ATLANTIC-CAMTRAPS: a dataset of medium and large terrestrial mammal communities in the Atlantic Forest of South America.

Our understanding of mammal ecology has always been hindered by the difficulties of observing species in closed tropical forests. Camera trapping has become a major advance for monitoring terrestrial mammals in biodiversity rich ecosystems. Here we compiled one of the largest datasets of inventories of terrestrial mammal communities for the Neotropical region based on camera trapping studies. The dataset comprises 170 surveys of medium to large terrestrial mammals using camera traps conducted in 144 areas by 74 studies, covering six vegetation types of tropical and subtropical Atlantic Forest of South America (Brazil and Argentina), and present data on species composition and richness. The complete dataset comprises 53,438 independent records of 83 species of mammals, includes 10 species of marsupials, 15 rodents, 20 carnivores, eight ungulates and six armadillos. Species richness averaged 13 species (±6.07 SD) per site. Only six species occurred in more than 50% of the sites: the domestic dog Canis familiaris, crab-eating fox Cerdocyon thous, tayra Eira barbara, south American coati Nasua nasua, crab-eating raccoon Procyon cancrivorus and the nine-banded armadillo Dasypus novemcinctus. The information contained in this dataset can be used to understand macroecological patterns of biodiversity, community, and population structure, but also to evaluate the ecological consequences of fragmentation, defaunation, and trophic interactions.

Can roads be used as transects for primate population surveys?.

Line transect distance sampling (LTDS) can be applied to either trails or roads. However, it is likely that sampling along roads might result in biased density estimates. In this paper, we compared the results obtained with LTDS applied on trails and roads for two primate species (Callithrix penicillata and Callicebus nigrifrons) to clarify whether roads are appropriate transects to estimate densities. We performed standard LTDS surveys in two nature reserves in south-eastern Brazil. Effective strip width and population density were different between trails and roads for C. penicillata, but not for C. nigrifrons. The results suggest that roads are not appropriate for use as transects in primate surveys, at least for some species. Further work is required to fully understand this issue, but in the meantime we recommend that researchers avoid using roads as transects or treat roads and trails as covariates when sampling on roads is unavoidable.

Molecular evidence for a diverse green algal community growing in the hair of sloths and a specific association with Trichophilus welckeri (Chlorophyta, Ulvophyceae).

BACKGROUND: Sloths are slow-moving arboreal mammals inhabiting tropical rainforests in Central and South America. The six living species of sloths are occasionally reported to display a greenish discoloration of their pelage. Trichophilus welckeri, a green algal species first described more than a century ago, is widely believed to discolor the animals fur and provide the sloth with effective camouflage. However, this phenomenon has not been explored in any detail and there is little evidence to substantiate this widely held opinion. RESULTS: Here we investigate the genetic diversity of the eukaryotic community present in fur of all six extant species of sloth. Analysis of 71 sloth hair samples yielding 426 partial 18S rRNA gene sequences demonstrates a diverse eukaryotic microbial assemblage. Phylogenetic analysis reveals that sloth fur hosts a number of green algal species and suggests that acquisition of these organisms from the surrounding rainforest plays an important role in the discoloration of sloth fur. However, an alga corresponding to the morphological description of Trichophilus welckeri was found to be frequent and abundant on sloth fur. Phylogenetic analysis demonstrated the retention of this alga on the fur of sloths independent of geographic location. CONCLUSIONS: These results demonstrate a unique diverse microbial eukaryotic community in the fur of sloths from Central and South America. Our analysis streghtens the case for symbiosis between sloths and Trichophilus welckeri.

Ecosystem services provided by armadillos.

Awareness of the natural ecological processes provided by organisms that benefit human well-being has significantly progressed towards the goal of making conservation a mainstream value. Identifying different services and the species that provide them is a vital first step for the management and maintenance of these so-called ecosystem services. Herein, we specifically address the armadillos, which play key functional roles in terrestrial ecosystems, including as ecosystem engineers, predators, and vectors of invertebrates and nutrients, although these roles have often been overlooked. Armadillos can control pests, disperse seeds, and be effective sentinels of potential disease outbreaks or bioindicators of environmental contaminants. They also supply important material (meat, medicines) and non-material (learning, inspiration) contributions all over the Americas. We identify key gaps in the understanding of ecosystem services provided by armadillos and areas for future research required to clarify their functional role in terrestrial ecosystems and the services they supply. Such information will produce powerful arguments for armadillo conservation.

DNA mini-barcoding of leporids using noninvasive fecal DNA samples and its significance for monitoring an invasive species.

Introduced in South America at the end of the 19th century, the European hare population has expanded dramatically and now represents a risk to native Brazilian forest rabbits. Monitoring the invasive Lepus europaeus and its coexistence with native Sylvilagus brasiliensis is a challenge that can be efficiently addressed by the use of molecular tools. This work describes a set of primers useful for amplifying three mini-barcodes for the molecular identification of both invasive and native leporid species using degraded fecal DNA. In addition, tests in silico indicate that these mini-barcodes can successfully amplify the DNA sequences of a number of leporids. These mini-barcodes constitute a powerful tool for the monitoring and management of the invasive L. europaeus and the conservation of native rabbits.

FragSAD: A database of diversity and species abundance distributions from habitat fragments.

Habitat destruction is the single greatest anthropogenic threat to biodiversity. Decades of research on this issue have led to the accumulation of hundreds of data sets comparing species assemblages in larger, intact, habitats to smaller, more fragmented, habitats. Despite this, little synthesis or consensus has been achieved, primarily because of non-standardized sampling methodology and analyses of notoriously scale-dependent response variables (i.e., species richness). To be able to compare and contrast the results of habitat fragmentation on species' assemblages, it is necessary to have the underlying data on species abundances and sampling intensity, so that standardization can be achieved. To accomplish this, we systematically searched the literature for studies where abundances of species in assemblages (of any taxa) were sampled from many habitat patches that varied in size. From these, we extracted data from several studies, and contacted authors of studies where appropriate data were collected but not published, giving us 117 studies that compared species assemblages among habitat fragments that varied in area. Less than one-half (41) of studies came from tropical forests of Central and South America, but there were many studies from temperate forests and grasslands from all continents except Antarctica. Fifty-four of the studies were on invertebrates (mostly insects), but there were several studies on plants (15), birds (16), mammals (19), and reptiles and amphibians (13). We also collected qualitative information on the length of time since fragmentation. With data on total and relative abundances (and identities) of species, sampling effort, and affiliated meta-data about the study sites, these data can be used to more definitively test hypotheses about the role of habitat fragmentation in altering patterns of biodiversity. There are no copyright restrictions. Please cite this data paper and the associated Dryad data set if the data are used in publications.

Landscape Use and Co-Occurrence Patterns of Neotropical Spotted Cats.

Small felids influence ecosystem dynamics through prey and plant population changes. Although most of these species are threatened, they are accorded one of the lowest research efforts of all felids, and we lack basic information about them. Many felids occur in sympatry, where intraguild competition is frequent. Therefore, assessing the role of interspecific interactions along with the relative importance of landscape characteristics is necessary to understand how these species co-occur in space. Here, we selected three morphologically similar and closely related species of small Neotropical cats to evaluate the roles of interspecific interactions, geomorphometry, environmental, and anthropogenic landscape characteristics on their habitat use. We collected data with camera trapping and scat sampling in a large protected Atlantic forest remnant (35,000 ha). Throughout occupancy modeling we investigated whether these species occur together more or less frequently than would be expected by chance, while dealing with imperfect detection and incorporating possible habitat preferences into the models. We used occupancy as a measure of their habitat use. Although intraguild competition can be an important determinant of carnivore assemblages, in our system, we did not find evidence that one species affects the habitat use of the other. Evidence suggested that proximity to the nature reserve (a more protected area) was a more important driver of Neotropical spotted cats' occurrence than interspecific interactions or geomorphometry and environmental landscape characteristics-even though our entire study area is under some type of protection. This suggests that small felids can be sensitive to the area protection status, emphasizing the importance of maintaining and creating reserves and other areas with elevated protection for the proper management and conservation of the group.

Occurrence of potential wild hosts of Echinococcus vogeli in the forests of southwestern Brazilian Amazonia / Ocorrência de potenciais hospedeiros silvestres de Echinococcus vogeli nas florestas do sudoeste da Amazônia brasileira

Abstract The helminth Echinococcus vogeliRausch & Bernstein, 1972 is a causative agent of Neotropical Echinococcosis, a chronic zoonotic disease which is endemic to the Neotropical region. This parasite is transmitted from bush dogs (Speothos venaticus) to their prey, which include lowland pacas (Cuniculus paca) and agoutis (Dasyprocta spp.). In Brazil, most human cases of Neotropical Echinococcosis have been recorded in the Amazonian states of Acre and Pará, although few data are available on the occurrence of the potential definitive or intermediate hosts of E. vogeli in the Amazon region. In the present study, we surveyed the forests surrounding 46 human communities located within and around of outside six sustainable-use protected areas in the southwestern Amazon basin of Brazil. The forests were surveyed using camera traps to determine the local presence of potential wild hosts of E. vogeli, and the exploitation of these hosts for game meat was evaluated through interviews with 136 subsistence hunters resident in the local communities. We recorded pacas, agoutis, and bush dogs, as well as domestic dogs (Canis familiaris), all potential reservoirs of Neotropical Echinococcosis, using the same habitats. We also confirmed the frequent consumption of paca and agouti meat by subsistence hunters and their families in the study communities. Our data contribute to the understanding of the occurrence of E. vogeli in Brazilian ecosystems.

Resumo O helminto Echinococcus vogeliRausch & Bernstein, 1972 é o agente causador da Equinococose Neotropical, uma doença zoonótica crônica e endêmica da região Neotropical. Este parasito é transmitido entre o cachorro-vinagre (Speothos venaticus) e suas presas, como pacas (Cuniculus paca) e cutias (Dasyprocta spp.). No Brasil, a maioria dos casos humanos de Equinococose Neotropical é registrada nos estados do Acre e Pará, embora existam poucos dados disponíveis sobre a ocorrência de potenciais hospedeiros definitivos e intermediários de E. vogeli na Amazônia. No presente estudo, foram investigadas áreas de floresta ao redor de 46 comunidades humanas localizadas no interior e entorno de seis unidades de conservação de uso sustentável no sudoeste da bacia amazônica brasileira e, por meio de armadilhas fotográficas, foram avaliadas as presenças de potenciais hospedeiros silvestres de E. vogeli. Adicionalmente, foram avaliados o padrão de consumo da carne dos hospedeiros silvestres por meio de entrevistas com 136 moradores dessas comunidades. Foram registradas pacas, cutias e cachorros-vinagre, bem como cães domésticos (Canis familiaris) utilizando os mesmos habitats, todos potenciais reservatórios da Equinococose Neotropical. Além disto, confirmamos a alto consumo de paca e cutia nas comunidades. Os dados do presente trabalho contribuem para pesquisas em andamento sobre a presença dos potenciais reservatórios de E. vogeli em ambientes brasileiros.

Mammals in São Paulo State: diversity, distribution, ecology, and conservation / Mamíferos do Estado de São Paulo: diversidade, distribuição, ecologia e conservação

Abstract Mammals are charismatic organisms that play a fundamental role in ecological functions and ecosystem services, such as pollination, seed dispersal, nutrient cycling, and pest control. The state of São Paulo represents only 3% of the Brazilian territory but holds 33% of its mammalian diversity. Most of its territory is dominated by agriculture, pastures, and urban areas which directly affect the diversity and persistence of mammals in the landscape. In addition, São Paulo has the largest port in Latin America and the largest offshore oil reservoir in Brazil, with a 600 km stretch of coastline with several marine mammal species. These human-made infrastructures affect the diversity, distribution, ecology, and the future of mammals in the state. Here, we answer five main questions: 1) What is the diversity of wild mammals in São Paulo state? 2) Where are they? 3) What is their positive and negative impact on human well-being? 4) How do mammals thrive in human-modified landscapes? 5) What is the future of mammals in the state? The state of São Paulo holds 255 species of native mammals, with four endemic species, two of them globally endangered. At least six species (two marsupials, Giant otter, Pampas deer, Brazilian dwarf brocket deer, and Giant armadillo) were extirpated from the state due to hunting and habitat loss. The intense human land use in the state forced many mammalian species to change their diet to cope with the intense fragmentation and agriculture. Large-scale monoculture has facilitated the invasion of exotic species such as wild boars (javali) and the European hare. Several "savanna-dwelling" species are expanding their ranges (Maned wolf, Brocket deer) over deforested areas and probably reflect changes towards a drier climate. Because the state has the largest road system, about 40,000 mammals from 33 species are killed per year in collisions causing an economic loss of 12 million dollars/year. The diversity of mammals is concentrated in the largest forest remnants of Serra do Mar and in the interior of the State, mainly in the regions of Ribeirão Preto and Jundiaí. Sampling gaps are concentrated throughout the interior of the state, particularly in the northwest region. Wild mammals play a fundamental role in many ecosystem services, but they can also be a concern in bringing new emergent diseases to humans. Although the taxonomy of mammals seems to be well known, we show that new species are continuously being discovered in the state. Therefore, continuous surveys using traditional and new technologies (eDNA, iDNA, drones), long-term population monitoring, investigation of the interface of human-wildlife conflict, and understanding of the unique ecosystem role played by mammals are future avenues for promoting sustainable green landscapes allied to human well-being in the state. The planting of forest or savanna corridors, particularly along with major river systems, in the plateau, controlling illegal hunting in the coastal areas, managing fire regimes in the Cerrado, and mitigating roadkill must be prioritized to protect this outstanding mammal diversity.

Resumo Os mamíferos são organismos carismáticos que desempenham um papel fundamental na função ecológica e nos serviços ecossistêmicos, como polinização, dispersão de sementes, ciclagem de nutrientes e controle de pragas. O Estado de São Paulo representa apenas 3% do território brasileiro, mas detém 33% da diversidade de mamíferos. A maior parte de seu território é dominado pela agricultura, pastagens e áreas urbanas que afetam diretamente a diversidade e a persistência dos mamíferos na paisagem. Além disso, São Paulo possui o maior porto da América Latina e o maior reservatório de petróleo costeiro do Brasil, com 600 km de extensão de litoral com diversas espécies de mamíferos marinhos. Essas infraestruturas afetam a diversidade, distribuição, ecologia e o futuro dos mamíferos no estado. Aqui, respondemos cinco perguntas principais: 1) Qual é a diversidade de mamíferos silvestres no Estado de São Paulo? 2) Onde eles ocorrem? 3) Qual é o seu impacto positivo e negativo no bem-estar humano? 4) Como os mamíferos persistem em paisagens modificadas pelo homem? 5) Qual é o futuro dos mamíferos no estado? O estado de São Paulo possui 255 espécies de mamíferos nativos, com quatro espécies endêmicas, duas delas globalmente ameaçadas de extinção. Pelo menos seis espécies (dois marsupiais, ariranha, veado-campeiro, veado-cambuta e tatu-canastra) foram extirpadas do estado devido à caça e perda de habitat. O intenso uso humano da terra no estado forçou muitas espécies de mamíferos a mudar sua dieta para lidar com a intensa fragmentação e agricultura. A monocultura em larga escala facilitou a invasão de espécies exóticas, como porcos selvagens (javaporco) e a lebre europeia. Várias espécies de áreas abertas estão expandindo suas áreas de distribuição (lobo-guará, veado-catingueiro) sobre áreas desmatadas e provavelmente refletem mudanças em direção a um clima mais seco. Como o estado possui o maior sistema rodoviário do Brasil, cerca de 40 mil mamíferos de 33 espécies são mortos por ano em colisões, causando um prejuízo econômico de 12 milhões de dólares/ano. A diversidade de mamíferos está concentrada nos maiores remanescentes florestais da Serra do Mar e no interior do Estado, principalmente nas regiões de Ribeirão Preto e Jundiaí. As lacunas amostrais estão concentradas em todo o interior do estado, principalmente na região noroeste. Os mamíferos silvestres desempenham um papel fundamental em muitos serviços ecossistêmicos, mas também podem ser uma preocupação em trazer novas doenças emergentes para as populações humanas. Embora a taxonomia de mamíferos pareça ser bem conhecida, mostramos que novas espécies estão sendo continuamente descobertas no estado. Portanto, pesquisas usando tecnologias tradicionais e novas (eDNA, iDNA, drones), monitoramento populacional de longo prazo, a investigação da interface do conflito homem-vida selvagem e a compreensão do papel único no ecossistema desempenhado pelos mamíferos são um caminho futuro para promover uma paisagem verde sustentável aliada ao bem-estar humano no estado. O plantio de corredores florestais ou de cerrado, principalmente junto aos principais sistemas fluviais, no planalto, o controle da caça ilegal nas áreas costeiras, o manejo dos regimes de fogo no Cerrado e a mitigação dos atropelamentos devem ser uma prioridade para proteger essa notável diversidade de mamíferos.

Density and Population Size of Mammals in Remnants of Brazilian Atlantic Forest.

From October 1994 to April 1996, I surveyed six Atlantic forest reserves, two large (approximately 20,000 ha each), two medium-sized (approximately 2000 ha each), and two small (approximately 200 ha each), located in northern Espírito Santo, southeastern Brazil, for mammals openface> 1 kg body weight. My main objective was to assess the effects of fragmentation on population sizes and densities of five abundant species of forest-dwelling species (three primates and two rodents). I used line-transect sampling to survey mammals and estimated densities through the DISTANCE program. The average density of mammals increased from small to medium to large fragments, with small fragments having an average mammal density ( 7.6 individuals/km2 ) significantly lower than that of large fragments (20.9 individuals/km2 ). This trend was not significant when species that were extinct or absent in some fragments were excluded from the analysis. Shortage of food ( fruits) and predation by small cats ( Leopardus sp.) are the likely factors contributing to the demise of mammals, most of which are frugivores, in small fragments. Estimates of population sizes were on the order of several hundred to thousands of individuals for the large reserves, whereas comparable estimates for the other areas indicate a few hundred individuals for the medium-sized reserves and <100 individuals per species in the small reserves. The estimates provided here indicate that only Atlantic forest reserves of ≥20,000 ha can sustain viable populations ( Ne ≅ 500 individuals) of the five species studied, which represent only about 14% of all medium-sized to large species of mammals known to be present in fragments of this size. Given that only about 20% of all protected areas remaining in the Atlantic forest are equal to or larger than this size, management measures are badly needed to improve mammal conservation in this biome.

RESUMEN: Entre los meses de octubre de 1994 a abril de 1996, estudié los mamíferos mayores de un kg de peso en seis reservas forestales, dos grandes (c. 20,000 ha cada una), dos de tamaño mediano (c. 2000 ha cada una) y dos pequeñas (c. 200 ha cada una), localizadas al sureste de Brasil, en la provincia de Espírito Santo. El principal objetivo fue evaluar los efectos de la fragmentación en los tamaños poblacionales y las densidades de cinco especies abundantes residentes del bosque (tres primates y dos roedores). Utilicé muestreos de transectos en línea para evaluar los mamíferos y estimé las densidades mediante el programa DISTANCE. La densidad promedio de los mamíferos incrementó de los fragmentos pequeños a los medianos, a los grandes. Los fragmentos pequeños tuvieron una densidad promedio ( 7.6 individuos/km2 ) significativamente menor que la de los fragmentos grandes (20.9 individuos/km2 ). Esta tendencia no fue significativa cuando las especies extintas o ausentes de algunos fragmentos fueron excluidas del análisis. La escasez de alimento ( frutas) y la depredación por gatos pequeños ( Leopardus spp.) son probablemente los factores que contribuyeron a la muerte de los mamíferos-la mayoría de los cuales son frugívoros- en los fragmentos pequeños. Las estimaciones de tamaño poblacional fueron de un orden de varios cientos a miles de individuos para las reservas grandes, mientras que las estimaciones para las otras áreas indican unos pocos cientos de individuos en las reservas de tamaño <100 individuos/especie en las reservas pequeñas. Las estimaciones proporcionadas aquí indican que solo las reservas de bosque del Atlántico ≥20,000 ha pueden sostener poblaciones viables ( Ne ≅ 500 individuos) de las cinco especies estudiadas, las cuáles representan solo el 14% del total de especies de mamíferos de tamaño mediano a grande que se sabe están presentes en fragmentos de ese tamaño. Dado que solo 20% del total de las áreas protegidas que persisten en el bosque del Atlántico son iguales o mayores a este tamaño, se necesitan urgentemente medidas de manejo para mejorar la conservación de los mamíferos en este bioma.