The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals

Abstract Aim To examine how the genetic diversity of selected taxa of forest‐dwelling small mammals is distributed between and within the major rain forest domains of Amazonia and Atlantic Forest and the intervening interior forests of Brazil, as inferred by the relationships between gene genealogies and geography. I also addressed the historical importance of the central Brazilian forests in connecting Amazon and Atlantic Forest populations of rodents and marsupials. Methods I evaluated variation in the mitochondrial cytochrome b gene to estimate the levels of sequence divergence between those taxa occurring throughout the Amazon, Atlantic Forest, and forests in the Cerrado and Caatinga regions. I inferred the hierarchical relationships between haplotypes, populations and formal taxa using the cladistic approach of maximum parsimony. I compared areas and the clades identified by superimposing cladograms on the geographical distribution of samples. The degree of concordance both in phylogeny and the depth of the nodes in these phylogenies, in addition to patterns of geographical distribution of clades, permitted me to make inferences on how, when and where the taxa differentiated. Results Sequence similarity is often greater between samples from the Atlantic Forest and either Amazon or central Brazilian forests than it is within each of the two rain forest domains. The Atlantic Forest clades are either not reciprocally monophyletic or are the sister group to all the other clades. There is some indication of northern and southern components in the Atlantic Forest. Given the geographical distribution of clades and the relatively deep levels of divergence, the central Brazilian area does not behave as a separate region but is complementary to either Amazon or Atlantic Forest. Patterns of area relationships differ across taxa, suggesting that different processes and/or historic events affected the diversification within each lineage. Main conclusions The Amazon and the Atlantic forests are not exclusive in terms of their small mammal faunas; both overlap broadly with taxa occurring in gallery forests and dry forests in central Brazil. Central Brazilian forests are an integral part of the evolutionary scenario of lowland small mammals, playing an important role as present and past habitats for rain forest species. Therefore, representatives from this area should always be included in analyses of the evolutionary history of lowland rain forest faunas. The incongruence of branching patterns among areas is in agreement with recent results presented for Neotropical passerine birds and indicates that a single hypothesis of Neotropical area relationships is unlikely. These findings reinforce the idea that speciation in the Neotropics will not be explained by any single model of vicariance or climatic changes.     

Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol

Automated species identification based on data produced with metabarcoding offers an alternative for assessing biodiversity of bulk insect samples obtained with traps. We used a standard two‐step PCR approach to amplify a 313 bp fragment of the barcoding region of the mitochondrial COI gene. The PCR products were sequenced on an Illumina MiSeq platform, and the OTUs production and taxonomic identifications were performed with a customized pipeline and database. The DNA used in the PCR procedures was extracted directly from the preservative ethanol of bulk insect samples obtained with automatic light traps in 12 sampling areas located in different biomes of Brazil, during wet and dry seasons. Agricultural field and forest edge habitats were collected for all sampling areas. A total of 119 insect OTUs and nine additional OTUs assigned to other arthropod taxa were obtained at a ≥97% sequence similarity level. The alpha and beta diversity analyses comparing biomes, habitats, and seasons were mostly inconclusive, except for a significant difference in beta diversity between biomes. In this study, we were able to metabarcode and HTS adult insects from their preservative medium. Notwithstanding, our results underrepresent the true magnitude of insect diversity expected from samples obtained with automatic light traps in Brazil. Although biological and technical factors might have impacted our results, measures to optimize and standardize eDNA HTS should be in place to improve taxonomic coverage of samples of unknown diversity and stored in suboptimal conditions, which is the case of most eDNA samples.     

Community structure and diversity of tropical forest mammals: data from a global camera trap network

Terrestrial mammals are a key component of tropical forest communities as indicators of ecosystem health and providers of important ecosystem services. However, there is little quantitative information about how they change with local, regional and global threats. In this paper, the first standardized pantropical forest terrestrial mammal community study, we examine several aspects of terrestrial mammal species and community diversity (species richness, species diversity, evenness, dominance, functional diversity and community structure) at seven sites around the globe using a single standardized camera trapping methodology approach. The sites-located in Uganda, Tanzania, Indonesia, Lao PDR, Suriname, Brazil and Costa Rica-are surrounded by different landscape configurations, from continuous forests to highly fragmented forests. We obtained more than 51 000 images and detected 105 species of mammals with a total sampling effort of 12 687 camera trap days. We find that mammal communities from highly fragmented sites have lower species richness, species diversity, functional diversity and higher dominance when compared with sites in partially fragmented and continuous forest. We emphasize the importance of standardized camera trapping approaches for obtaining baselines for monitoring forest mammal communities so as to adequately understand the effect of global, regional and local threats and appropriately inform conservation actions.     

Identifying error and accurately interpreting environmental DNA metabarcoding results: A case study to detect vertebrates at arid zone waterholes

Environmental DNA (eDNA) metabarcoding surveys enable rapid, noninvasive identification of taxa from trace samples with wide‐ranging applications from characterizing local biodiversity to identifying food‐web interactions. However, the technique is prone to error from two major sources: (a) contamination through foreign DNA entering the workflow, and (b) misidentification of DNA within the workflow. Both types of error have the potential to obscure true taxon presence or to increase taxonomic richness by incorrectly identifying taxa as present at sample sites, but multiple error sources can remain unaccounted for in metabarcoding studies. Here, we use data from an eDNA metabarcoding study designed to detect vertebrate species at waterholes in Australia's arid zone to illustrate where and how in the workflow errors can arise, and how to mitigate those errors. We detected the DNA of 36 taxa spanning 34 families, 19 orders and five vertebrate classes in water samples from waterholes, demonstrating the potential for eDNA metabarcoding surveys to provide rapid, noninvasive detection in remote locations, and to widely sample taxonomic diversity from aquatic through to terrestrial taxa. However, we initially identified 152 taxa in the samples, meaning there were many false positive detections. We identified the sources of these errors, allowing us to design a stepwise process to detect and remove error, and provide a template to minimize similar errors that are likely to arise in other metabarcoding studies. Our findings suggest eDNA metabarcoding surveys need to be carefully conducted and screened for errors to ensure their accuracy.     

笼捕法和陷阱法对森林小型兽类多样性监测效率比较

<正>小型兽类包括食虫目(Insectivora)、啮齿目(Rodentia)、翼手目(Chiroptera)、兔形目(Lagomorpha)等,物种数量多,分布广,适应能力强,对环境变化敏感,因此其群落组成和种群数量变化可较好地反映生境变化的质量和人类活动的干扰程度(肖治术等,2002;李俊生等,2003;仝磊和路纪琪,2010)。小型兽类多样性一直是生物多样性和生态环境监测与评价的重要指示类群之一(周立志和马勇,2002)。统计动物毛发、粪便、巢穴、叫声、足迹等动物痕迹以及直接观察等方法已被广泛用于兽类物种监测和种群密度估计(Eberhardt and Van Etten,1956;Bider,1968;Gannon     

Comparing motion capture cameras versus human observer monitoring of mammal movement through fence gaps: a case study from Kenya

Monitoring the movement and distribution of wildlife is a critical tool of an adaptive management framework for wildlife conservation. We installed motion‐triggered cameras to capture the movement of mammals through two purpose‐built migration gaps in an otherwise fenced conservancy in northern Kenya. We compared the results to data gathered over the same time period (1 Jan 2011–31 Dec 2012) by the human observers monitoring mammal tracks left at the same fence gaps in a sandy loam detection strip. The camera traps detected more crossing events, more species and more individuals of each species per crossing event than did the human track observers. We tested for volume detection differences between methods for the five most common species crossing each gap and found that all detection rates were heavily weighted towards the camera‐trap method. We review some of the discrepancies between the methods and conclude that although the camera traps record more data, the management of that data can be time‐consuming and ill‐suited to some time‐sensitive decision‐making. We also discuss the importance of daily track monitoring for adaptive management conservation and community security.     

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Aquatic environmental DNA (eDNA) surveys are transforming how marine ecosystems are monitored. The time-consuming preprocessing step of active filtration, however, remains a bottleneck. Hence, new approaches that eliminate the need for active filtration are required. Filter-feeding invertebrates have been proven to collect eDNA, but side-by-side comparative studies to investigate the similarity between aquatic and filter-feeder eDNA signals are essential. Here, we investigated the differences among four eDNA sources (water; bivalve gill-tissue; sponges; and ethanol in which filter-feeding organisms were stored) along a vertically stratified transect in Doubtful Sound, New Zealand using three metabarcoding primer sets targeting fish and vertebrates. Combined, eDNA sources detected 59 vertebrates, while concurrent diver surveys observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was successfully extracted from the ethanol in which sponges were stored, although a reduced number of species were detected. Bivalve gill-tissue dissections, on the other hand, failed to reliably detect eDNA. Overall, our results show that vertebrate eDNA signals obtained from water samples and marine sponges are highly concordant. The strong similarity in eDNA signals demonstrates the potential of marine sponges as an additional tool for eDNA-based marine biodiversity surveys, by enabling the incorporation of larger sample numbers in eDNA surveys, reducing plastic waste, simplifying sample collection, and as a cost-efficient alternative. However, we note the importance to not detrimentally impact marine communities by, for example, nonlethal subsampling, specimen cloning, or using bycatch specimens.     

Birds and army ants in a fragment of the Atlantic Forest of Brazil

ABSTRACT Little is known about the birds associated with army‐ant swarms in the Brazilian Atlantic forest. Our objectives were to locate and monitor army‐ant swarms in the Atlantic rainforest of Brazil and to identify the species of birds that attended the swarms and exhibited bivouac‐checking behavior. From July 2004 to August 2005, we located 49 swarms of army ants, including 28 Eciton burchelli, 19 Labidus praedator, and 2 Eciton vagans swarms. No birds were present at 17 (35%) swarms. At 32 swarms where birds were present, 22 (69%) were E. burchelli swarms and 10 (31%) were L. praedator swarms. No birds were observed at the two E. vagans swarms. We identified 66 species of birds attending the swarms, but only 43 species were observed foraging on prey flushed by the ants. Eighteen of these species had not been previously reported to forage in association with army‐ant swarms. Most birds observed during our study attended army‐ant swarms opportunistically, with White‐shouldered Fire‐eyes (Pyriglena leucoptera) the only obligate ant follower. Our observations suggest that the arthropods and other organisms flushed by army ants represent an important food resource for several species of birds in the Atlantic forest ecosystem.     

Taxonomy and molecular phylogeny of the Neotropical genus Atlantoscia (Oniscidea,Philosciidae): DNA barcoding and description of two new species

Identification to the species level using morphology is challenging when usual diagnostic characters are similar amongst related taxa. Within the Neotropical genus Atlantoscia, differences between nominal species are generally small and restricted to a few characters. Despite the power of DNA sequencing to identify and distinguish between species, molecular phylogenies of terrestrial isopods from the Neotropics have not been determined. In this study, two new species of Atlantoscia were described and molecular markers were used to verify both the validity of the current taxonomy and the relationships amongst the species within this genus. All of the recognized Atlantoscia species were strongly supported in the generated phylogenetic trees. The average congeneric distance was 14.7%, with Atlantoscia ituberasensis and Atlantoscia rubromarginata showing the highest genetic divergence. Our results demonstrate the utility of the cytochrome c oxidase subunit I gene together with DNA barcoding to reliably distinguish Atlantoscia species. They also show that DNA barcoding may be helpful in those cases in which classical taxonomy does not provide clear‐cut species resolution. © 2015 The Linnean Society of London     

八大公山自然保护区地栖性小兽多样性初步研究

湖南省八大公山自然保护区自1982年设立以来, 尚未进行过兽类资源的深入研究。为此, 作者于2012年9–10月, 采用笼捕法、陷阱法和红外相机法等对保护区内森林动态永久监测样地及周边常见植被类型中的地栖性小型兽类多样性进行了初步研究。共捕获小型兽类12种, 其中啮齿目8种, 食虫目4种。结合以往记录, 该保护区现已记录的小型兽类有20种, 而本次调查新增分布记录物种6种, 即黑腹绒鼠(Eothenomys melanogaster)、猪尾鼠(Typhlomys cinereus)、中华姬鼠(Apodemus draco)、四川短尾鼩(Anourosorex squamipes)、灰黑齿鼩鼱(Blarinella griselda)和藏鼩鼱(Sorex thibetanus)。陷阱法所捕获个体的体重显著小于笼捕法。此外, 不同生境类型对小兽多样性有重要影响。建议综合采用多种调查方法对整个保护区兽类多样性资源进行深入监测与研究。     

Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding

Environmental DNA (eDNA) metabarcoding is an increasingly popular tool for measuring and cataloguing biodiversity. Because the environments and substrates in which DNA is preserved differ considerably, eDNA research often requires bespoke approaches to generating eDNA data. Here, we explore how two experimental choices in eDNA study design—the number of PCR replicates and the depth of sequencing of PCR replicates—influence the composition and consistency of taxa recovered from eDNA extracts. We perform 24 PCR replicates from each of six soil samples using two of the most common metabarcodes for Fungi and Viridiplantae (ITS1 and ITS2), and sequence each replicate to an average depth of ~84,000 reads. We find that PCR replicates are broadly consistent in composition and relative abundance of dominant taxa, but that low abundance taxa are often unique to one or a few PCR replicates. Taxa observed in one out of 24 PCR replicates make up 21–29% of the total taxa detected. We also observe that sequencing depth or rarefaction influences alpha diversity and beta diversity estimates. Read sampling depth influences local contribution to beta diversity, placement in ordinations, and beta dispersion in ordinations. Our results suggest that, because common taxa drive some alpha diversity estimates, few PCR replicates and low read sampling depths may be sufficient for many biological applications of eDNA metabarcoding. However, because rare taxa are recovered stochastically, eDNA metabarcoding may never fully recover the true amplifiable alpha diversity in an eDNA extract. Rare taxa drive PCR replicate outliers of alpha and beta diversity and lead to dispersion differences at different read sampling depths. We conclude that researchers should consider the complexity and unevenness of a community when choosing analytical approaches, read sampling depths, and filtering thresholds to arrive at stable estimates.     

Assessing the impact of deforestation and climate change on the range size and environmental niche of bird species in the Atlantic forests,Brazil

Aim Habitat loss and climate change are two major drivers of biological diversity. Here we quantify how deforestation has already changed, and how future climate scenarios may change, environmental conditions within the highly disturbed Atlantic forests of Brazil. We also examine how environmental conditions have been altered within the range of selected bird species. Location Atlantic forests of south‐eastern Brazil. Methods The historical distribution of 21 bird species was estimated using Maxent . After superimposing the present‐day forest cover, we examined the environmental niches hypothesized to be occupied by these birds pre‐ and post‐deforestation using environmental niche factor analysis (ENFA). ENFA was also used to compare conditions in the entire Atlantic forest ecosystem pre‐ and post‐deforestation. The relative influence of land use and climate change on environmental conditions was examined using analysis of similarity and principal components analysis. Results Deforestation in the region has resulted in a decrease in suitable habitat of between 78% and 93% for the Atlantic forest birds included here. Further, Atlantic forest birds today experience generally wetter and less seasonal forest environments than they did historically. Models of future environmental conditions within forest remnants suggest generally warmer conditions and lower annual variation in rainfall due to greater precipitation in the driest quarter of the year. We found that deforestation resulted in a greater divergence of environmental conditions within Atlantic forests than that predicted by climate change. Main conclusions The changes in environmental conditions that have occurred with large‐scale deforestation suggest that selective regimes may have shifted and, as a consequence, spatial patterns of intra‐specific variation in morphology, behaviour and genes have probably been altered. Although the observed shifts in available environmental conditions resulting from deforestation are greater than those predicted by climate change, the latter will result in novel environments that exceed temperatures in any present‐day climates and may lead to biotic attrition unless organisms can adapt to these warmer conditions. Conserving intra‐specific diversity over the long term will require considering both how changes in the recent past have influenced contemporary populations and the impact of future environmental change.     

A study of Culicoides in Rondônia,in the Brazilian Amazon: species composition,relative abundance and potential vectors

There is very little information available about Culicoides species (Diptera: Ceratopogonidae) in the western Brazilian Amazon. However, studies of the fauna of this region are essential to knowledge of the species and potential vectors within it. Thus, the present study aims to evaluate the abundance, richness and composition of Culicoides species in rural areas in the state of Rondônia, Brazil. Culicoides specimens were collected in forest and pasture environments in the municipality of Porto Velho, using light traps. A total of 1708 individuals (1136 females and 572 males) belonging to 33 species were collected; 28 of these samples represent new records for the state of Rondônia and include the first record of Culicoides contubernalis in Brazil. Culicoides insignis was the most abundant species (86.1%). Species richness was greater in forest areas (32 species, 96.96%), whereas pastures presented the greatest number of Culicoides captured (n = 1540, 90.1%). This study shows that Culicoides populations differ between forest and pasture environments and indicates that the abundance of C. insignis is an important factor in epidemiological vigilance studies in the region.     

Medicinal Plants in the Atlantic Forest (Brazil): Knowledge, Use, and Conservation

This study focuses on knowledge of medicinal plants among the Caiçaras (rural inhabitants of the Atlantic Forest coast, Brazil). In particular, we examine the use of medicinal plants according to sex and age to reveal general patterns of Caiçara knowledge and use of plant resources. Data collected through 449 interviews at 12 Caiçara communities (Rio de Janeiro and São Paulo coastal sites) include citations of 249 plants and identification of 227 species. We show the importance of introduced as opposed to native plants and of key individuals for the conservation of the Caiçaras-Atlantic Forest.     

Morphogenia: a new genus of the Neotropical tribe Jubini (Coleoptera,Staphylinidae, Pselaphinae) from the Brazilian Amazon

A new genus and species of the large Neotropical pselaphine tribe Jubini is described from Manaus, Brazil, based on material preserved in the Natural History Museum, London. Morphogenia struhligen. et sp. n. represents the possible sister taxon of the abundant and speciose genus Barrojuba Park, sharing with it the putatively derived condition of anterolaterally shifted vertexal foveae, producing a smoothly convex vertex devoid of fovea or sulci. However, unlike Barrojuba, Morphogenia retains a plesiomorphic antebasal sulcus on the pronotum in both sexes, and additionally lacks elaborate abdominal fovea-like pockets and teeth on the lateral margins of the pronotum that are typical of Barrojuba. The genus is also unusual among jubine genera in lacking the characteristic V- or Y-shaped gular carina. In contrast to the commonly-collected Barrojuba, specimens of Morphogenia are absent in extensive jubine collections housed in museums in the United States, indicating that the new taxon may be relatively scarce or localised.     

Influence of water chemistry and environmental degradation on macroinvertebrate assemblages in a river basin in south-east Brazil

Benthic macroinvertebrate assemblages, water chemistry variables and environmental degradation were investigated in an Atlantic Forest region in Brazil. Seven sites of the Guapimirim river basin were studied during three sampling periods based on the rain regime: end of wet season (May 1998), dry season (August 1998), and wet season (January 1999). Four substrates were collected at each site: sand, stony substrates, litter in pool areas and litter in riffle areas. Relationships between macroinvertebrate assemblages, water chemistry variables and environmental degradation were examined using canonical correspondence analysis (CCA). According to CCA, concentrations of dissolved oxygen and chloride, and the environmental degradation, measured by the Riparian Channel Environment index, exhibited the strongest relationship to macroinvertebrate assemblages. Overall, the loss of community diversity measured by the Shannon Index along the degradation gradient was observed. Some taxa were shown to be sensitive to water pollution, especially among Plecoptera, Trichoptera, Coleoptera and some Ephemeroptera, while others such as Simuliidae, Odonata and molluscs were tolerant to moderate levels of pollutants. The Chironomidae were the only group tolerant to a high level of pollutants and degradation.     

Diet of the Neotropical Otter,Lontra longicaudis,in an Atlantic Forest Area,Santa Catarina State,Southern Brazil

The diet of the neotropical otter (Carnivora, Mustelidae) was studied from September 1995 to March 1997, in Volta Velha, an Atlantic Forest reserve in the coastal plain of Santa Catarina State, southern Brazil. Fecal samples were collected monthly along the rivers Saí-Mirim, Braço do Norte and Volta Velha. Additionally, from October 1996 to June 1997, a qualitative and quantitative study of fish species available in the studied rivers was performed. The analysis of 202 collected fecal samples indicated a diet based on fish (mainly Hoplias malabaricus and Geophagus brasiliensis) and crustaceans (mainly Trichodactylus fluviatilis, a river crab), characterizing the neotropical otter as piscivorous-cancrivorous in the study area. The presence of fruits, reptiles, birds and mammals in the diet is occasional and opportunistic. Probably the higher consumption of a certain fish species compared to its availability and the high percentage of occurrence of T. fluviatilis in scats of the neotropical otter reflect their higher catchability.     

Sampling large geographic areas for rare species using environmental DNA: a study of bull trout Salvelinus confluentus occupancy in western Montana

This study tested the efficacy of environmental DNA (eDNA) sampling to delineate the distribution of bull trout Salvelinus confluentus in headwater streams in western Montana, U.S.A. Surveys proved fast, reliable and sensitive: 124 samples were collected across five basins by a single crew in c. 8 days. Results were largely consistent with past electrofishing, but, in a basin where S. confluentus were known to be scarce, eDNA samples indicated that S. confluentus were more broadly distributed than previously thought.     

Reproduction and Activity of the Snail-Eating Snake,Dipsas albifrons (Colubridae), in the Southern Atlantic Forest in Brazil

A study in a remnant of cerrado vegetation in São Paulo State, Brazil, was carried out to investigate the possible role of leaf-cutting ants in the creation of nutrient-rich patches and their consequent influence on plant establishment and growth. The results showed that leaf-cutting ants had neither detectable effect on local nutrient enrichment nor on plant community structure. It is suggested that leaf-cutting ants may affect early successional stages of the vegetation, when colonies are more abundant and disperse into the habitat. Foi feito um estudo em um remanescente de vegetação de cerrado no Estado de São Paulo, com o objetivo de testar o papel das sa£vas na criação de manchas ricas em nutrientes e sua conseqüente influência no estabelecimento e crescimento das plantas. Os resultados mostraram que as saúvas não tiveram nenhum efeito detectável no enriquecimento local de nutrientes e nem na estrutura das comunidades vegetais. Sugere-se que as saúvas possam afetar os estádios iniciais da sucessão vegetal, quando as colônias são mais abundantes e dispersam-se mais no habitat.     

Scaling body mass and use of space in three species of marsupials in the Atlantic Forest of Brazil

Abstract Body mass is considered a major determinant of home range size, but usually at a large scale of body mass variation. The exact scale where body size becomes more important than particular adaptations of each species is not clear, and uncertainty in the estimate of home range size is a possible cause of weak intraspecific scaling. We determine the scaling to body mass of two alternative movement measurements, daily home range (DHR) and its intensity of use (IU), in three species of didelphid marsupials, Didelphis aurita, Philander frenatus, and Metachirus nudicaudatus (Didelphimorphia, Didelphidae). The expected scaling exponents DHR ≈ M^0.5 and IU ≈ M^?0.25 were derived from the scaling to body mass of home range and daily movement distance. Animals were tracked in Serra dos Órgãos, Rio de Janeiro, Brazil, using a spool‐and‐line device. Individuals of the three species were compared combining intra and interspecific variation in a single analysis, with species, body mass, and thread tracked as covariates. The model best supported included only body mass as the independent variable, with DHR ≈ M^0.435 and IU ≈ M^?0.218, close to the expected values. The second best supported model included species identity, but with a non‐significant effect. It was surprising that body mass was more important than species identity in a comparison involving only three species, and considering the morphological and locomotory adaptations of the three species. Body mass may become more important than species identity when the scale of variation approaches one order of magnitude.