Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest,Brazil

The application of environmental DNA (eDNA) metabarcoding as a biomonitoring tool has greatly increased, but studies have focused on temperate aquatic macro-organisms. We apply eDNA metabarcoding to detecting the mammalian community in two high-biodiversity regions of Brazil: the Amazon and Atlantic Forests. We identified Critically Endangered and Endangered mammalian species and found overlap with species identified via camera trapping. We highlight the potential for using eDNA monitoring for mammals in biodiverse regions and identify challenges: we need a better understanding of the ecology of eDNA within variable environments and more appropriate reference sequences for species identification in these anthropogenically impacted biomes.     

Diversity and abundance of climbers from the Atlantic Forest, southeastern Brazil

Climbing plant community composition and abundance was compared between the Alto da Serra de Paranapiacaba Biological Reserve (ASPRB) and the Nascentes de Paranapiacaba Municipal Natural Park (NPMNP), two protected areas in the largest Atlantic Forest remnant, southeastern Brazil. Climbing plants ≥1 cm in diameter were sampled in 52 quadrats of 10 × 20 m (1.04 ha). From these data we calculated the Shannon–Wiener diversity index, calculated abundance and importance values for families, performed a principal coordinate analysis, and created a similarity dendrogram (TWINSPAN). The composition and abundance of species between ASPRB and NPMNP differed significantly due to the successional state of the ASPRB forest, which was affected by more recent disturbance. There we found 34 species, while in the NPMNP, species richness was 72, with only 24 species in common. The two areas formed two groups corresponding to two distinct floristic subsets. These montane forests were characterized by a predominance of species of the Asteraceae. The high species richness, floristic composition, and community composition reflect the greater degree of conservation in the area of NPMNP. The high density and community composition of climbers in the more conserved area of rainforest may be due to the low intensity of disturbance.     

SHOREBIRDS OF COASTAL BUENOS AIRES PROVINCE, ARGENTINA

The Pampas shorebird community is comprised of species from diverse taxonomic and faunal origin. Four major groups can be recognized: North American migrants residing in coastal Buenos Aires Province during their non-breeding season, Patagonian species wintering locally but breeding further south, Pampean species breeding locally, and Brazil–Paraguayan species present during their breeding season. Because of differences among these groups in the timing and migration patterns, community composition shows marked seasonal variation. Both nesting and non-breeding birds use a diversity of habitat types ranging from littoral sandy beaches to upland grasslands. Throughout the year, however, and in all habitat types, non-breeders predominate in species number and abundance. Intra- and inter-specific patterns of aggression suggest both that resources are limiting, and that non-breeding migrants may play an important role in determining breeding community composition.     

Patterns and partitioning of food resources by elasmobranchs in southern Brazil

Our study sought to analyze patterns and overlap in prey items consumed by elasmobranch species in southern Brazil through a complex network analysis. We hypothesized that species with the same habitat use would show greater trophic niche overlap and lower diet specialization than species with different habitat use. We conducted a literature survey of the species recorded in southern Brazil and analyzed publications with quantitative data on the diet of each species. We found records of 103 species in the region, of which 58 had their diets analyzed and had quantitative data to contribute to this analysis. The results suggest nested diet patterns in this community. Nestedness may arise for different reasons, and suggests that species might be balancing their high feeding niche overlap through compensatory mechanisms. There are no prior records of such a pattern in elasmobranch communities, which brings to light important information about their feeding niche. Data on prey consumption and temporal and spatial patterns of elasmobranch feeding may yield further insight into how these species are interacting in the environment and assist the investigation of the processes that shaped the current community’s trophic structure.

     

Helminth community structure of Tropidurus torquatus (Squamata: Tropiduridae) in a rocky outcrop area of Minas Gerais state, southeastern Brazil

The helminth community of Tropidurus torquatus (Squamata: Tropiduridae) from a rocky outcrop area located in the state of Minas Gerais, southeastern Brazil, was studied. Ninety-two of the 110 individuals examined (83.6%) harbored helminths. Five species were found, including 3 nematodes ( Physaloptera lutzi , Parapharyngodon bainae , and Oswaldofilaria chabaudi ), 1 unidentified cestode species, and 1 acanthocephalan cystacanth also not identified. Only the nematode species had sufficient data to perform ecological analysis, with P. lutzi exhibiting the highest prevalence (67.3%). Prevalence between male and female hosts differed only for Oswaldofilaria chabaudi , with males exhibiting the highest values. The intensities of infection by P. lutzi and O. chabaudi were different among male and female hosts, with males also exhibiting the highest values. The host body size was positively related to intensity of infection for all nematode species. Local seasonality had some influence on the helminth community structure. Host diet, sexual dimorphism, and behavior (territorialism, forage strategy) represented important factors for the structure of this parasite community. In general, the helminth community was species poor, depauperate, and non-interactive, representing a typical structure observed in lizard hosts.     

Examining variation in the leaf mass per area of dominant species across two contrasting tropical gradients in light of community assembly

Understanding variation in key functional traits across gradients in high diversity systems and the ecology of community changes along gradients in these systems is crucial in light of conservation and climate change. We examined inter‐ and intraspecific variation in leaf mass per area (LMA) of sun and shade leaves along a 3330‐m elevation gradient in Peru, and in sun leaves across a forest–savanna vegetation gradient in Brazil. We also compared LMA variance ratios (T‐statistics metrics) to null models to explore internal (i.e., abiotic) and environmental filtering on community structure along the gradients. Community‐weighted LMA increased with decreasing forest cover in Brazil, likely due to increased light availability and water stress, and increased with elevation in Peru, consistent with the leaf economic spectrum strategy expected in colder, less productive environments. A very high species turnover was observed along both environmental gradients, and consequently, the first source of variation in LMA was species turnover. Variation in LMA at the genus or family levels was greater in Peru than in Brazil. Using dominant trees to examine possible filters on community assembly, we found that in Brazil, internal filtering was strongest in the forest, while environmental filtering was observed in the dry savanna. In Peru, internal filtering was observed along 80% of the gradient, perhaps due to variation in taxa or interspecific competition. Environmental filtering was observed at cloud zone edges and in lowlands, possibly due to water and nutrient availability, respectively. These results related to variation in LMA indicate that biodiversity in species rich tropical assemblages may be structured by differential niche‐based processes. In the future, specific mechanisms generating these patterns of variation in leaf functional traits across tropical environmental gradients should be explored.     

Distribution of Satyrini (Lepidoptera, Nymphalidae) in Rio Grande do Sul State, southern Brazil

Knowledge of species distribution is important for effective conservation measures. Considering that habitat features and abiotic factors can influence local community structure of butterflies, this study aimed to verify the existence of a pattern in the distribution of Satyrini in southern Brazil. For this objective, we updated the regional Satyrini species list based on field studies and literature, resulting in a total of 54 species. For those studies that presented clearly defined sampling sites, we analyzed the faunal similarity by site and by phytoecological region and verified the influences of environmental (altitude, average annual temperature and precipitation, and phytoecological region) and spatial variables (PCNM) in species distribution. We analyzed 156 records of 40 species at 14 sites and eight phytoecological regions. Environmental variables—namely, differences in temperature and phytoecological region—and spatial position proved to effect the distribution of Satyrini in southern Brazil. We thus urge that the future Conservation Units should be well spaced and properly distributed through environmentally distinct units in the landscape, representing different phytoecological regions. These conclusions shall provide subsidies to biodiversity conservation.     

Syncephalis aggregata, a new species from the semiarid region of Brazil

A new species of Syncephalis (Zoopagales) was isolated from soil in a semiarid area of northeastern Brazil. Syncephalis aggregata is distinguished from the other species of the genus by the production of merosporangiophores in dense tufts and with randomly spaced, irregular swellings and simple merosporangia produced over the upper 50% of a globose to ovoid vesicle. An identification key for the species of Syncephalis found in Brazil is provided.     

Bat Community in a Cave From Eastern Brazil,Including a New Record of Lionycteris (Phyllostomidae,Glossophaginae)

A cave bat community from a semiarid region in eastern Brazil was studied during the dry season. A high diversity was observed, with thirteen species recorded. Except for Micronycteris minuta and Lionycteris spurrelli, these bats were also found in other Brazilian karstic areas. The commonest species were the hematophague Desmodus rotundus, the omnivore Carollia perspicillata, and the insectivore Natalus stramineus. The bats formed itinerant colonies, moving frequently inside the cave. L. spurrelli was previously known from Amazonia, usually associated with evergreen forests. The present record extends its range 1600 km to the south. A disjunct distribution explains some morphological differentiation between Amazonia and Olhos d'Água cave populations. The latter may be a relict of former continuous forest vegetation, which has been fragmented after the climatic optimum. Dispersion through the Cerrado forest gallery is also possible.     

Habitat loss and mammalian extinction patterns: are the reserves in the Quadrilátero Ferrífero, southeastern Brazil, effective in conserving mammals?

Habitat loss is considered to be the principal cause of the local extinction of mammals worldwide. We assessed the extinction pattern of medium- and large-sized mammals caused by the effects of habitat loss in reserves in the Quadrilátero Ferrífero, southeastern Brazil, and discussed the effectiveness of these natural remnants for conserving mammals. A literature review and field collections were conducted from 2006 to 2011 to estimate the composition and richness of mammals in nine remnants of different sizes, including reserves and non-protected areas. A species–area relation and a nested subset analysis were performed, and a degree of sensitivity to habitat loss was obtained for each species according to its frequency of occurrence. Forty-five species of mammals were recorded. There was a strong species–area relation involving the legal size of reserves. High species richness was associated with large reserves, and the z value was within the range of very isolated continental remnants. The mammalian community exhibited a nested occurrence pattern, suggesting that most species were part of a more continuous ecosystem and that non-random extinction caused by habitat loss occurred in southeastern Brazil. The negative relation found between species frequencies and body weights suggested that selective species loss is associated with decreases in the size of the reserves. The estimated viable size required to conserve all of the sensitive species is greater than the size of the largest reserve inventoried. We recommend the aggregation of neighboring natural remnants and the creation of new reserves to reduce extinction risks.     

Diversity of arbuscular mycorrhizal fungi in restinga and dunes areas in Brazilian Northeast

Strong anthropogenic pressure, mainly mineral extraction, is one of the main factors leading to degradation of the Brazilian coastal environment. Strategies to recover these areas include replanting native plant species, and symbiotic fungi from the neighboring area might be important for the establishment of the new vegetation. Species richness, diversity and community composition of arbuscular mycorrhizal fungi (AMF) were investigated in NE Brazil in two natural areas, ‘restinga’ forest and seaside ‘restinga’, and in two areas of revegetated dunes after mining activity 20 and 8?years ago. Soil samples were collected during the dry (March) and wet (September) seasons of 2009 in Mataraca, Paraíba State, Brazil. Based on glomerospore morphology, 34 species of AMF were recorded, of which 29 were identified in field samples and five after trap culturing, with the greatest diversity and richness found in the dune revegetated 8?years ago. The sampling effort allowed an assessment of between 70 and 80?% of the species estimated for the areas by the first-order Jackknife index. Among the generalist species Gigaspora margarita was the only one found in all areas and during both collection periods. The similarity of AMF species between the revegetated areas and the seaside ‘restinga’ was >60?%, supporting the hypothesis that this area represents a source of propagules, but the substrate used for seedling production may also bring other species, enabling the recovery of the AMF community in the mined and revegetated dunes.     

Use of Terra Firme Forest by Caicubi Caboclos,Middle Rio Negro,Amazonas, Brazil. A Quantitative Study

Use of Terra Firme Forest by Caicubi Caboclos, Middle Rio Negro, Amazonas, Brazil. A Quantitative Study. An ethnobotanical study was carried out with caboclos from the village of Caicubi, Roraima State, Brazil. This village is located between the Rio Negro and Rio Branco. The data were collected in 1 ha of terra firme forest and involved caboclo knowledge of the tree species with individuals dbh ≥ 10 cm. A total of 11 informants between 34 to 74 years of age were interviewed. The caboclos used 185 (98%) of the 189 species analyzed. The family with the highest use value for the community was Arecaceae. The species with the highest use value was Bertholletia excelsa. Arecaceae, Lecythidaceae, and Sapotaceae showed a wide variety of uses. The uses were grouped into eight categories; those with the highest use values were firewood, technology, and construction. The mean use value for species was 1.6. The most intensely used resources in the forest were wood, leaves, spines, and exudates.     

The Impact of Industrial Anthropization on Mosquito (Diptera, Culicidae) Communities in Mangrove Areas of Guanabara Bay (Rio de Janeiro, Brazil)

The effects of industrial anthropization on species composition and community diversity of Culicidae (Diptera) were studied in a mangrove area impacted by industrial activities as compared to a preserved area, both around Guanabara Bay in the state of Rio de Janeiro, Brazil. Diversity, equitability, and species richness in Culicidae community differed between the studied areas. Indicator species analysis and correspondence analysis were carried out and indicated that the Sabethini, especially Wyeomyia (Phoniomyia) theobaldi Lane, Wyeomyia (Phoniomyia) fuscipes (Edwards), and a non-identified species of Wyeomyia sp. were associated to the preserved area, whereas Aedes taeniorhynchus Wiedemann and Aedes scapularis (Rondani) to the impacted area.     

Anthropic effects on the fish community of Ribeir?o Claro, Rio Claro, SP, Brazil.

The effect of anthropic alterations such as drain discharge on a fish community was studied in the Ribeir?o Claro River, municipality of Rio Claro, State of S?o Paulo, southeastern Brazil. Samples were made monthly in three different points along the river (headwaters, mid course, and confluence) between December, 2003 and March, 2004, which is the reproductive period for the majority of the species. The fish community of the Ribeir?o Claro River showed a fair composition and diversity, with species rarely observed in studies made in the region, such as Paravandellia oxyfera and Callichthys callichthys. Indices of diversity and equitability showed different results when weight or the number of individuals were considered. Moreover, these indices did not reveal the typical increase in diversity from the headwaters toward the confluence, nor the loss of richness in the part altered by drain discharge. An interpretation should be made with caution, taking into account the diverse factors included in the computation. Similar to the diversity indices, the Morisita-Horn similarity index did not reveal a great difference in the fish community of the confluence of the river, mainly in relation to its mid course. The decline of species richness and trophic composition alteration in the disturbed part is clear, which shows a great dominance of piscivorous species.     

Resource Partitioning between Highly Eusocial Bees and Possible Impact of the Introduced Africanized Honey Bee on Native Stingless Bees in the Brazilian Atlantic Rainforest

The highly eusocial bee community of the neotropical Atlantic Rainforest was studied at Boracéia Biological Station in the state of São Paulo, Brazil. In this reserve, 17 species of stingless bees and the introduced Africanized honey bee were found, the latter being the most abundant flower visitor. Of all flowering plants, Asteraceae and Myrtaceae were particularly important as resources for bees. Trophic niche overlap between the various species of stingless bees is evident, and it was generally larger within the tribes Meliponini and Trigonini than between members of different tribes. Nevertheless, in the stingless bee community the competitive pressure is rather uniformly spread. The trophic niche of the Africanized honey bee can be positioned between those of Meliponini and Trigonini. Today this introduced species represents the main competitor in this bee community. However, its impact on native stingless bee populations is apparently buffered by mass-flowering trees which are the most important food plants of the indigenous highly eusocial bees.     

Influence of vegetation regeneration and agricultural land use on lizard composition,taxonomic and functional diversity between different vegetation types in Caatinga domain,Brazil

Anthropogenic changes in habitats are one of the main threats to biodiversity. Understanding how species diversity and their functions are affected by these changes is crucial to assess environmental impacts. In this work, we aim to understand how lizard composition, taxonomic and functional diversity respond to differences in native vegetation regeneration stages (conserved vegetation and open secondary vegetation) and agricultural land use in different vegetation types (Caatinga sensu stricto, Cerrado sensu stricto and Relictual Humid Forest) in Caatinga domain, Brazil. In more degraded areas (open secondary vegetation and agricultural areas), we found a decline in species evenness, shown by greater dominance of few species. Moreover, we found a lower functional evenness in agricultural areas than in areas of conserved vegetation, which suggests that a smaller portion of functional traits present greater dominance in more anthropized areas. We did not detect any significant differences in species richness, but we did registered differences in species composition in Relictual Humid Forest. Contrary to our expectations, lizard abundance was also greater in more degraded areas, probably as a result of the increased abundance of species benefited by anthropization. In this work, we advance the knowledge of how anthropogenic changes influence lizard diversity and emphasize the importance of analysing different facets of diversity and different habitat environments to understand how anthropization affects patterns in community ecology.     

Plankton richness in a eutrophic reservoir (Barra Bonita Reservoir,SP, Brazil)

Species richness of plankton was studied in a eutrophic reservoir (Barra Bonita Reservoir) of the Middle Tietê River, São Paulo State, Brazil, during the period 1985–1986. This reservoir is formed by two rivers: the Tietê and the Piracicaba (the main tributaries), of which the Tiête is more eutrophic, having conductivity and nutrient concentration values twice those of the Piracicaba. In addition, the reservoir is fed by 114 smaller tributaries. Monthly sampling was carried out at three stations representing different environmental conditions: St1 on the Tietê, S2 on the Piracicaba, and St3 at the confluence of the two rivers. For the phytoplankton community, the Piracicaba River (St2) proved the richest site, with a listed 72 species with abundance of Chlorophyta, while St1 and St3 registered 59 and 50 species, respectively, with abundance of Cyanophyta. For the zooplankton community a great difference was not registered in species number at the three stations but the species composition and dominant species of rotifers and copepods were quite different. The occurrence of Mesocyclops meridianus and Metacyclops mendocinus, specific for St2;Mesocyclops ogunnus and Notodiaptomus iheringi, specific for St1, and that of these two species plus Mesocyclops meridianusat St3 shows that the conditions combining at this station were favorable to Mesocyclops meridianus but not to Metacyclops mendocinus. Both for phytoplankton and zooplankton, high values found of species richness were compared to species richness of natural lakes, e.g., Dom Helvecio, a monomictic stable lake in eastern Brazil, and another fifteen lakes in the same region.In conclusion, this work shows that environmental gradients are strong selective factors that enhance plankton richness in eutrophic reservoirs exhibiting environmental instability. This fact could explain the presence of a high number of plankton species associated with a high number of individuals in Barra Bonita Reservoir, supporting the effects of the intermediate disturbance hypothesis.     

Helminths of the horned leaf frog, Proceratophrys appendiculata, from southeastern Brazil

The helminth fauna of the horned leaf frog, Proceratophrys appendiculata (Anura: Leptodactylidae), was studied from 17 adult individuals from an island in Rio de Janeiro state, southeastern Brazil. A total of five nematode species (Aplectana delirae, Cosmocerca brasiliense, Schulzia travassosi, Rhabdias androgyna and Physaloptera sp.) and an unidentified cestode were recovered from the digestive tract, lungs and gall bladder of P. appendiculata and all the nematode species are new host records. Aplectana delirae had the highest values for the prevalence and intensity of infection and can thus be considered a core species in the helminth community of P. appendiculata. Aplectana crossodactyli Baker, 1980 is synonymized with Aplectana delirae (Fabio, 1971). The helminth fauna of P. appendiculata presents characteristics typical of those in amphibians.     

Shade cacao plantations (<Emphasis Type="Italic">Theobroma cacao</Emphasis>) and bat conservation in southern Bahia,Brazil

Nearly 40% of the remaining Atlantic Forest in southern Bahia state, Brazil, is a rustic agroforest of cacao (Theobroma cacao). These traditional shade plantations, locally known as ‘cabrucas’, are habitats for forest dwelling species. Here we investigated the potential role of this traditional crop as a support for bat assemblages in southern Bahia, establishing the extent to which the bat community structure found in this agricultural system is influenced by the proximity of forest tracts. We compared the bat community attributes (richness, diversity and dominance) and species-level response (capture frequency) between native forest tracts and shade cacao plantations located in two distinct landscapes, which varied in total amount of forest (patch sizes and total forested area) and in their proximity to forest tracts. The cabrucas contiguous to forest tracts showed a rich and abundant bat community, with samples showing capture rates, species richness, diversity and evenness significantly higher than those reported for forest tracts. This situation changes, however, when shade plantations are located at some distance from forest tracts ( > 1000 m). Bat communities in these isolated cabrucas are less diverse than those found in forests and nearby cabrucas, but in both cases, species usually associated with pristine habitats were found. These findings suggest that cabrucas per se are not forest surrogates, and their potential to harbor forest dwelling bat species is closely linked with the existence of nearby forest tracts that may act as a source for species populations. Therefore, the entire landscape should be considered for management, taking into account that maintenance of cabrucas together with the preservation and restoration of forest patches is probably direly needed if one wishes to conserve the bat diversity in southern Bahia for the long term.