63 Works

A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae

Johanna Jantzen, Prabha Amarasinghe, Ryan Folk, Marcelo Reginato, Fabian Michelangeli, Douglas Soltis, Nico Cellinese & Pamela Soltis
Premise of the study: Putatively single-copy nuclear (SCN) loci, identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment in the distantly related Memecylon and Tibouchina (Melastomataceae). Methods: We present a two-tiered pipeline. First, we identified...

Evoregions: mapping shifts in phylogenetic turnover across biogeographic regions

Renan Maestri & Leandro Duarte
1. Biogeographic regionalization offers context to the geographical evolution of clades. The positions of bioregions inform both the spatial location of clusters in species distribution and where their most important boundaries are. Nevertheless, defining bioregions based on species distribution alone only incidentally recover regions that are important during the evolution of the focal group. The extent to which bioregions correspond to centers of independent diversification depends on how clusters of species composition naturally reflect the...

Data from: Mechanisms and implications of a type IV functional response for short-term intake rate of dry matter in large mammalian herbivores

Jean C. Mezzalira, Olivier J. F. Bonnet, Paulo C. De F. Carvalho, Lidiane Fonseca, Carolina Bremm, Carlos C. Mezzalira & Emilio A. Laca
1. The functional response (i.e. the relationship between consumers’ intake rate and resource density) is central in plant-herbivore interactions. Its shape and the biological processes leading to it have significant implications for both foraging theory and ecology of grazing systems. 2. A type IV functional response (i.e. dome-shaped relationship) of short-term intake rate of dry matter (intake while grazing) has rarely been reported for large herbivores and the conditions that can lead to it are...

Data from: Factors affecting the structure of Coleoptera assemblages on bracket fungi (Basidiomycota) in a Brazilian forest

Leticia V. Graf, Fabrícia Barbieri, Edilena Sperb, Daniela Soares Rivaldo, Luciano De A. Moura, Rosa Mara B. Da Silveira, Mateus A. Reck & Flavia Nogueira-De-Sa
Insect–fungal interactions are an important but understudied aspect of tropical forest ecology. Here we present the first large-scale study of insect communities feeding on the reproductive structures of macrofungi (basidiomes) in the Neotropics. This trophic interaction is not well characterized in most ecosystems; however, beetle consumption of basidiomes is thought to be affected by fungal factors, via mechanisms analogous to those observed in plant–herbivore interactions and in some interactions with fungi as hosts in the...

Data from: Evolutionary history as a driver of ecological networks: a case study of plant-hummingbird interactions

Rômulo S. Vitória, Jeferson Vizentin-Bugoni & Leandro D.S. Duarte
Multiple factors drive species interactions in ecological networks, such as morphological barriers, spatio-temporal distribution, abundances and evolutionary histories of species. Novel methods are making it possible to evaluate the relative importance of each of these drivers. However, the lack of appropriate methods has prevented evaluating the extent to which interaction networks are shaped by species’ evolutionary histories. This study includes the evolutionary histories of species among the potential drivers of interactions, allowing the comparative analysis...

Data from: Molecular phylogenetics of Maxillaria and related genera (Orchidaceae: Cymbidieae) based on combined molecular data sets

W. Mark Whitten, Mario A. Blanco, Norris H. Williams, Samantha Koehler, Germán Carnevali, Rodrigo B. Singer, Lorena Endara & Kurt M. Neubig
The orchid genus Maxillaria is one of the largest and most common of neotropical orchid genera, but its current generic boundaries and relationships have long been regarded as artificial. Phylogenetic relationships within subtribe Maxillariinae sensu Dressler (1993) with emphasis on Maxillaria s.l. were inferred using parsimony analyses of individual and combined DNA sequence data. We analyzed a combined matrix of nrITS DNA, the plastid matK gene and flanking trnK intron, and the plastid atpB-rbcL intergenic...

Data from: Reverse diel vertical movements of oceanic manta rays off the northern coast of Peru and implications for conservation

Samantha Andrzejaczek, Robert Schallert, Kerstin Forsberg, Natalie Arnoldi, Mariano Cabanillas, Wilmer Purizaca & Barbara Block
An understanding of the vertical movements of elasmobranchs across their range is crucial to defining critical habitat use, its overlap with anthropogenic activities, and subsequently managing such interactions. In this study, satellite telemetry was used to investigate the vertical habitat use of three oceanic manta rays (Mobula birostris) tagged on the northern coast of Peru. All three oceanic mantas exhibited patterns of reverse diel vertical migration, where vertical movements were significantly deeper at night than...

Supplemental material: Astrocyte biomarkers in Alzheimer’s disease: a systematic review and meta-analysis

Bruna Bellaver, João Pedro Ferrari-Souza, Lucas Uglione Da Ros, Stephen F. Carter, Elena Rodriguez-Vieitez, Agneta Nordberg, Luc Pellerin, Pedro Rosa-Neto, Douglas Teixeira Leffa & Eduardo R. Zimmer
Objective: To perform a systematic review and meta-analysis to determine whether fluid and imaging astrocyte biomarkers are altered in Alzheimer's disease (AD). Methods: PubMed and Web of Science databases were searched for articles reporting fluid or imaging astrocyte biomarkers in AD. Pooled effect sizes were determined with mean differences (SMD) using the Hedge’s G method with random-effects to determine biomarker performance. Adapted questions from QUADAS-2 were applied for quality assessment. A protocol for this study...

Disentangling drivers of small mammal diversity in a highly fragmented forest system

Noé De La Sancha, Renan Maestri, Ricardo Bovendorp & Christopher Higgins
The Atlantic Forest is the second most diverse forest system in South America and only a fraction of its original distribution remains. In this study, we aim to use robust datasets of small mammals along the entire forest system to disentangle the main drivers for diversity along this gradient. More specifically we aim to disentangle if deforestation (recent), biogeographical variables, including 19 bioclimatic variables (historic), or historical trapping bias best describe patterns of taxonomic, functional,...

A comprehensive sampling of species sheds light on the molecular phylogenetics of Calothecinae (Poaceae, Pooideae): evidence for a new subtribe and multiple genera within the Chascolytrum clade

Leonardo Nogueira Da Silva, Jeffery Saarela, Liliana Essi & Tatiana Souza-Chies
The circumscription of subtribe Calothecinae has undergone several changes since its description. Currently, three genera are considered in the subtribe: Chascolytrum, Laegaardia and Paramochloa, although no phylogenetic evidence for the placement of the two last genera was published so far. In this study we aim to evaluate the circumscription of Calothecinae and the infrageneric classification recently proposed for Chascolytrum using a more comprehensive sampling of taxa and molecular markers. We included species of all genera...

Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile–Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground

Emma L Carroll, Paulo Ott, Louise McMillan, Bárbara Galletti Vernazzani, Petra Neveceralova, Els Vermeulen, Oscar Gaggiotti, Artur Andriolo, C. Scott Baker, Connor Bamford, Peter Best, Elsa Cabrera, Susannah Calderan, Andrea Chirife, Rachel M. Fewster, Paulo A. C. Flores, Timothy Frasier, Thales R. O. Freitas, Karina Groch, Pavel Hulva, Amy Kennedy, Russell Leaper, Mathew S. Leslie, Michael Moore, Larissa Oliviera … & Jennifer A Jackson
As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds...

Data from: Advanced glycation end products (AGE) and receptor for AGE (RAGE) in patients with active tuberculosis, and their relationship between food intake and nutritional status

Lívia F. Da Silva, Erika C. Skupien, Tássia K. Lazzari, Sizuane R. Holler, Ellis G.C. De Almeida, Luísa R. Zampieri, Sandra E. Coutinho, Michael Andrades & Denise R. Silva
Introduction: The receptor for advanced glycation end products (RAGE) is expressed in normal lungs and is upregulated during infection. AGEs and RAGE cause oxidative stress and apoptosis in lung cells. The objective of this study is to evaluate levels of AGEs and its soluble receptor (sRAGE), and to investigate their relationship with food intake and nutritional status, in a university-affiliated hospital in Brazil. Methods: Case-control study, from June 2017 to June 2018. AGE (carboxymethyl lysine,...

Influence of past and current factors on the beta diversity of coastal lagoon fish communities in South America

Taís De Fátima Ramos Guimarães, Ana Cristina Petry, Sandra Maria Hartz & Fernando Gertum Becker
Aim: We aimed to assess the relative influence of past (Quaternary paleodrainage characteristics) and current factors on the beta diversity of freshwater fishes in coastal lagoons and explore the main processes involved. Location: Atlantic coast of South America. Taxon: Fishes (173 species) Methods: We built a dataset of species occurrence in 129 lagoons across eight freshwater ecoregions of the world (FEOWs) located between latitudes 0° and 36° and calculated beta diversity (βjac) and its turnover...

Evolutionary tradeoffs between male secondary sexual traits revealed by a phylogeny of the hyperdiverse tribe Eumaeini (Lepidoptera: Lycaenidae)

Wendy A. Valencia-Montoya, Tiago B. Quental, João Filipe R. Tonini, Gerard Talavera, James D. Crall, Gerardo Lamas, Robert C. Busby, Ana Paula S. Carvalho, Ana B. Morais, Nicolás Oliveira Mega, Helena Piccoli Romanowski, Marjorie A. Liénard, Shayla Salzman, Melissa R. L. Whitaker, Akito Y. Kawahara, David J. Lohman, Robert K. Robbins & Naomi E. Pierce
Male butterflies in the hyperdiverse tribe Eumaeini possess an unusually complex and diverse repertoire of secondary sexual characteristics involved in pheromone production and dissemination. Maintaining multiple sexually selected traits is likely to be metabolically costly, potentially resulting in trade-offs in the evolution of male signals. However, a phylogenetic framework to test hypotheses regarding the evolution and maintenance of male sexual traits in Eumaeini has been lacking. Here, we infer a comprehensive, time-calibrated phylogeny from 379...

Focus group transcripts for Influenza vaccination hesitancy in large urban centers in South America. Qualitative analysis of confidence, complacency and convenience across risk groups

Miguel Ángel Gonzalez-Block, Blanca Estela Pelcastre-Villafuerte, Daniela Riva Knauth, Andréa Fachel- Leal, Yamila Comes, Pedro Crocco, Laura Noboa, Berenice Rodríguez-Zea, Mónica Ruoti, Sandra Patricia Díaz-Portillo & Elsa Sarti
Influenza vaccination coverage in countries of Latin America is low among priority risk groups, ranging from 5 to 75% among older people. This paper aims to describe and analyze the determinants of influenza vaccination hesitancy through the lens of the 3C model of confidence, complacency and convenience among middle-class, urban risk group populations in Brazil, Chile, Paraguay, Peru, Uruguay, countries in South America with contrasting vaccination coverage. Focus groups were conducted among four risk groups:...

Seascape genetics of the Atlantic spotted dolphin (Stenella frontalis) based on mitochondrial DNA

Karina Bohrer Do Amaral, Dalia C. Barragán-Barrera, Roosevelt A. Mesa-Gutiérrez, Nohelia Farias-Curtidor, Susana J. Caballero Gaitán, Paula Méndez-Fernandez, Marcos C. Oliveira Santos, Caroline Rinaldi, Renato Rinaldi, Salvatore Siciliano, Vidal Martín, Manuel Carillo, Ana Carolina O. De Meirelles, Valentina Franco-Trecu, Nelson J. R. Fagundes, Ignacio Benites Moreno, L. Lacey Knowles & Ana Rita Amaral
The Atlantic spotted dolphin (Stenella frontalis) is endemic to tropical, subtropical, and warm temperate waters of the Atlantic Ocean. Throughout its distribution, both geographic distance and environmental variation may contribute to population structure of the species. In this study we follow a seascape genetics approach to investigate population differentiation of Atlantic spotted dolphins based on a large worldwide dataset and the relationship with marine environmental variables. The results revealed that the Atlantic spotted dolphin exhibits...

ESRC Newton Healthy Urban Mobility

Tim Jones, H Günther, Sue Brownill, Ramin Keivani, I Neto, E D'Orsi, Ben Spencer, J Vargas & G Butina-Watson
The Healthy Urban Mobility (HUM) project was a study to understand the impact of everyday (im)mobility on health and wellbeing with a variety of social groups living in different neighbourhoods in Brazil and the UK, and also to explore the potential for participatory mobilities planning with local communities to support and develop solutions for healthy urban mobility.

Data from: Resilience of an integrated crop-livestock system to climate change: a simulation analysis of cover crop grazing in southern Brazil

Caitlin Peterson, Lindsay Bell, Paulo Carvalho & Amelie Gaudin
Integrated crop-livestock systems are a form of sustainable intensification of agriculture that rely on synergistic relationships between plant and animal components to bolster critical agroecosystem processes. We simulated cash crop and cover crop productivity dynamics in an integrated beef-soybean cover crop grazing system typical of southern Brazil to gain a better understanding of the impacts of livestock integration on system performance. Long-term historical simulations in APSIM showed that the integrated system resulted in greater system-wide...

Data from: Population-specific genetic modification of Huntington's disease in Venezuela

Michael J. Chao, Kyung-Hee Kim, Jun Wan Shin, Diane Lucente, Vanessa C. Wheeler, Hong Li, Jared C. Roach, Leroy Hood, Nancy S. Wexler, Laura B. Jardim, Peter Holmans, Lesley Jones, Michael Orth, Seung Kwak, James F. Gusella, Marcy E. MacDonald & Jong-Min Lee
Modifiers of Mendelian disorders can provide insights into disease mechanisms and guide therapeutic strategies. A recent genome-wide association (GWA) study discovered genetic modifiers of Huntington's disease (HD) onset in Europeans. Here, we performed whole genome sequencing and GWA analysis of a Venezuelan HD cluster whose families were crucial for the original mapping of the HD gene defect. The Venezuelan HD subjects develop motor symptoms earlier than their European counterparts, implying the potential for population-specific modifiers....

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

Jonathan M. Chase, Mario Liebergesell, Alban Sagouis, Felix May, Shane A. Blowes, Åke Berg, Enrico Bernard, Berry J. Brosi, Marc W. Cadotte, Luis Cayuela, Adriano G. Chiarello, Jean-François Cosson, Will Cresswell, Filibus Danjuma Dami, Jens Dauber, Christopher R. Dickman, Raphael K. Didham, David P. Edwards, Fabio Z. Farneda, Yoni Gavish, Thiago Gonçalves-Souza, Demetrio Luis Guadagnin, Mickaël Henry, Adrià López-Baucells, Heike Kappes … & Yaron Ziv
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...

Data from: Population genetics of jaguars (Panthera onca) in the Brazilian Pantanal: molecular evidence for demographic connectivity on a regional scale

Fernanda Pedone Valdez, Taiana Haag, Fernando C. C. Azevedo, Leandro Silveira, Sandra M. C. Cavalcanti, Francisco M. Salzano & Eduardo Eizirik
Habitat loss and fragmentation are important threats to carnivores worldwide, and can be especially intense for large predators. Jaguars have already been extirpated from over half of their original area of distribution, and few regions still maintain large populations. For these, detailed understanding is crucial for setting appropriate recovery targets in impacted areas. The Pantanal is among the best examples of a region with a large jaguar population in a healthy environment. Here, we analyzed...

Data from: Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits

Andréa T. Thomaz, Dahiana Arcila, Guillermo Ortí & Luiz R. Malabarba
Background The subfamily Stevardiinae is a diverse and widely distributed clade of freshwater fishes from South and Central America, commonly known as “tetras” (Characidae). The group was named “clade A” when first proposed as a monophyletic unit of Characidae and later designated as a subfamily. Stevardiinae includes 48 genera and around 310 valid species with many species presenting inseminating reproductive strategy. No global hypothesis of relationships is available for this group and currently many genera...

Seasonality and interspecific competition shape individual niche variation in co-occurring tetra fish in Neotropical streams

Mayara Neves, Raul Costa-Pereira, Rosilene Luciana Delariva & Clarice Bernhardt Fialho
The drivers of intraspecific niche variation and its effects on species interactions are still unclear, especially in species-rich Neotropical environments. Here, we investigated how ecological opportunity and interspecific competition affect the degree of individual trophic specialization and the population niche breadth in tetra fish. We studied the four ecologically similar species (Psalidodon aff. gymnodontus, P. aff. paranae, P. bifasciatus, and Bryconamericus ikaa) in subtropical headwater streams (three sites with two co-occurring species and three sites...

Harrison’s rule scales up to entire parasite assemblages but is determined by environmental factors

Renan Maestri, Maico Fiedler, Georgy Shenbrot, Elena Surkova, Sergei Medvedev, Irina Khokhlova & Boris Krasnov
Harrison’s rule states that parasite body size and the body size of their hosts tend to be positively correlated. After it was proposed a century ago, a number of studies have investigated this trend, but the support level has varied greatly between parasite/host associations. Moreover, while the rule has been tested at the individual species level, we still lack knowledge on whether Harrison’s rule holds at the scale of parasite and host communities. Here, we...

Data from: Impact of introduction of Xpert MTB/RIF test on tuberculosis (TB) diagnosis in a city with high TB incidence in Brazil

Giovana Rodrigues Pereira, Márcia Silva Barbosa, Natan José Dutra Dias, Carlos Podalirio Borges De Almeida & Denise Rossato Silva
Background: Xpert MTB/RIF is increasingly used in many countries as the initial diagnostic test for tuberculosis (TB). Few studies have evaluated the effect of Xpert on TB diagnosis under programmatic conditions in Brazil. The aim of the present study was to evaluate the impact of introduction of Xpert MTB/RIF on TB diagnosis in a city with high TB incidence in Brazil. Methods: We included patients evaluated with conventional diagnostic tests during one year before Xpert...

Registration Year

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Resource Types

  • Dataset
    63

Affiliations

  • Federal University of Rio Grande do Sul
    63
  • University of Sao Paulo
    6
  • Sao Paulo State University
    4
  • University of Pretoria
    4
  • Field Museum of Natural History
    3
  • Duke University
    3
  • Royal Botanic Gardens
    3
  • Hospital de Clínicas de Porto Alegre
    3
  • Universidade Estadual de Santa Cruz
    3
  • State University of Campinas
    3