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.

Epidemiological compatibility of Amblyomma sculptum as possible vector and Panthera onca as reservoir of Cytauxzoon spp. in Midwestern Brazil

Cytauxzoonosis is an acute and highly lethal tick-borne disease of wild and domestic cats, and is widely distributed in Africa, Asia, Europe, the USA and Brazil. So far, only two tick species present on the USA are experimentally confirmed in Cytauxzoon transmission however, in Brazil and other continents, the epidemiology of the disease remains unknown. Evidences points to Panthera onca as a possible reservoir, but there is no evidence to point the vector. Therefore, this study evaluates the presence of Cytauxzoon spp. in wild felids from areas with and without records of Amblyomma sculptum this ixodid for comparison. Overall, 53 blood samples of P. onca, Puma concolor, and Leopardus pardalis from the Midwest region (MR; region with A. sculptum) and 143 blood and/or spleen samples from Leopardus geoffroyi, Leopardus wiedii, Leopardus munoai, Leopardus guttulus, Herpailurus yagouaroundi, L. pardalis, and P. concolor from Rio Grande do Sul State (RS; without A. sculptum). Only one feline sample was negative for Cytauxzoon sp. from MR; no samples from RS were positive. In total, 507 ticks were identified from MR felids, with predominance of A. sculptum (69.23%). In RS, there were 93 ixodids, of which 90.32% were Amblyomma aureolatum. The difference in the tick fauna of the two regions studied (presence/absence of A. sculptum) reflects the results found. This study highlighted A. sculptum as a possible vector since this hemoparasite was abundantly observed in areas where it occurs, also, there was no evidence of Cytauxzoon spp. where it was absent. Additionally, the study supported the suggestion that P. onca is the reservoir for the agent in MR.

Molecular and Serological Survey of the Cat-Scratch Disease Agent (Bartonella henselae) in Free-Ranging Leopardus geoffroyi and Leopardus wiedii (Carnivora: Felidae) From Pampa Biome, Brazil

The genus Bartonella comprises emerging bacteria that affect humans and other mammals worldwide. Felids represent an important reservoir for several Bartonella species. Domestic cats are the main reservoir of Bartonella henselae, the agent of cat scratch disease (CSD). It can be transmitted directly by scratches and bites from infected cats and via cat fleas. This study aims to investigate the circulation of Bartonella spp. in free-ranging Neotropical wild felids from Southern Brazil using serological and molecular methods. In this study, 53 live-trapped free-ranging wild felids were sampled, 39 Leopardus geoffroyi and 14 Leopardus wiedii, from five municipalities in the Rio Grande, do Sul state, southern Brazil. All captured animals were clinically healthy. Two blood samples of L. geoffroyi were positive, by PCR, for the presence of B. henselae DNA. Conversely, none of L. wiedii blood samples were positive when tested using PCR. Indirect immunofluorescence assay (IFA) showed that 28% of serum samples of wild felids were reactive (seropositive) for B. henselae by immunofluorescence, with titers ranging from 64 to 256. The results presented here provide the first evidence of a Bartonella-enzootic cycle involving L. geoffroyi and L. wiedii, which may account for the spillover of the emerging zoonotic pathogen B. henselae for the indigenous fauna in Southern Brazil.

NEOTROPICAL CARNIVORES: a data set on carnivore distribution in the Neotropics

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data.

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.

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.

Landscape features lead to shifts in communities of medium- to large-bodied mammals in subtropical Atlantic Forest

Defaunation is a key ecological issue that has only recently been given sufficient attention. As predicted, evidence so far indicates loss of larger species followed by medium-sized species, leading to cascading effects that propagate throughout entire communities and ecosystems. The Atlantic Forest is among the most important global biodiversity hotspots. These regions have historically been impacted by habitat loss and fragmentation, resulting in landscape changes and negative impacts upon animal communities. This study evaluates community characteristics of medium- and large-sized mammals in subtropical Atlantic Forest, southern Brazil. We gathered data on mammal occurrence using 108 cameras traps located across 8 protected areas. We then tested whether landscape differences impact mammal richness, composition, and community complexity. Specifically, we used a regression tree to evaluate compositional differences as a function of landscape configuration. We analyzed data for 26 species in total, with the number of species per area ranging from 9 to 17. Changes in mammal composition at the landscape scale were most strongly associated with human occupation. Areas with strong human occupation had low species richness, with a predominance of medium-sized omnivores and insectivores species; these conditions led to high defaunation indices. Community complexity was greater in areas with low human occupation, where carnivores (Felidae) were more abundant. Differences in species composition were also linked to altitudinal bands and the ratio of period of time with protected status versus history of land exploitation in a particular area. Analysis of functional groups indicated that intense human occupation had negative effects on larger species, a process that may have impending consequences. Despite defaunation being a serious ecological issue, we assert that taking prompt action may limit or potentially reverse effects of defaunation before the most dramatic changes take place.

Defaunação é uma questão ecológica chave e que só recentemente tem recebido atenção suficiente. Como previsto, as evidências até agora indicam perda de espécies de maior porte, seguida por espécies de médio porte, levando à efeitos em cascata que se propagam em todas as comunidades e ecossistemas. A Mata Atlântica está entre os mais importantes hotspots de biodiversidade mundiais. Essa região tem sido historicamente impactada pela perda e fragmentação de hábitat, resultando em mudanças na paisagem e impactos negativos nas comunidades animais. Este estudo avalia características de comunidades de mamíferos de médio e grande porte na Mata Atlântica subtropical, sul do Brasil. Nós reunimos dados sobre ocorrência de mamíferos utilizando 108 armadilhas fotográficas instaladas em oito áreas protegidas. Em seguida, avaliamos se as diferenças de paisagem impactam a riqueza, composição e a complexidade das comunidades de mamíferos. Especificamente, nós usamos uma análise de árvore de regressão para avaliar as diferenças na composição das comunidades em função da configuração da paisagem. Analisamos ​​dados de 26 espécies no total, com o número de espécies por área variando 9 a 17. As alterações na composição de mamíferos na escala da paisagem foram mais fortemente associadas à ocupação humana. As áreas com maior ocupação humana tiveram baixa riqueza de espécies, com predominância de espécies onívoras e insetívoras de médio porte, e, estas condições geraram índices de defaunação elevados. A complexidade das comunidades foi maior em áreas com baixa ocupação humana, onde carnívoros (Felidae) foram mais frequentes. As diferenças na composição de espécies também foram ligadas às quotas de altitude, assim como à razão entre o período de tempo com estatuto de proteção e o tempo de exploração de cada área. A análise com abordagem de grupos funcionais indicou que a maior ocupação humana teve efeitos negativos sobre as espécies maiores, um processo com consequências negativas iminentes. Apesar da defaunação ser uma importante questão ecológica, nós acreditamos que um conjunto de ações conservacionistas imediatas podem potencialmente limitar ou reverter os efeitos da defaunação antes que mudanças mais dramáticas acontecem.

The role of melanism in oncillas on the temporal segregation of nocturnal activity

The occurrence of coat colour polymorphisms in populations may promote the ecological success of species by permitting a wider spectrum of use of different subsets of available resources. We conducted an analysis of temporal segregation by comparing night brightness with nocturnal activity of spotted and melanistic oncillas (Leopardus tigrinus). Melanistic oncillas were more active during bright nights and spotted oncillas and other species were more active during dark nights. Each colour morph occupied a temporal niche outside the confidence interval of the other colour morph, demonstrating the ecological significance of polymorphic colour patterns in this felid species.