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.

NEOTROPICAL FRESHWATER FISHES: A dataset of occurrence and abundance of freshwater fishes in the Neotropics

The Neotropical region hosts 4225 freshwater fish species, ranking first among the world's most diverse regions for freshwater fishes. Our NEOTROPICAL FRESHWATER FISHES data set is the first to produce a large-scale Neotropical freshwater fish inventory, covering the entire Neotropical region from Mexico and the Caribbean in the north to the southern limits in Argentina, Paraguay, Chile, and Uruguay. We compiled 185,787 distribution records, with unique georeferenced coordinates, for the 4225 species, represented by occurrence and abundance data. The number of species for the most numerous orders are as follows: Characiformes (1289), Siluriformes (1384), Cichliformes (354), Cyprinodontiformes (245), and Gymnotiformes (135). The most recorded species was the characid Astyanax fasciatus (4696 records). We registered 116,802 distribution records for native species, compared to 1802 distribution records for nonnative species. The main aim of the NEOTROPICAL FRESHWATER FISHES data set was to make these occurrence and abundance data accessible for international researchers to develop ecological and macroecological studies, from local to regional scales, with focal fish species, families, or orders. We anticipate that the NEOTROPICAL FRESHWATER FISHES data set will be valuable for studies on a wide range of ecological processes, such as trophic cascades, fishery pressure, the effects of habitat loss and fragmentation, and the impacts of species invasion and climate change. There are no copyright restrictions on the data, and please cite this data paper when using the data in publications.

Human-modified landscapes narrow the isotopic niche of neotropical birds

Deforestation and habitat loss resulting from land use changes are some of the utmost anthropogenic impacts that threaten tropical birds in human-modified landscapes (HMLs). The degree of these impacts on birds' diet, habitat use, and ecological niche can be measured by isotopic analysis. We investigated whether the isotopic niche width, food resources, and habitat use of bird trophic guilds differed between HMLs and natural landscapes (NLs) using stable carbon (δ¹³C) and nitrogen isotopes (δ¹⁵N). We analyzed feathers of 851 bird individuals from 28 landscapes in the Brazilian Atlantic Forest. We classified landscapes into two groups according to the percentage of forest cover (HMLs ≤ 30%; NLs ≥ 47%), and compared the isotopic niche width and mean values of δ¹³C and δ¹⁵N for each guild between landscape types. The niches of frugivores, insectivores, nectarivores, and omnivores were narrower in HMLs, whereas granivores showed the opposite pattern. In HMLs, nectarivores showed a reduction of 44% in niche width, while granivores presented an expansion of 26%. Individuals in HMLs consumed more resources from agricultural areas (C₄ plants), but almost all guilds showed a preference for forest resources (C₃ plants) in both landscape types, except granivores. Degraded and fragmented landscapes typically present a lower availability of habitat and food resources for many species, which was reflected by the reduction in niche width of birds in HMLs. Therefore, to protect the diversity of guilds in HMLs, landscape management strategies that offer birds more diverse habitats must be implemented in tropical regions.

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.

Good times, bad times: Resource pulses influence mammal diversity in meridional Brazilian highlands

Understanding spatiotemporal patterns of species distributions and their determinants is paramount in ecology. Here, we explore the relationship between the diversity of surviving mammals and two of the main alimentary resources (araucaria seeds and feijoa fruits) across the Araucaria Forest (FOM) in South America. First, we investigated the influence of landscape and environment on the species distribution and pulse of forest productivity. Then, we evaluated how these spatiotemporal pulses in resource availability influence the mammalian diversity. We analyzed the data via diversity descriptors, Morisita index and multiple regressions. Our findings highlighted that climate, tree density, and other environmental variables explained the pulses of productivity. Mammalian diversity of first-order consumers mammals-all those immediately feeding on seeds and fruits-was partially related to resource pulses. Our results revealed that the pulses of forest resources can influence mammal diversity over the years, including delayed responses and asynchronous oscillations. The integrity of vegetal elements of the FOM is key to maintain several mammal-mediated ecological processes. Maintaining the viability of tree populations, encouraging the sustainable use of non-timber resources, and promoting the conservation of the mammalian fauna, which is undergoing an unprecedented diversity crisis worldwide, can help to preserve the remaining ecological processes.

Can taxonomic and functional metrics explain variation in the ecological uniqueness of ecologically-associated animal groups in a modified rainforest?

The conservation of biodiversity requires adequate information about species and ecosystem attributes. The local contribution to β-diversity (LCBD) is a community composition-based metric of ecological uniqueness of sites. Here, we tested the capability of taxonomic and functional attributes of biological communities to explain variation in LCBD at a large spatial extent. We approached this idea using data on dung beetles and mammals (medium-to-large, small and volant) recorded across the Atlantic Forest of South America due to their millennial-scale evolutionary relationship (food providers and consumers). We related LCBD values to both taxonomic and functional metrics via beta regression. Our results revealed that taxonomic and functional features of assemblages can be used to predict variation in ecological uniqueness (LCBD). High LCBD values were associated with low species and functional richness for all animal groups. For dung beetles, high LCBD values were associated with low values of all functional metrics. For mammalian groups high ecological uniqueness was associated with low abundance, low Rao's quadratic entropy, as well as high functional divergence, functional evenness, functional originality, and either low or high functional specialization. This implies that variation in ecological uniqueness can be explained by functional features at large spatial extents, although the type of functional metrics' response of assemblages may be animal group specific. The potential of the LCBD metric to inform about both taxonomic and functional changes at large scales makes its use in conservation planning a highly promising approach.

Melanism evolution in the cat family is influenced by intraspecific communication under low visibility

Melanism in the cat family has been associated with functions including camouflage, thermoregulation and parasite resistance. Here we investigate a new hypothesis proposing that the evolution of melanism in cats has additionally been influenced by communication functions of body markings. To evaluate this hypothesis, we assembled a species-level data set of morphological (body marks: white marks on the backs of ears) and ecological (circadian activity: arrhythmic/nocturnal, and environmental preference: open/closed) characteristics that could be associated with communication via body markings, and combined these data with a dated molecular phylogeny. Next, we tested the association between melanism and communication, first by relating species’ body marks with their ecological conditions, using a Bayesian implementation of the threshold model. Second, to explore the evolution of characteristics potentially influencing melanism in cat species, we modeled their evolution relative to melanism using models of coordinated vs. independent character changes. Our results suggest that white marks are associated with intraspecific communication between individuals that have non-melanistic phenotypes, as well as towards melanistic individuals (without white marks). The absence of white marks in a melanistic individual tends to be a limiting condition for intraspecific visual communication at night, resulting in an evolutionary dilemma for these species, i.e. to be almost invisible at night, but not to communicate visually. The comparative analysis of several evolutionary models indicated more support for the evolution of melanism being coordinated with the evolution of arrhythmic activity and white marks on the backs of ears.

ATLANTIC MAMMALS: a data set of assemblages of medium- and large-sized mammals of the Atlantic Forest of South America

Biodiversity inventories contain important information about species richness, community structure, and composition, and are the first step in developing any conservation and mitigation strategies. The Atlantic Forest of South America is home to around 334 species of small-, medium-, and large-sized mammals, and is currently restricted to less than 12% of its original cover. Here, we present the ATLANTIC MAMMALS, an open data set on information on medium- and large-sized mammal assemblages in the Atlantic Forest of Brazil, Paraguay, and Argentina. A total of 129 studies were compiled, including published and in press peer-reviewed papers, book chapters, theses and unpublished data. We mapped 244 assemblages, eight orders, 63 genera, and 94 species (24 of which are classified as threatened by the IUCN Red List) distributed in 128 protected and 116 unprotected areas. Species richness of the mammalian assemblages varied from 1 to 39 species (mean 15). The most recorded species in the entire biome was Dasypus novemcinctus, followed by Cerdocyon thous and Procyon cancrivorous. These data can be useful in support of macroecological studies and conservation planning strategies. 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.

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.

Wish you were here: How defaunated is the Atlantic Forest biome of its medium- to large-bodied mammal fauna?

Mammals represent the largest-bodied elements of the world's surviving megafauna and provide several key ecosystems services, yet their populations are often under steep decline throughout the tropics. Anthropogenic defaunation is one the most important contemporary threats to modern mammal faunas. Although the Atlantic Forest biome of South America shows several clear signs of defaunation, the extent to which this biome has lost its mammal fauna remains poorly understood. Here, we collate and analyze a comprehensive body of secondary data to quantitatively assess the spatial patterns of defaunation of all medium- to large-bodied Atlantic Forest mammals which were then classed by morpho-ecological traits. We used a Defaunation Index, which was scaled-up to the entire biome using kriging interpolation, to examine the integrity of site-specific mammal faunas. We further use environmental and socioeconomic predictors to explain the drivers of defaunation. Our results show high levels of defaunation (>0.5) for most of the Atlantic Forest. Apex predators, other carnivores, large-bodied mammals and large herbivores were among the most defaunated functional groups. Remaining native vegetation cover, forest fragment size, and the largest neighboring forest remnant were the main negative predictors of defaunation. We conclude that medium- to large-bodied Atlantic Forest mammals are under high levels of threat due to historical population losses that continue today. A conservation action plan thus becomes imperative to prevent this biome from becoming an even "emptier forest", severely compromising patterns of diversity, ecological processes and ecosystem functioning.

The ecological footprint of Acca sellowiana domestication maintains the residual vertebrate diversity in threatened highlands of Atlantic Forest

Past and contemporary human actions are causing numerous changes in patterns and processes at various ecosystem scales and trophic levels, including unintended downstream changes, such as species interactions. In its native range Acca sellowiana (Feijoa) combines some characteristics of human interactions: incipient domestication, restricted to subtropical Atlantic Forest highlands, associated with the threatened conifer Araucaria angustifolia (Araucaria), within a domesticated landscape with anthropogenic forest patches, and provides fruit at a time of resource shortage (Araucaria seeds—pinhão). We quantify the trophic relationships between Feijoa and vertebrates, and evaluate the influences on interactions caused by environmental variations, Feijoa domestication evidences, spatial distance and fruit availability. In four sites within protected areas, we selected 28 focal individuals of Feijoa (seven/site) and collected three temporal replicas between 2015 and 2016, when we measured productivity and frugivory via 45-second videos taken with camera traps. Using ecological network, rarefaction curves and variation partitioning analyses, we evaluate the frugivory network topology, the spatiotemporal structure of communities in relation to fruit availability and the influence of predictive variables on frugivory. We found a large spatiotemporal variation in productivity of Feijoa and that 20 species consumed Feijoa fruits, with a species degree of 2.8 (±5.7) and average Feijoa degree of 14.4 (±10.1), in a modular network with intermediary connectance. Rarefaction curves showed that richness and the independent records are congruent with the fruit amount. Variation partitioning showed that, for the focal individuals, canopy area, green coverage, patch size and distance to water influenced frugivory, and the Feijoa domestication influenced significantly the mammalian frugivory. Feijoa is an important resource that provides food during the time of year when Pinhão is absent, and attracts frugivores, maintain the residual diversity of vertebrates contributing to the structure of communities in highlands. Our insights allowed us to evaluate the magnitude of the interactions between vertebrates and an incipient domesticated tree, in a cultural landscape and highly threatened environment, under a basal foodweb approach with implications for bottom-up and top-down forces. The results contribute to understanding animal-plant relationships, including concepts that can be replicated for other sessile prey and mobile predators in any region or habitat under different gradients of management. Thus, this work shows how human actions can change not only patterns of distribution and abundance but also the diversity and direction of interspecific interactions among species.

Chemical communication in free-ranging gray brocket deer (Mazama gouazoubira)

http://dx.doi.org/10.5007/2175-7925.2017v30n1p113A comunicação química, em especial a marcação odorífera, é intensa em veados, com a marcação de território feita principalmente pelos machos. Apresentamos gravações em vídeo de pelo menos dois veados-catingueiros (macho e fêmea) que estão desenvolvendo comunicação química através de marcas de cheiro. Os vídeos demonstram a deposição de fezes e urina várias vezes pelos animais, provavelmente para o desenvolvimento de interação intrassexual e secundariamente para demarcações territoriais. A comunicação química observada é possivelmente relacionada à reprodução. Essas marcas territoriais são particularmente importantes para evitar a competição intraespecífica por recursos e parceiros sexuais.

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.

Genotoxicity in Astyanax bimaculatus (Twospot Astyanax) exposed to the waters of Engano River (Brazil) as determined by micronucleus tests in erythrocytes

Changes in aquatic environments are potentially large, and effects on biota are highly variable. In Santa Catarina State, Brazil, the main sources of pollution in headwaters are wastewater, pesticides, and animal waste, which contain chemical and organic additives, and there is little knowledge about their effects on aquatic organisms. This study was aimed at investigating the possible genotoxic effects of the waters of the Engano River through the micronucleus (MN) test in Astyanax bimaculatus erythrocytes. Samplings were performed at two sites on the river, and there were six temporal repetitions with collection of blood from six individuals per site/repetition. For the negative-control treatment, we used fish from organic culture; cyclophosphamide was inoculated to constitute the positive-control treatment. MN was obtained in 3,000 erythrocytes/individual. Kruskal-Wallis analysis of variance, Scott-Knott test, and Spearman correlation were employed for data analysis. We found 124 MN in fish from the river, with 70 and 54 MN, respectively, for each site and 16 and 59 MN in negative and positive controls, respectively. The results showed a statistical difference for the formation of MN between river fish and fish in the positive-control treatment. Considering the average MN, we found the formation of three distinct groups: (1) fish from site no. 1 and those in the negative-control group, (2) fish from site no. 2, and (3) fish in the positive-control group. The greater values of chromosomal damage were found during periods of lower rainfall. The test used indicated the presence in the water of substances likely to cause clastogenic and aneugenic effects.