27 Works

Data from: The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae)

Pedro L. V. Peloso, Darrel R. Frost, Stephen J. Richards, Miguel T. Rodrigues, Stephen Donnellan, Masafumi Matsui, Cristopher J. Raxworthy, S. D. Biju, Emily Moriarty Lemmon, Ward C. Wheeler, Alan R. Lemmon, Pedro L.V. Peloso & S.D. Biju
Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: Incompatible ages for clearwing butterflies based on alternative secondary calibrations

Ivonne J. Garzón-Orduña, Karina L. Silva-Brandão, Keith R. Willmott, André V. L. Freitas & Andrew V. Z. Brower
The recent publication of a time-tree for the plant family Solanaceae (nightshades) provides the opportunity to use independent calibrations to test divergence times previously inferred for the diverse Neotropical butterfly tribe Ithomiini. Ithomiini includes clades that are obligate herbivores of Solanaceae, with some genera feeding on only one genus. We used 8 calibrations extracted from the plant tree in a new relaxed molecular-clock analysis to produce an alternative temporal framework for the diversification of ithomiines....

Data from: Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat

Marcela Guidugli, Alison G Nazareno, Juliana Feres, Eucleia Contel, Moacyr Mestriner & Ana Lilia Alzate-Marin
Here, we explore the mating pattern and genetic structure of a tropical tree species, Cariniana estrellensis, in a small population in which progeny arrays (n=399), all adults (n=28) and all seedlings (n=39) were genotyped at nine highly informative microsatellite loci. From progeny arrays we were able to identify the source tree for at least 78% of pollination events. The gene immigration rates, mainly attributable to pollen, were high, varying from 23.5 to 53%. Although gene...

Data from: Environmental gradients and the evolution of successional habitat specialization: a test case with 14 Neotropical forest sites

Susan G. Letcher, Jesse R. Lasky, Robin L. Chazdon, Natalia Norden, S. Joseph Wright, Jorge A. Meave, Eduardo A. Pérez-García, Rodrigo Muñoz, Eunice Romero-Pérez, Ana Andrade, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Tony V. Bentos, Radika Bhaskar, Frans Bongers, Vanessa Boukili, Pedro H. S. Brancalion, Ricardo G. César, Deborah A. Clark, David B. Clark, Dylan Craven, Alexander DeFrancesco, Juan M. Dupuy, Bryan Finegan … & G. Bruce Williamson
1. Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late successional stages in wet forest. 2....

Data from: Geographic mosaic of plant evolution: extrafloral nectary variation mediated by ant and herbivore assemblages

Anselmo Nogueira, Pedro J. Rey, Julio M. Alcántara, Rodrigo M. Feitosa & Lúcia G. Lohmann
Herbivory is an ecological process that is known to generate different patterns of selection on defensive plant traits across populations. Studies on this topic could greatly benefit from the general framework of the Geographic Mosaic Theory of Coevolution (GMT). Here, we hypothesize that herbivory represents a strong pressure for extrafloral nectary (EFN) bearing plants, with differences in herbivore and ant visitor assemblages leading to different evolutionary pressures among localities and ultimately to differences in EFN...

Data from: A case study of extant and extinct Xenarthra cranium covariance structure: implications and applications to paleontology

Alex Hubbe, Diogo Melo & Gabriel Marroig
Most of the mammalian diversity is known only from fossils, and only a few of these fossils are well preserved or abundant. This under sampling poses serious problems for understanding mammalian phenotypic evolution under a quantitative genetics framework, since this framework requires estimation of a group's additive genetic variance-covariance matrix (G-matrix), which is impossible, and estimating a phenotypic variance-covariance matrix (P-matrix) requires larger sample sizes then what is often available for extinct species. One alternative...

Data from: Population differentiation and behavioural association of the two ‘personality’ genes DRD4 and SERT in dunnocks (Prunella modularis)

Benedikt Holtmann, Stefanie Grosser, Malgorzata Lagisz, Sheri R. Johnson, Eduardo S. A. Santos, Carlos E. Lara, Bruce Robertson, Shinichi Nakagawa, S. L. Johnson & B. C. Robertson
Quantifying the variation in behaviour-related genes within and between populations provides insight into how evolutionary processes shape consistent behavioural traits (i.e. personality). Deliberate introductions of non-native species offer opportunities to investigate how such genes differ between native and introduced populations and how polymorphisms in the genes are related to variation in behaviour. Here, we compared the genetic variation of the two ‘personality’ genes, DRD4 and SERT, between a native (United Kingdom, UK) and an introduced...

Data from: Prospective randomized trial comparing hepatic venous outflow and renal function after conventional versus piggyback liver transplantation

Marília D’Elboux Guimarães Brescia, Paulo Celso Bosco Massarollo, Ernesto Sasaki Imakuma & Sérgio Mies
Background: This randomized prospective clinical trial compared the hepatic venous outflow drainage and renal function after conventional with venovenous bypass (n = 15) or piggyback (n = 17) liver transplantation. Methods: Free hepatic vein pressure (FHVP) and central venous pressure (CVP) measurements were performed after graft reperfusion. Postoperative serum creatinine (Cr) was measured daily on the first week and on the 14th, 21st and 28th postoperative days (PO). The prevalence of acute renal failure (ARF)...

Data from: Plasmodium vivax diversity and population structure across four continents

Cristian Koepfli, Priscila T. Rodrigues, Tiago Antao, Pamela Orjuela-Sánchez, Peter Van Den Eede, Dionicia Gamboa, Nguyen Van Hong, Jorge Bendezu, Annette Erhart, Céline Barnadas, Arsène Ratsimbasoa, Didier Menard, Carlo Severini, Michela Menegon, Baki Y. M. Nour, Nadira Karunaweera, Ivo Mueller, Marcelo U. Ferreira, Ingrid Felger & Bakri Y. M. Nour
Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999–2008. Diversity was highest in South-East Asia (mean allelic richness 10.0–12.8), intermediate in the South Pacific (8.1–9.9) Madagascar and Sudan (7.9–8.4), and lowest in South America and Central Asia (5.5–7.2). A...

Data from: Population genetic structure in hyacinth macaws (Anodorhynchus hyacinthinus) and identification of the probable origin of confiscated individuals

Flavia T. Presti, Neiva M. R. Guedes, Paulo T. Z. Antas & Cristina Y. Miyaki
Understanding the intraspecific genetic composition of populations in different geographic locations is important for the conservation of species. If genetic variability is structured, conservation strategies should seek to preserve the diversity of units. Also, origin of individuals can be determined, which is important for guiding actions against animal trafficking. The hyacinth macaw (Anodorhynchus hyacinthinus) is located in allopatric regions, vulnerable to extinction and suffering animal trafficking pressure. Therefore, we characterized its population genetic structure based...

Data from: Extreme operative temperatures are better descriptors of the thermal environment than mean temperatures

Agustín Camacho, Miguel Trefaut Rodrigues, Carlos Arturo Navas & Carlos Navas
In ecological studies of thermal biology the thermal environment is most frequently described using the mean or other measures of central tendency in environmental temperatures. However, this procedure may hide biologically relevant thermal variation for ectotherms, potentially misleading interpretations. Extremes of operative temperatures (EOT) can help with this problem by bracketing the thermal environment of focal animals. Within this paper, we quantify how mean operative temperatures relate to the range of simultaneously available operative temperatures...

Data from: Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation

Leonardo Campagna, Ilan Gronau, Luís Fábio Silveira, Adam Siepel & Irby J. Lovette
Recently diverged taxa provide the opportunity to search for the genetic basis of the phenotypes that distinguish them. Genomic scans aim to identify loci that are diverged with respect to an otherwise weakly differentiated genetic background. These loci are candidates for being past targets of selection because they behave differently from the rest of the genome that has either not yet differentiated or that may cross species barriers through introgressive hybridization. Here we use a...

Data from: Relationship among medical student resilience, educational environment and quality of life

Patricia Tempski, Itamar S. Santos, Fernanda B. Mayer, Sylvia C. Enns, Bruno Perotta, Helena B. M. S. Paro, Silmar Gannam, Munique Peleias, Vera Lucia Garcia, Sergio Baldassin, Katia B. Guimaraes, Nilson R. Silva, Emirene M. T. Navarro Da Cruz, Luis F. Tofoli, Paulo S. P. Silveira & Milton A. Martins
Context: Resilience is a capacity to face and overcome adversities, with personal transformation and growth. In medical education, it is critical to understand the determinants of a positive, developmental reaction in the face of stressful, emotionally demanding situations. We studied the association among resilience, quality of life (QoL) and educational environment perceptions in medical students. Methods: We evaluated data from a random sample of 1,350 medical students from 22 Brazilian medical schools. Information from participants...

Data from: Carbon assimilation and habitat segregation in resurrection plants: a comparison between desiccation- and non-desiccation-tolerant species of Neotropical Velloziaceae (Pandanales)

Suzana Alcantara, Renato De Mello-Silva, Grazielle S. Teodoro, Kamila Drequeceler, David Ackerly & Rafael S. Oliveira
Desiccation tolerance is the ability that some organisms show to equilibrate their water content with that of dry air and recover when water supplies are re-established. This is a widespread although rare strategy in angiosperms, and most desiccation-tolerant (DT) species are restricted to tropical rock outcrops. Such restricted ecological range is attributed to weak competitive potential caused by low productivity, due to the temporal limitation in carbon assimilation that occurs when plants desiccate. However, few...

Data from: Speciation with gene flow in whiptail lizards from a Neotropical xeric biome

Eliana F. Oliveira, Marcelo Gehara, Vinícius A. São Pedro, Xin Chen, Edward A. Myers, Frank T. Burbrink, Daniel O. Mesquita, Adrian A. Garda, Guarino R. Colli, Miguel T. Rodrigues, Federico J. Arias, Hussam Zaher, Rodrigo M. L. Santos & Gabriel C. Costa
Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure, and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein we analyze genetic diversity and structure, phylogeographic history, and diversification of a widespread...

Data from: Diffusion tensor imaging in patients with glioblastoma multiforme using the supertoroidal model

Choukri Mekkaoui, Philippe Metellus, William J. Kostis, Roberto Martuzzi, Fabricio R. Pereira, Jean-Paul Beregi, Timothy G. Reese, Todd R. Constable & Marcel P. Jackowski
Purpose: Diffusion Tensor Imaging (DTI) is a powerful imaging technique that has led to improvements in the diagnosis and prognosis of cerebral lesions and neurosurgical guidance for tumor resection. Traditional tensor modeling, however, has difficulties in differentiating tumor-infiltrated regions and peritumoral edema. Here, we describe the supertoroidal model, which incorporates an increase in surface genus and a continuum of toroidal shapes to improve upon the characterization of Glioblastoma multiforme (GBM). Materials and Methods: DTI brain...

Data from: Network analyses support the role of prey preferences in shaping resource use patterns within five animal populations

Paula Lemos-Costa, Mathias M. Pires, Márcio S. Araújo, Marcus A. M. De Aguiar &
Individual variation is an inherent aspect of animal populations and understanding the mechanisms shaping resource use patterns within populations is crucial to comprehend how individuals partition resources. Theory predicts that differences in prey preferences among consumers and/or differences in the likelihood of adding new resources to their diets are key mechanisms underlying intrapopulation variation in resource use. We developed network models based on optimal diet theory that simulate how individuals consume resources under varying scenarios...

Data from: Natural light exposure, sleep and depression among day workers and shiftworkers at Arctic and Equatorial latitudes

Elaine Cristina Marqueze, Suleima Vasconcelos, Johanna Garefelt, Debra J. Skene, Claudia Roberta Moreno & Arne Lowden
Objectives: This study aimed to investigate the relationship between individual natural light exposure, sleep need, and depression at two latitudes, one extreme with a few hours of light per day during winter, and the other with equal hours of light and darkness throughout the year. Methods: This cross-sectional study included a sample of Brazilian workers (Equatorial, n = 488 workers) and a Swedish sample (Arctic, n = 1,273). Results: The reported mean total natural light...

Data from: Soil microbiome responses to the short-term effects of Amazonian deforestation

Acácio A. Navarrete, Siu M. Tsai, Lucas W. Mendes, Karoline Faust, Mattias De Hollander, Noriko A. Cassman, Johannes A. Van Veen, Eiko E. Kuramae & Jeroen Raes
Slash-and-burn clearing of forest typically results in increase in soil nutrient availability. However, the impact of these nutrients on the soil microbiome is not known. Using next generation sequencing of 16S rRNA gene and shotgun metagenomic DNA, we compared the structure and the potential functions of bacterial community in forest soils to deforested soils in the Amazon region and related the differences to soil chemical factors. Deforestation decreased soil organic matter content and factors linked...

Data from: Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation

Arthur Porto, Harley Sebastião, Silvia Eliza Pavan, John L. VandeBerg, Gabriel Marroig & James M. Cheverud
We tested the hypothesis that the rate of marsupial cranial evolution is dependent on the distribution of genetic variation in multivariate space. To do so, we carried out a genetic analysis of cranial morphological variation in laboratory strains of Monodelphis domestica and used estimates of genetic covariation to analyze the morphological diversification of the Monodelphis brevicaudata species group. We found that within-species genetic variation is concentrated in only a few axes of the morphospace and...

Data from: Multi-objective optimization for plant germplasm collection conservation of genetic resources based on molecular variability

Shana Schlottfeldt, Maria Emília M. T. Walter, Andre Carlos P. L. F. Carvalho, Thannya N. Soares, Mariana P. C. Telles, Rafael D. Loyola & Jose Alexandre F. Diniz-Filho
Germplasm collections play a significant role among strategies for conservation of diversity. It is common to select a core collection to represent the genetic diversity of a germplasm collection, in order to minimize the cost of conservation, while ensuring the maximization of genetic variation. We aimed to solve two main problems: (1) to select a set of individuals, from an in situ data set, that is genetically complementary to an existing germplasm collection, and (2)...

Data from: A landscape triage approach: combining spatial and temporal dynamics to prioritize restoration and conservation

Danielle I. Rappaport, Leandro R. Tambosi & Jean Paul Metzger
1. The spatial and temporal dynamics of landscape structure yield ecological constraints that may limit or promote the recovery of functioning habitat within human-modified ecosystems. In planning restoration and conservation measures to optimize outcomes for biodiversity, such constraints should be evaluated at multiple scales. 2. This paper presents a multi-scale methodology based on the concept of triage that incorporates landscape and regional spatial context and temporal dynamics to prioritize restoration and conservation. 3. In applying...

Data from: Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression

Martín O. Pereyra, Diego Baldo, Boris L. Blotto, Patricia P. Iglesias, Maria T. C. Thomé, Célio F. B. Haddad, César Barrio-Amorós, Roberto Ibáñez & Julián Faivovich
The Rhinella granulosa group consists of 13 species of toads distributed throughout open areas of South America and Panama. In this paper we perform a phylogenetic analysis considering all but one species of the group, employing five nuclear and four mitochondrial genes, for up to 7910 bp per specimen. Separate phylogenetic analyses under direct optimization (DO) of nuclear and mitochondrial sequences recovered the R. granulosa group as monophyletic and revealed topological incongruence that can be...

Data from: Ultraconserved elements sequencing as a low-cost source of complete mitochondrial genomes and microsatellite markers in non-model amniotes

Fábio Raposo Do Amaral, Leandro G. Neves, , Flávia Mobili, Cristina Y. Miyaki, Katia C. M. Pellegrino & Cibele Biondo
Sequence capture of ultraconserved elements (UCEs) associated with massively parallel sequencing has become a common source of nuclear data for studies of animal systematics and phylogeography. However, mitochondrial and microsatellite variation are still commonly used in various kinds of molecular studies, and probably will complement genomic data in years to come. Here we show that besides providing abundant genomic data, UCE sequencing is an excellent source of both sequences for microsatellite loci design and complete...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Sao Paulo
  • Sao Paulo State University
  • State University of Campinas
  • City University of New York
  • Federal University of São Carlos
  • University of Otago
  • University of Chicago
  • Federal University of Sao Paulo
  • University of Missouri
  • Smithsonian Tropical Research Institute