ants have various nesting resources available, such as live or dead trunks, twigs, leaves, fruits and seeds. On the twigs, there are adults and immature individuals, but also the queen and winged. The production of wings requires time and energy from the colony. The objective of this study was to investigate the presence of winged in ant colonies in twigs on the leaf litter. Our prediction is that the richness and abundance of winged in twigs are the greatest in rainy months. We collected all twigs with ants in 552 plots with 16 m2, totaling 8,832 m2 of leaf litter, in areas located in the Brazilian Atlantic Domain. We compared the species richness and the number of colonies with and without winged, as well as the number of winged over a year. In total, we collected 1,521 twigs with colonies belonging to 92 species of ants. The rate of twigs with winged was low, about 12%. In colonies with winged, the total number of twigs, species and amount of winged does not differ between the months considered dry and rainy. The majority of winged species are leaf litter dwellers, such as Linepithema neotropicum, recorded with the highest amount of winged irrespective of the period. Arboreal species colonized 15% of the twigs and, in 1/3 of these species, winged were recorded as part of the composition of the colony. Although winged represent a small percentage of the colony in twigs, our results indicate that this feature is important for the life cycle of 44% of the species that occupy twigs, considering that winged are fundamental for the dispersion of the colony.

ATLANTIC-PRIMATES: a dataset of communities and occurrences of primates in the Atlantic Forests of South America

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.

Homogenization and impoverishment of taxonomic and functional diversity of ants in Eucalyptus plantations

Despite its negative impacts on the environment and biodiversity, tree plantations can contribute to biodiversity conservation in fragmented landscapes, as they harbor many native species. In this study, we investigated the impact of Eucalyptus plantations on the taxonomic and functional diversity of ant communities, comparing ant communities sampled in managed and unmanaged (abandoned for 28 years) Eucalyptus plantations, and native Atlantic rain forests. Eucalyptus plantations, both managed and unmanaged, reduced the functional diversity and increased the similarity between ant communities leading to functional homogenization. While communities in managed plantations had the lowest values of both taxonomic and functional ant diversities, ant communities from unmanaged plantations had similar values of species richness, functional redundancy and Rao's Q compared to ant communities from forest patches (although functional richness was lower). In addition, communities in unmanaged Eucalyptus plantations were taxonomically and functionally more similar to communities located in managed plantations, indicating that Eucalyptus plantations have a severe long-term impact on ant communities. These results indicate that natural regeneration may mitigate the impact of Eucalyptus management, particularly regarding the functional structure of the community (α diversity), although it does not attenuate the effects of long term homogenization in community composition (β diversity).

Ant communities (Hymenoptera: Formicidae) in urban centers of the Alto Tietê, São Paulo, Brazil

The Alto Tietê municipalities have rich remnants of Dense Rain Forest in their vicinities. Considering the environmental importance of the Alto Tietê as water source and that of ants as components of tropical biodiversity, this paper aimed at describing the diversity, composition and similarity of the ant fauna in urban centers of different cities. Samples were collected in houses and city squares. Seven subfamilies and 87 species were recorded, of which 39% are commonly found in the Atlantic Forest remnants adjacent to the cities. Linepithema neotropicum is dominant in areas outside the houses and in squares. In each municipality, in the area inside the houses, there is a dominant species. Tapinoma melanocephalumwas recorded preferably in the area inside the houses. Five exotic species were recorded mainly in the city of Mogi das Cruzes, SP, Brazil.

Diversidade e riqueza de formigas (Hymenoptera: Formicidae) em remanescentes de Mata Atlântica na Bacia Hidrográfica do Alto Tietê, SP

O objetivo deste estudo foi descrever a diversidade, composição e a similaridade da fauna de formigas entre sete remanescentes de Floresta Ombrófila Densa da Bacia Hidrográfica do Alto Tietê. Dois desses remanescentes pertencem à Unidades de Conservação, quatro estão sob proteção e um fragmento pertence à propriedade particular. Em cada área foram coletadas 50 m2 de serapilheira, que foram submetidas à extratores do tipo mini-Winkler, onde permaneceram por 48 h. Todas as coletas ocorreram no período chuvoso. No total foram registradas 11 subfamílias, 44 gêneros e 158 morfoespécies/espécies de formigas. As espécies mais frequentes em todas as áreas foram Pheidole sp.7, Solenopsis sp.1, Hypoponera sp.1 e Strumigenys denticulate. O maior valor de diversidade α foi registrado na unidade de conservação com composição florística de Mata Atlântica; o menor valor em florestas com influência antrópica. A variação na composição de espécies entre as áreas indica a substituição de espécies entre os remanescentes de Floresta Ombrófila Densa da Bacia Hidrográfica do Alto Tietê, o que sugere a importância da preservação dessas áreas para a conservação da diversidade regional da fauna de formigas.

Fauna de formigas (Hymenoptera: Formicidae) atraídas a armadilhas subterrâneas em áreas de Mata Atlântica

Este estudo teve como objetivo avaliar a composição da fauna de formigas que forrageia abaixo da superfície do solo de áreas de Floresta Atlântica em estágio avançado de regeneração. Foram estudadas duas áreas similares em relação às características abióticas do solo, sendo uma localizada na Serra do Mar e a outra na Serra do Itapeti, ambas no Estado de São Paulo, Brasil. Em cada área foram distribuídos, a cada dois meses, 20 conjuntos de três armadilhas subterrâneas, contendo iscas atrativas, em buracos de 30 cm de profundidade, e equidistantes 20 m um do outro. As armadilhas permaneceram no campo por 24 horas. Foram registradas no total sete subfamílias, 16 gêneros e 42 morfoespécies/espécies. Três destas espécies, Acanthostichus quadratus, Labidus coecus e L. mars, podem ser consideradas criptobióticas. A riqueza observada não difere em relação aos meses de coleta e, independentemente da época do ano, as comunidades são similares. Houve registro de uma espécie nova pertencente ao gênero Megalomyrmex, além de táxons normalmente pouco coletados, como Acanthostichus. Os resultados demonstram a importância de estudos sobre a fauna que forrageia abaixo da superfície do solo para a taxonomia, dado seu potencial para revelar novas espécies ou pouco representadas em coleções.

Composição da fauna de formigas (Hymenoptera: Formicidae) de serapilheira em florestas semidecídua e de Eucalyptus spp., na região sudeste do Brasil

Este estudo teve como objetivo avaliar a composição da fauna de formigas de serapilheira em áreas de floresta semidecídua com plantio de eucalipto sem manejo durante diferentes períodos. Foram estudadas quatro áreas, sendo três com eucalipto e uma formada por vegetação nativa; todas estão localizadas no município de Rio Claro (SP), sudeste do Brasil. Em cada área foram coletadas 100 amostras de 1 m² de serapilheira, abrangendo os períodos seco e chuvoso da região. Cada amostra foi submetida a extratores do tipo mini-winkler, onde permaneceram por 48 horas. Foram amostradas 58.410 formigas, distribuídas em 10 subfamílias, 42 gêneros e 120 morfoespécies/espécies. Destas, 85 espécies foram encontradas na floresta semidecídua e 84 na floresta de Eucalyptus tereticornis com 100 anos sem manejo. Já nas florestas de E. tereticornis e E. urophylla com 22 anos sem manejo foram encontradas 73 e 56 espécies, respectivamente. Baseando-se em estudos anteriores, este inventário proporcionou o conhecimento de mais 16 gêneros e 24 espécies para a região estudada, sendo três exóticas. A ordenação das amostras com o escalonamento multidimensional não-métrico (NMDS) indicou diferença na similaridade entre as amostras das áreas, especialmente àquelas pertencentes à floresta de E. urophylla. Além do período sem manejo, a presença de substâncias alelopáticas na serapilheira pode estar interferindo no número de espécies e nas comunidades. Os resultados demonstram a importância das florestas abandonadas de eucaliptos para a manutenção da diversidade de formigas em uma região em que a vegetação nativa é escassa.

Ant community richness and composition across a gradient from Eucalyptus plantations to secondary Atlantic Forest

Secondary forests and exotic tree plantations are expanding across tropical landscapes. However, our current understanding of the value of these human-dominated forest landscapes for invertebrate biodiversity conservation is still very poor. In this paper, we use the leaf-litter ant fauna to assess invertebrate diversity in one commercially managed Eucalyptus plantation (four years old), two abandoned plantations of different regeneration ages (16 and 31 years), and one neighboring secondary Atlantic Forest in Southeastern Brazil. There was a clear gradient in species richness from the secondary forest to the managed Eucalyptus plantation; richness and diversity peaked in secondary forest and in the older regenerating Eucalyptus plantation. Significantly more species were recorded in secondary forest samples than in Eucalyptus plantations, but Eucalyptus plantations had a similar level of richness. Furthermore, a non-metric multidimensional scaling analysis revealed clear differences in species composition between the younger managed Eucalyptus plantation (understory absent) and habitats with sub-developed or developed understory. Eucalyptus plantations were characterized by an assemblage of widespread, generalist species very different from those known to occur in core forest habitats of southeastern Brazil. Our results indicate that while older regenerating Eucalyptus plantations can provide habitat to facilitate the persistence of generalist ant species, it is unlikely to conserve most of the primary forest species, such as specialized predators, Dacetini predators, and nomadic species.

Description of the immatures of the ant, Myrmelachista catharinae

The Neotropical ant genus Myrmelachista Roger comprises 69 described species and subspecies, and still is a poorly studied group. Larvae play a paramount role in colony nutrition in social hymenopterans and bear considerable value in the reconstruction of group phylogenies, however, they are generally neglected. Larvae of different instars of Myrmelachista catharinae Mayr (Hymenoptera: Formicidae) are herein described in detail by light and scanning electron microscopy. The number of larval instars was estimated as three based on the frequency distribution of maximum head capsule widths. The described larvae confirmed some traits typical of the genus: general shape of body and mandibles, general aspect and distribution of body hairs, and the number of sensilla on the palps and galea. Differently from other Myrmelachista larvae previously described, M. catharinae presented two distinct kinds of second instars, some additional types of body hairs, different number of antennal sensilla, and a distinct labrum shape. M. catharinae presented ten pairs of spiracles, which is the first record for this genus.

Identification and characterization of Wolbachia in Solenopsis saevissima fire ants (Hymenoptera: Formicidae) in southeastern Brazil

The genus Solenopsis appears to have evolved and radiated very rapidly in South America and then spread throughout the rest of the continent. As part of the expansion process, distribution patterns and different degrees of geographic isolation among populations of S. saevissima can be observed. We have investigated the presence of Wolbachia in 52 colonies and 1623 individuals in southeastern Brazil. Detection of Wolbachia infection was based on amplification of the 16S rRNA and wsp genes by polymerase chain reactions. Wolbachia was found in only one of the four locations investigated and it was observed that the populations were polymorphic for infection. The infection level observed increased during the period of screening. In particular, double infection (16SWA and B) increased from 44% in 2005 to 90% in 2006. The A-group of Wolbachia from the wsp sequences was determined by sequencing. However, two variant wsp sequences were detected in Wolbachia present in these populations. The alignment of our sequences with those deposited in GenBank indicated significant differences in relation to homologous sequences. Phylogenetic relationships were inferred using parsimony, and confidence intervals were estimated by bootstrapping. Then the divergence of the Wolbachia of S. saevissima in the populations studied with other variants allowed us to verify that wSS1 and dwSS2 formed a distinct clade within the A-group (>75%). These results can be useful in studies on the dynamics of ant populations.