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.

Direct development in Atlantic Forest anurans: What can environmental and biotic influences explain about its evolution and occurrence?

Different environmental and biological factors can originate and support different alternative life histories in different taxonomic groups. Likewise, these factors are important for the processes that assemble and structure communities. Amphibians, besides being highly susceptible to environmental conditions, have various reproductive strategies, such as the direct development of individuals. Several hypotheses have been raised about possible selective pressures related to the emergence of direct development in anurans, as well as the relationship between environmental characteristics and the occurrence of these species. Such investigations, however, have mainly focused on specific clades and/or regions. Here, we use structural equation modelling to investigate the relationships between different abiotic (temperature, precipitation, humidity, and terrain slope) and biotic (phylogenetic composition and functional diversity) factors and the proportion of species with direct development in 766 anuran communities of the Atlantic Forest, a biome with a vast diversity of anuran species and high environmental complexity. Anuran communities with higher proportions of direct developing species were found to be mainly influenced by low potential evapotranspiration, low temperature seasonality, and high functional diversity. Phylogenetic composition and terrain slope were also found to be important in determining the occurrence of these species in Atlantic Forest communities. These results show the importance of these factors in the structuring of these communities and provide important contributions to the knowledge of direct development in anurans.

Anthropogenic influences on the distribution of a threatened apex-predator around sustainable-use reserves following hydropower dam installation

Although previous studies demonstrate declines in many large bodied species following hydropower dam installation, others suggest that some species, including the giant otter (Pteronura brasiliensis) may return to newly created reservoir habitats. Yet, there is a lack of evidence to support such theories. Here, we analyzed the effects of a hydropower dam on giant otters using a before-after control-impact study design in the eastern Brazilian Amazon. We collected data 3 years before (2011-2012 and 2015) and after (2017-2019) dam construction, totaling 6,459 km of surveys along rivers with 43 direct sightings of giant otters. Contrary to expectations, our results revealed that giant otters did not remain nor did they return to the dam reservoir. Beyond the zone directly impacted by the dam giant otter occurrence and relative abundance declined next to sustainable-use reserves where the river was more intensely used by people. Our study showed that in the absence of active management sustainable-use reserves and low human density were not sufficient to maintain this apex-predator. Our findings suggest a need to proactively create and maintain areas with low levels of anthropogenic disturbance to enable sustainable coexistence between energy demands and biodiversity across Amazonia.

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.

Is evolution faster at ecotones? A test using rates and tempo of diet transitions in Neotropical Sigmodontinae (Rodentia, Cricetidae)

We evaluated whether evolution is faster at ecotones as niche shifts may be needed to persist under unstable environment. We mapped diet evolution along the evolutionary history of 350 sigmodontine species. Mapping was used in three new tip-based metrics of trait evolution - Transition Rates, Stasis Time, and Last Transition Time - which were spatialized at the assemblage level (aTR, aST, aTL). Assemblages were obtained by superimposing range maps on points located at core and ecotone of the 93 South American ecoregions. Using Linear Mixed Models, we tested whether ecotones have species with more changes from the ancestral diet (higher aTR), have maintained the current diet for a shorter time (lower aST), and have more recent transitions to the current diet (lower aLT) than cores. We found lower aTR, and higher aST and aLT at ecotones than at cores. Although ecotones are more heterogeneous, both environmentally and in relation to selection pressures they exert on organisms, ecotone species change little from the ancestral diet as generalist habits are necessary toward feeding in ephemeral environments. The need to incorporate phylogenetic uncertainty in tip-based metrics was evident from large uncertainty detected. Our study integrates ecology and evolution by analyzing how fast trait evolution is across space.

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.

Database of bird species composition in natural habitats and forest plantations

In southeastern South America, the afforestation over grasslands imposes a severe threat to the grassy landscapes and associated biodiversity. To analyze the effect of forest plantations on grassland birds, we present a new database that considers the composition of bird communities in natural habitats, as well as in eucalyptus plantations from the southeastern South American grasslands. Data were previously used to investigate the effectiveness of legally protected grasslands in private lands to protect birds in “Bird-grassland associations in protected and non-protected areas in the southern Brazil” [1] and also the effects of afforestation of grasslands on different dimensions of bird diversity in “The effects of grassland ecosystem afforestation on avian phylogenetic diversity, taxonomic diversity and evolutionary distinctiveness” [2]. Data were collected during the breeding period of bird species (spring/austral summer), covering three breeding seasons during the years 2014–2016. Species presence and number of individuals were recorded, totaling 107 species and 1175 individuals. The dataset will be useful for researchers interested in conservation studies as it includes data from globally threatened bird species.

A global database on non-volant small mammal composition in natural and human-modified habitats

Non-volant small mammals, which include small-bodied representatives from several mammal orders, have been used as a model group to test the effects of habitat conversion and edge creation on biodiversity. Small mammals occupy a large variety of habitat types and vegetation strata, and have varied lifestyles and diets. They include species with slow-to fast-life history (the Etruscan shrew Suncus etruscus and European Hare Lepus europaeus, respectively) and with very specialized to very generalist habits and diets (the Atlantic bamboo rat Kannabateomys amblyonyx and house mouse Mus musculus, respectively). There are no databases with global coverage focusing on small mammal composition in natural and human-modified habitats and that include neglected natural habitats (e.g. grasslands and savannas). Here, peer-reviewed articles were searched in the primary literature to synthesize almost half century (1973–2017) of research on small mammal composition in natural forests, grasslands and their natural edges, and in five types of human-modified habitats (human-induced forest edges, human-induced grassland edges, crop fields, clear-cuts and tree plantations). The complete database includes information from 199 peer-reviewed articles. Presence data were obtained for 534 species (including 30 unidentified) in 551 sites distributed in 45 countries, 92 ecoregions, 10 biomes and six realms. Measurements of sampling effort and number of species records (number of individuals, captures) per habitat were also obtained, from which researchers can calculate a measure of abundance standardized by the sampling effort. The database will be useful for researchers interested in local-to broad-scale patterns of alpha- and beta-diversity in natural and human-modified habitats.

Influences of the area, shape and connectivity of coastal lakes on the taxonomic and functional diversity of fish communities in Southern Brazil

In this study we investigated the influence of landscape variables on the alpha taxonomic and functional diversity of fish communities in coastal lakes. We built an analytical framework that included possible causal connections among variables, which we analyzed using path analysis. We obtained landscape metrics for the area, shape and connectivity (estuary connectivity and primary connectivity to neighboring lakes) of 37 coastal lakes in the Tramandaí River Basin. We collected fish data from 49 species using standardized sampling with gillnets and obtained a set of traits related to dispersal abilities and food acquisition. The model that best explained the taxonomic diversity and functional richness took into account the shape of the lakes. Functional richness was also explained by estuary connectivity. Functional evenness and dispersion were not predicted by area or connectivity, but they were influenced by the abundant freshwater species. This indicates that all lakes support most of the regional functional diversity. The results highlight the importance of the dispersal process in this lake system and allow the conclusion that considering multiple diversity dimensions can aid the conservation of local and regional fish communities.

Movement and longitudinal distribution of a migratory fish ( Salminus brasiliensis) in a small reservoir in southern Brazil

ABSTRACT We investigated whether the movement and distribution of the migratory fish, Salminus brasiliensis, were affected by a small reservoir. We also examined how movement and distribution were related to water temperature, flow, and rainfall. In December 2011 and January 2012, 24 individuals were captured downstream from the dam, tagged with radio transmitters and released in the reservoir (5.46 km² total area). After being released in the reservoir, 18 of the 24 tagged fish travelled upstream, taking an average of 16.6 days to leave the reservoir, with daily movements varying from < 5 km/day to > 24 km/day. However, only seven tagged specimens (29.16%) returned to the lower reservoir section, while the rest remained in the intermediate and upper reservoir sections. Longitudinal distributions and movements were positively related to both upstream flow into the reservoir and water temperature. We found evidence that S. brasiliensis can recognize the longitudinal gradient and is able to continue its upstream migration. On the other hand, the reservoir negatively affected downstream movements, possibly because disorientation prevented movement to the lower reservoir section. Based on these results, we suggest that the impact of small reservoirs on migratory fish species should be objectively addressed in environmental impact assessments and management programs.

Structure of bird communities in eucalyptus plantations: nestedness as a pattern of species distribution

Replacement of native habitats by tree plantations has increased dramatically in Brazil, resulting in loss of structural components for birds, such as appropriate substrates for foraging and nesting. Tree plantations can also reduce faunal richness and change the composition of bird species. This study evaluated the structure of avian communities in eucalyptus plantations of different ages and in a native forest. We classified species as habitat specialists or generalists, and assessed if the species found in eucalyptus plantations are a subset of the species that occur in the native forest. Forty-one sampling sites were evaluated, with three point counts each, in a native forest and in eucalyptus plantations of four different ages. A total of 71 bird species were identified. Species richness and abundance were higher in the native forest, reflecting the greater heterogeneity of the habitat. The composition of bird species also differed between the native forest and plantations. The species recorded in the plantations represented a subset of the species of the native forest, with a predominance of generalist species. These species are more tolerant of habitat changes and are able to use the plantations. The commercial plantations studied here can serve as a main or occasional habitat for these generalists, especially for those that are semi-dependent on edge and forest. The bird species most affected by silviculture are those that are typical of open grasslands, and those that are highly dependent on well-preserved forests.

Fish composition and species richness in eastern South American coastal lagoons: additional support for the freshwater ecoregions of the world

The relationships between fish composition, connectivity and morphometry of 103 lagoons in nine freshwater ecoregions (FEOW) between 2·83° S and 37·64° S were evaluated in order to detect possible congruence between the gradient of species richness and similarities of assemblage composition. Most lagoons included in the study were <2 km(2) , with a maximum of 3975 km(2) in surface area. Combined surface area of all lagoons included in the study was 5411 km(2) . Number of species varied locally from one to 76. A multiple regression revealed that latitude, attributes of morphometry and connectivity, and sampling effort explained a large amount of variability in species richness. Lagoon area was a good predictor of species richness except in low latitude ecoregions, where lagoons are typically small-sized and not affected by marine immigrants, and where non-native fish species accounted for a significant portion of species richness. Relationships between species and area in small-sized lagoons (<2 km(2) ) is highly similar to the expected number in each ecoregion, with systems located between 18·27° S and 30·15° S attaining higher levels of species richness. Similarities in species composition within the primary, secondary and peripheral or marine divisions revealed strong continental biogeographic patterns only for species less tolerant or intolerant to salinity. Further support for the FEOW scheme in the eastern border of South America is therefore provided, and now includes ecotonal systems inhabited simultaneously by freshwater and marine species of fishes.

Phylogenetic and morphological relationships between nonvolant small mammals reveal assembly processes at different spatial scales

The relative roles of historical processes, environmental filtering, and ecological interactions in the organization of species assemblages vary depending on the spatial scale. We evaluated the phylogenetic and morphological relationships between species and individuals (i.e., inter- and intraspecific variability) of Neotropical nonvolant small mammals coexisting in grassland-forest ecotones, in landscapes and in regions, that is, three different scales. We used a phylogenetic tree to infer evolutionary relationships, and morphological traits as indicators of performance and niche similarities between species and individuals. Subsequently, we applied phylogenetic and morphologic indexes of diversity and distance between species to evaluate small mammal assemblage structures on the three scales. The results indicated a repulsion pattern near forest edges, showing that phylogenetically similar species coexisted less often than expected by chance. The strategies for niche differentiation might explain the phylogenetic repulsion observed at the edge. Phylogenetic and morphological clustering in the grassland and at the forest interior indicated the coexistence of closely related and ecologically similar species and individuals. Coexistence patterns were similar whether species-trait values or individual values were used. At the landscape and regional scales, assemblages showed a predominant pattern of phylogenetic and morphological clustering. Environmental filters influenced the coexistence patterns at three scales, showing the importance of phylogenetically conserved ecological tolerances in enabling taxa co-occurrence. Evidence of phylogenetic repulsion in one region indicated that other processes beyond environmental filtering are important for community assembly at broad scales. Finally, ecological interactions and environmental filtering seemed important at the local scale, while environmental filtering and historical colonization seemed important for community assembly at broader scales.

Checklist of climbing plants in an Araucaria forest of Rio Grande do Sul State, Brazil

Climbing plants are remarkable components of forests, highly contributing for the diversity and dynamics of communities. Studies focusing on climbing plants are scarce and for many vegetation types little is known about climbing species composition and their traits relevant for dispersal and establishment. The focus of this study is to provide the first floristic inventory of climbing plants in an Araucaria forest of Brazil, describing the dispersal syndromes and climbing mechanisms of species and comparing these traits and species composition patterns with other study sites in Southern Brazil. We found 104 taxa belonging to 33 families, with Asteraceae (22 spp.) and Apocynaceae (14 spp.) being the richest families. Among climbing mechanisms, stem twiner (50 spp.) is the most common, followed by tendril (20 spp.) and scrambler (12 spp.), while in relation to the dispersal syndromes, anemochoric species (65 spp.) are the most relevant followed by endozoochoric (28 spp.). Three new species registries were found for Rio Grande do Sul State expanding their occurrence range towards South Brazil. The comparison of climbers’ survey sites showed two sharp groups in relation to species composition and traits proportion, Seasonal and Araucaria/Atlantic forest sites, but with no difference of traits frequency between sites. There is a predominance of stem twiners species in all sites, but the relative difference for tendril species increases in Araucaria and Atlantic forest sites. The Asteraceae and Apocynaceae families were the most relevant, contrasting to Seasonal forests of Southeast Brazil. Interesting patterns can be achieved with a more detailed classification of climbing mechanisms and the results found in this study contributes to enhance the knowledge on climbers’ traits and diversity in South Brazil.

Life-history of the South American darter, Characidium pterostictum (Crenuchidae): evidence for small scale spatial variation in a piedmont stream

The present study compares the reproduction, condition and size of the small characiform fish, Characidium pterostictum, sampled at close sites differing in severity of flash flood effects. Data were obtained from seasonal samples in two sites situated 8 km apart in the same stream. In the upstream site, habitat is more severely affected by flash floods than in the downstream site, and this difference was hypothesized to produce differences in life history and individual reproduction trade-off patterns, as predicted by life-history theory. The results provided evidence for small-scale spatial variation in life-history and trade-off patterns within the studied population. At the most severely disturbed site, C. pterostictum displayed a trade-off pattern that favored reproductive life-span (e.g., larger size, higher and seasonally stable condition, larger mean size of mature females) over instantaneous reproductive output (lower gonadosomatic index), while the opposite pattern was observed in the less disturbed site. Because of the differences in disturbance effects between each sampling site, these results suggest that within-stream variability in the severity of hydrological disturbance can influence life-history patterns at small spatial scales. An implication of the results is that fish occupying areas that are hydrologically more variable within a stream are not necessarily at an energetic or reproductive disadvantage, but may be simply under environmental conditions that favor distinct patterns of energy allocation (or trade-offs) and population persistence, as predicted by life-history theory. Therefore, plasticity in life-history is expected to be common in stream fish populations that are widespread in a stream system with spatially variable or patchy habitat characteristics.

Feeding dynamics and ecomorphology of Oligosarcus jenynsii (Gunther, 1864) and Oligosarcus robustus (Menezes, 1969) in the Lagoa Fortaleza, southern Brazil

Oligosarcus jenynsii and Oligosarcus robustus are fishes of Characidae family that occur in Rio Grande do Sul, Uruguay and northern Argentina. This work purported to study the feeding dynamics (repletion and hepatosomatic indexes and condition factor) over time, and to investigate the coexistence of these two species by evaluating the partition of resources using qualitative and quantitative analyses of diet, temporal and spatial segregation throughout the water column and some ecomorphological aspects of the species in the Lagoa Fortaleza. Specimens were sampled monthly, from May 2000 to April 2001 during 24 h/month, using stationary gill nets of different mesh sizes. The records of each individual included total and standard length; total, stomach and liver weight; sex and stomach repletion. The variation of the mean values of repletion index and relative frequencies of stomach repletion stages indicate that O. jenynsii and O. robustus do not present seasonal differences in feeding intensity. The hepatosomatic index shows an allocation of energy to the liver during every period except reproduction, when part of the energy is used for gonad maturation. The estimated condition factor for both species reveals an increase in the reproductive period, evidencing the influence of gonads upon the condition of the fish. The diet analysis revealed that O. robustus is piscivorous, whereas O. jenynsii is a generalist carnivore, tending to piscivory as well. The active period of O. robustus is more concentrated at sunrise and sunset, whereas O. jenynsii is continually active, a characteristic related to hunting for prey. The ecomorphological analysis revealed differences between the two species in the dimensions of the mouth. Evidence suggests that the species coexist, sharing food sources, differing in oral morphology but ingesting similar prey, possibly because food is not a limiting factor in the environment.

Persistency of lactation yield: a novel approach

The objectives of our study were to propose a new, simple, and easy-to-understand definition for persistency of lactation yield and to develop a new mathematical model to describe a lactation curve, one that includes a measure for persistency of lactation yield according to the proposed definition. Our definition of persistency is the number of days during which the level of constant yield is maintained. No lactation model exists that includes a measure of persistency in terms of duration of time or that allows this measure of persistency to be derived from model parameters. It was necessary, therefore, to develop a new model to describe the lactation curve: [formula: see text] where yt = yield at time t, t1 = time at transition from increased yield to constant yield, yP = level of constant yield, b3 = rate of decline in yield from the end of constant yield to the end of lactation, and P = persistency of constant yield. These four parameters measured directly the important biological characteristics of a lactation curve. Two test day data sets, one for individual records from a high-producing cow and one for average records from 17,607 cows, were used to illustrate the model and to estimate persistency. The proposed measure of persistency should be important for genetic selection because it might be desirable to select for increased persistency (e.g., for extended lactations) without increasing peak yield and, hence, subjecting the cow to undesirable stress.