70 Works

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: 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: 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...

Bridging macroecology and macroevolution in the radiation of sigmodontine rodents

Renan Maestri, André L. Luza, Sandra M. Hartz, Thales R.O. De Freitas & Bruce D. Patterson
Investigations of phenotypic disparity across geography often ignore macroevolutionary processes. As a corollary, the random null expectations to which disparity is compared and interpreted may be unrealistic. We tackle this issue by representing, in geographical space, distinct processes of phenotypic evolution underlying ecological disparity. Under divergent natural selection, assemblages in a given region should have empirical disparity higher than expected under an evolutionarily-oriented null model, while the opposite may indicate constraints on phenotypic evolution. We...

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: 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...

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...

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,...

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...

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...

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...

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...

Genomic population reveals potential micro-refuge and riverine barriers in southern South American grasslands: An example in nightshade: VCF file (16,128 SNPs)

Giovanna Giudicelli
Aim: Pleistocene climate oscillations influenced the species distribution and genetic diversity in South American grasslands. Paleoclimate changes promoted expansion and contraction cycles that could lead to fragmentation and isolation of evolutionary lineages in refuges. Moreover, sea-level oscillations led to defrosting in some areas, affecting the river dynamics and influencing South American species' evolutionary history. This study aimed to infer which evolutionary processes most influenced the lineages differentiation in South American nightshade Petunia inhabiting subtropical grasslands...

Ground-foraging ant communities in invaded (by Hovenia dulcis) and non-invaded Atlantic Forest sites, and ant-H. dulcis diaspore interactions

Luciana Podgaiski, William Drose, Mauricio Almerão & Gabriel Guimarães
Biological invasions are a worldwide threat to biodiversity. Invasive species can affect biodiversity in many ways, such as by altering habitat properties and structure to which native species are dependent. Recipient communities that have mutualistic interactions with invasive species, such as seed dispersal mutualistic networks, are more vulnerable to invasion. The japanese raisin tree, Hovenia dulcis Thunberg (Rhamnaceae), is an example of a successful invasive tree in the Brazilian Atlantic Forest, where it alters plant...

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...

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,...

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: 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....

Data from: Characteristics of patients with smear-negative pulmonary tuberculosis (TB) in a region with high TB and HIV prevalence

Leandro C. Campos, Marcus V. V. Rocha, Denise Maria Cunha Willers, Denise Rossato Silva & Marcos Vinícius Vieira Rocha
Introduction: Smear-negative pulmonary TB (SNPT) represents 30–60% of all pulmonary TB cases. The mortality of these patients can reach 25% in populations with high prevalence of HIV infection, and 10–20% of TB transmission at the population level are attributable to SNPT cases. Methods: We conducted a retrospective study to evaluate epidemiological, clinical, and radiological characteristics of patients with SNPT and to compare these with patients who were diagnosed as having smear-positive pulmonary TB (SPPT). All...

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: 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...

Data from: The effect of habitat fragmentation on the genetic structure of a top predator: loss of diversity and high differentiation among remnant populations of Atlantic Forest jaguars (Panthera onca)

Taiana Haag, Anelisie Santos, Denis Sana, Ronaldo Morato, , , Carlos De Angelo, Mario Di Bitetti, Francisco Salzano & Eduardo Eizirik
Habitat fragmentation may disrupt original patterns of gene flow and lead to drift-induced differentiation among local population units. Top predators such as the jaguar may be particularly susceptible to this effect, given their low population densities, leading to small effective sizes in local fragments. On the other hand, the jaguar's high dispersal capabilities and relatively long generation time might counteract this process, slowing the effect of drift on local populations over the time frame of...

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...

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