Trypanosoma cruzi in Brazilian Amazonia: Lineages TCI and TCIIa in wild primates, Rhodnius spp. and in humans with Chagas disease associated with oral transmission

In this study, we provide phylogenetic and biogeographic evidence that the Trypanosoma cruzi lineages T. cruzi I (TCI) and T. cruzi IIa (TCIIa) circulate amongst non-human primates in Brazilian Amazonia, and are transmitted by Rhodnius species in overlapping arboreal transmission cycles, sporadically infecting humans. TCI presented higher prevalence rates, and no lineages other than TCI and TCIIa were found in this study in wild monkeys and Rhodnius from the Amazonian region. We characterised TCI and TCIIa from wild primates (16 TCI and five TCIIa), Rhodnius spp. (13 TCI and nine TCIIa), and humans with Chagas disease associated with oral transmission (14 TCI and five TCIIa) in Brazilian Amazonia. To our knowledge, TCIIa had not been associated with wild monkeys until now. Polymorphisms of ssrDNA, cytochrome b gene sequences and randomly amplified polymorphic DNA (RAPD) patterns clearly separated TCIIa from TCIIb-e and TCI lineages, and disclosed small intra-lineage polymorphisms amongst isolates from Amazonia. These data are important in understanding the complexity of the transmission cycles, genetic structure, and evolutionary history of T. cruzi populations circulating in Amazonia, and they contribute to both the unravelling of human infection routes and the pathological peculiarities of Chagas disease in this region.     

New and interesting species of Hymenochaetaceae from the Brazilian Amazonia

Coltricia globispora sp. nov. is described as new based on specimens collected in the Parque Natural Municipal de Porto Velho, in the state of Rondônia, Brazilian Amazonia. It is characterized by small pores (7–8 per mm), monomitic hyphal system, and globose, smooth and guttulate basidiospores (5.5–6.6 (?7) μm). Phellinus griseoporus has been found for the first time in Brazil, and Cyclomyces iodinus, P. merrillii, P. membranaceus and P. umbrinellus in the Brazilian Amazonia. Coltricia cinnamomea, P. calcitratus and Phylloporia chrysites are new occurrences to the state Rondônia, while C. hamata and Phylloporia spathulata to the state of Pará. The knowledge about Hymenochaetaceae in the Brazilian Amazonia is briefly discussed, and a key to the neotropical species of Coltricia is provided.     

The geographical pattern of distribution of the genus Teuthraustes Simon (Scorpiones, Chactidae) in South America and description of a new species

A new species of scorpion, Teuthraustes braziliensis sp. n. (Scorpiones, Chactidae), is described from the State of Amazonas, Brazil. This is the second species of the genus to be collected in the lowlands of South America, and the third record of a scorpion of the genus Teuthraustes to be recorded from Brazilian Amazonia. The total number of species of Teuthraustes is now raised to 21. The patterns of distribution of the genus are commented upon, and its geographical distribution is also enlarged.     

The mitogenome of Onchocerca volvulus from the Brazilian Amazonia focus

We report here the first complete mitochondria genome of Onchocerca volvulus from a focus outside of Africa. An O. volvulus mitogenome from the Brazilian Amazonia focus was obtained using a combination of high-throughput and Sanger sequencing technologies. Comparisons made between this mitochondrial genome and publicly available mitochondrial sequences identified 46 variant nucleotide positions and suggested that our Brazilian mitogenome is more closely related to Cameroon-origin mitochondria than West African-origin mitochondria. As well as providing insights into the origins of Latin American onchocerciasis, the Brazilian Amazonia focus mitogenome may also have value as an epidemiological resource.     

Chloroplast DNA Microsatellites Reveal Contrasting Phylogeographic Structure in Mahogany (Swietenia macrophylla King, Meliaceae) from Amazonia and Central America

Big-leaf mahogany (Swietenia macrophylla King) is one of the most valuable and overharvested timber trees of tropical America. In order to better characterize geographic patterns of genetic variation, we performed a phylogeographic analysis of S. macrophylla based on six polymorphic chloroplast genome simple sequence repeat loci (cpSSRs) analyzed in 16 populations (N?=?245 individuals) distributed across Central America and the Brazilian Amazon. Of the 31 total cpDNA haplotypes identified, 16 occurred in Central America and 15 in Amazonia with no single haplotype shared between the two regions. Populations from Central America showed moderate differentiation (F _ST ?=?0.36) while within population genetic diversity was generally high (mean Nei’s H _E ?=?0.639). In contrast, the Amazonian populations were strongly differentiated (F _ST ?=?0.91) and contained relatively low genetic diversity (mean H _E ?=?0.176), except for one highly diverse population (H _E ?=?0.925) from eastern Amazonia. Spatial analysis of molecular variance (SAMOVA) identified a single Central American phylogroup and four Amazonian phylogroups, indicating stronger phylogeographic structure within Amazonia. The results demonstrate distinctive regional patterns of S. macrophylla differentiation, and the first evidence of a strong phylogeographic break between Central American and South American mahogany populations. We suggest that the frequent occurrence of hurricanes in Central America, the differences in the glacial histories and in the duration and intensity of anthropogenic disturbance during the late Holocene may have played important roles in the geographic structuring of cpDNA lineages in the two regions. The high private haplotype diversity in Brazilian populations suggests that cpSSRs can be used as DNA barcodes for regional timber certification.     

Arapaima co-management through the lens of the Protected Areas Assets Framework

An extensive network of Protected Areas (PA) has been established across the Brazilian Amazon, but this PA system still suffers from a shortage of funding resources and environmental managers. New conservation strategies that successfully align social aspirations with biodiversity conservation are therefore imperative. Although approaches exist that demonstrate the value of biodiversity conservation for society and the local/national economy, these do not always manage to capture intrinsic values or local perspectives on natural resource conservation, and this can generate limitations in the use of these approaches as conservation tools. Here, we assessed the case of arapaima (Arapaima spp.) co-management, a well-consolidated community-based conservation initiative, through the lens of the Protected Areas Asset Framework (PAAF) to investigate the material and immaterial value of PA assets. Arapaima was clearly recognized as a key biophysical natural asset by local communities, with a significant role in terms of food, cultural, economic and conservation importance, in addition to its status as an iconic and emblematic species. This study reinforces the potential of the PAAF to identify the diverse range of values associated with PAs. Our results also encourage wider support to strengthen collaborative sustainable natural resource management programmes such as arapaima co-management, which is achieving remarkable social and ecological outcomes in rural Amazonia.     

Locality or habitat? Exploring predictors of biodiversity in Amazonia

Amazonia is an environmentally heterogeneous and biologically megadiverse region, and its biodiversity varies considerably over space. However, existing knowledge on Amazonian biodiversity and its environmental determinants stems almost exclusively from studies of macroscopic above‐ground organisms, notably vertebrates and trees. In contrast, diversity patterns of most other organisms remain elusive, although some of them, for instance microorganisms, constitute the overwhelming majority of taxa in any given location, both in terms of diversity and abundance. Here, we use DNA metabarcoding to estimate prokaryote and eukaryote diversity in environmental soil and litter samples from 39 survey plots in a longitudinal transect across Brazilian Amazonia using 16S and 18S gene sequences, respectively. We characterize richness and community composition based on operational taxonomic units (OTUs) and test their correlation with longitude and habitat. We find that prokaryote and eukaryote OTU richness and community composition differ significantly among localities and habitats, and that prokaryotes are more strongly structured by locality and habitat type than eukaryotes. Our results 1) provide a first large‐scale mapping of Amazonian soil biodiversity, suggesting that OTU richness patterns might follow substantially different patterns from those observed for macro‐organisms; and 2) indicate that locality and habitat factors interact in determining OTU richness patterns and community composition. This study shows the potential of DNA metabarcoding in unveiling Amazonia's outstanding diversity, despite the lack of complete reference sequence databases for the organisms sequenced.     

Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata,Ciliophora)

Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN‐BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN‐BC proposes to populate The Ciliate Guide, an online database, with biodiversity‐related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.     

Two new species of Amazonian Lecythidaceae

Two new species of Lecythidaceae from Brazilian Amazonia are described and illustrated:Cariniana penduliflora andCouratari atrovinosa. Details of the pollination ofCouratari atrovinosa are given, the principal pollinator being a Euglossine bee,Eulaema meriana Oliv.     

Phylogeographical, ecological and biological patterns shown by nuclear (ssrRNA and gGAPDH) and mitochondrial (Cyt b) genes of trypanosomes of the subgenus Schizotrypanum parasitic in Brazilian bats

The genetic diversity and phylogeographical patterns of Trypanosoma species that infect Brazilian bats were evaluated by examining 1043 bats from 63 species of seven families captured in Amazonia, the Pantanal, Cerrado and the Atlantic Forest biomes of Brazil. The prevalence of trypanosome-infected bats, as estimated by haemoculture, was 12.9%, resulting in 77 cultures of isolates, most morphologically identified as Trypanosoma cf. cruzi, classified by barcoding using partial sequences from ssrRNA gene into the subgenus Schizotrypanum and identified as T. cruzi (15), T. cruzi marinkellei (37) or T. cf. dionisii (25). Phylogenetic analyses using nuclear ssrRNA, glycosomal glyceraldehyde 3-phosphate dehydrogenase (gGAPDH) and mitochondrial cytochrome b (Cyt b) gene sequences generated three clades, which clustered together forming the subgenus Schizotrypanum. In addition to vector association, bat trypanosomes were related by the evolutionary history, ecology and phylogeography of the bats. Trypanosoma cf. dionisii trypanosomes (32.4%) infected 12 species from four bat families captured in all biomes, from North to South Brazil, and clustered with T. dionisii from Europe despite being separated by some genetic distance. Trypanosoma cruzi marinkellei (49.3%) was restricted to phyllostomid bats from Amazonia to the Pantanal (North to Central). Trypanosoma cruzi (18.2%) was found mainly in vespertilionid and phyllostomid bats from the Pantanal/Cerrado and the Atlantic Forest (Central to Southeast), with a few isolates from Amazonia.     

High Species Richness of Scinax Treefrogs (Hylidae) in a Threatened Amazonian Landscape Revealed by an Integrative Approach

Rising habitat loss is one of the main drivers of the global amphibian decline. Nevertheless, knowledge of amphibian diversity needed for effective habitat protection is still highly inadequate in remote tropical regions, the greater part of the Amazonia. In this study we integrated molecular, morphological and bioacoustic evidence to evaluate the species richness of the treefrogs genus Scinax over a 1000 km transect across rainforest of the Purus-Madeira interfluve, and along the east bank of the upper Madeira river, Brazilian Amazonia. Analysis revealed that 82% of the regional species richness of Scinax is still undescribed; two nominal species, seven confirmed candidate species, two unconfirmed candidate species, and one deep conspecific lineage were detected in the study area. DNA barcoding based analysis of the 16s rRNA gene indicates possible existence of three discrete species groups within the genus Scinax, in addition to the already-known S. rostratus species Group. Quantifying and characterizing the number of undescribed Scinax taxa on a regional scale, we provide a framework for future taxonomic study in Amazonia. These findings indicate that the level to which Amazonian anura species richness has been underestimated is far greater than expected. Consequently, special attention should be paid both to taxonomic studies and protection of the still-neglected Amazonian Scinax treefrogs.     

Two new species of <Emphasis Type="Italic">Miconia</Emphasis> (Melastomataceae,Miconieae) from the Brazilian northern border and adjacent French Guiana

Two new species of Miconia from northern Amazonia area described. Miconia amapaënsis has been collected in the Brazilian state of Amapá and in nearby locations in northern Pará and southern French Guiana. It has remarkable seeds, with both the appendix and seed coat covered with long papillae. Miconia forzzae has been collected on the Brazilian side of the Neblina Massif, in the Brazilian state of Amazonas, close to the border with Venezuela. It has 4-merous flowers, with a terete hypanthium, yellow stamens, the ovary apex with unbranched trichomes, and a punctiform stigma. This species may be endangered, considering its narrow distribution, and the fact that it was collected between 2000 and 2100 m elevation in an isolated mountain range with no neighboring mountains with similar height, but we assess its conservation status as “data deficient”, due to a lack of knowledge on the situation of the populations and the number of individuals.     

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.     

Dacryodes edilsonii, a new species from southwestern Amazonia. Studies in neotropical Burseraceae XII

Dacryodes edilsonii Daly (Burseraceae) is one of at least 14 still undescribed neotropical species in the genus; it is also one of a large number of new species emerging from intensified botanical exploration of the Brazilian state of Acre in southwestern Amazonia. The new species is easily distinguished from most other Neotropical species of the genus by its usually densely long-pubescent petiole, rachis, petiolules, and abaxial midvein.     

Secondary Forests on Anthropogenic Soils of the Middle Madeira River: Valuation,Local Knowledge,and Landscape Domestication in Brazilian Amazonia

Secondary Forests on Anthropogenic Soils of the Middle Madeira River: Valuation, Local Knowledge, and Landscape Domestication in Brazilian Amazonia. Anthropogenic forests and soils are widespread throughout Amazonia and are the product of the landscape domestication process carried out by Amazonian societies since pre-Colombian times. Areas of Terra Preta de índio (TPI, Amazonian Dark Earths) are recognized by local rural residents and associated with specific forms of use and management of these soils and associated secondary forests. We used a quantitative approach to investigate how secondary forests on TPI are recognized and used by local residents along the middle Madeira River, Central Amazonia. Sixty-two residents were interviewed in three riverside communities and listed the ethnospecies and their uses in secondary forests on TPI and on non-anthropogenic soils (NAS). Local residents mentioned more ethnospecies on TPI (mean ± standard deviation: 19.5 ± 8.9) than on NAS (17.4 ± 8.5), and the use value of the environment to the informants (UVia) was higher on TPI (19 ± 5.7) than on NAS (16.2 ± 6.0). Eleven ethnospecies were classified as anthropogenic soil indicators, among which three intensively used palms are widely recognized as indicators of anthropogenic areas and two are domesticated to some degree. The intimate and lasting interactions between humans and TPI have favored the maintenance of secondary forests in these domesticated landscapes with a diverse assemblage of useful and domesticated species. Rural residents in Amazonia recognize these forests as an important source of food and other resources. The use, management, and traditional knowledge related to these domesticated landscapes may provide useful information for the understanding of Amazonian historical ecology and for the design of more efficient biodiversity management and conservation plans.