358 Works

Using a coalescent approach to assess gene flow and effective population size of Acrocomia aculeata (Jacq.) Lodd. Ex Mart. in the Brazilian Atlantic Forest

Renan Marcelo Portela, Evandro Vagner Tambarussi, João Ricardo Bachega Feijó Rosa, Ananda Virginia De Aguiar, Fabiana Schmidt Bandeira Peres & Flávio Bertin Gandara
Acrocomia aculeata is a tropical palm tree native to Central and South America that has significant economic, social, and environmental potential. However, land encroachment due to the expansion of agribusiness, and other factors such as urban sprawl, have resulted in the fragmentation and destruction of its habitat, leading to the loss of genes and genotypes in A. aculeata populations. In this context, the objective of this study was to characterize the genetic variability of A....

Investigating morphological complexes using informational dissonance and bayes factors: A case study in corbiculate bees

Diego Porto, Eduardo Almeida & Matthew Pennell
It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here we investigate patterns of discordance among 282 morphological characters, which we scored...

Coronavirus prevalence in Brazilian Amazon and Sao Paulo city

Tassila Salomon, Oliver Pybus, Rafael França, Marcia Castro, Ester Cerdeira Sabino, Christopher Dye, Michael Busch, Moritz U. G. Kraemer, Charles Whittaker, Andreza Santos, Nuno Faria, Rafael Pereira, Lewis Buss, , Claudia Abrahim, Maria Carvalho, Allyson Costa, Manoel Barral-Netto, Crispim Myuki, Brian Custer, Cesar De Almeida-Neto, Suzete Ferreira, Nelson Fraiji, Susie Gurzenda, Leonardo Kamaura … & Maria Belotti
SARS-CoV-2 spread rapidly in the Brazilian Amazon. Mortality was elevated, despite the young population, with the health services and cemeteries overwhelmed. The attack rate in this region is an estimate of the final epidemic size in an unmitigated epidemic. Here we show that by June, one month after the epidemic peak in Manaus, capital of the Amazonas state, 44% of the population had detectable IgG antibodies. This equates to a cumulative incidence of 52% after...

Total Ortholog Median Matrix (TOMM): an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes

Sandra R. Maruyama, Luana A. Rogerio, Patrícia Domingues Freitas, Marta Maria Teixeira & José Marcos Ribeiro
The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs...

Diversification history of clown tree frogs in Neotropical rainforests (Anura, Hylidae, Dendropsophus leucophyllatus group)

Renata Pirani, Pedro Peloso, Joyce Prado, Érico Polo, Lacey Knowles, Santiago Ron, Miguel Rodrigues, Marcelo Sturaro & Fernanda Werneck
General consensus emphasizes that no single biological process can explain the patterns of species’ distributions and diversification in the Neotropics. Instead, the interplay of several processes across space and time must be taken into account. Here we investigated the phylogenetic relationships and biogeographic history of tree frogs in the Dendropsophus leucophyllatus species group (Amphibia: Hylidae), which is distributed across Amazonia and the Atlantic rainforests. Using Next Generation Sequencing (NGS) and double digest restriction-site associated DNA...

Variation in the production of plant tissues bearing extrafloral nectaries explains temporal patterns of ant attendance in Amazonian understory plants

Anselmo Nogueira, Fabricio Baccaro, Laura Leal, Pedro Rey, Lúcia Lohmann & Judith Bronstein
1. Information on direct and indirect drivers of temporal variation in ant-plant interactions is scarce, compromising our ability to predict the functioning of these ecologically important interactions. 2. We investigated the roles of precipitation, ant activity, abundance of young plant tissues bearing extrafloral nectaries (EFNs), and EFN phenotypes in the establishment of EFN-mediated ant-plant interactions throughout the year in Amazonia, Brazil. We hypothesized that the frequency of ant-plant interactions follows a predictable seasonal pattern, being...

Data from: Bee pollinator functional responses and functional effects in restored tropical forests

Paula María Montoya-Pfeiffer, Ricardo Ribeiro Rodrigues & Isabel Alves Dos Santos
Wild pollinators are necessary for ensuring plant reproduction not only among crop fields but also remnant and restored ecosystems. Restoration activities should, therefore, lead to wild pollinator recovery, and thus be monitored to evaluate effects on pollinator diversity and functionality. We assessed bee pollinator functional responses in restoration plantings by creating functional groups (traits: body size, nesting location, sociality and foraging strategy), comparing their abundance and diversity to that of other habitats (i.e. conserved and...

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: 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: 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: Prediction of phylogeographic endemism in an environmentally complex biome.

Ana Carolina Carnaval, Eric Waltari, Miguel T. Rodrigues, Dan Rosauer, Jeremy VanDerWal, Roberta Damasceno, Ivan Prates, Maria Strangas, Zoe Spanos, Danielle Rivera, Marcio R. Pie, Carina R. Firkowski, Marcos R. Bornschein, Luiz F. Ribeiro & Craig Moritz
Phylogeographic endemism, the degree to which the history of recently evolved lineages is spatially restricted, reflects fundamental evolutionary processes such as cryptic divergence, adaptation and biological responses to environmental heterogeneity. Attempts to explain the extraordinary diversity of the tropics, which often includes deep phylogeographic structure, frequently invoke interactions of climate variability across space, time and topography. To evaluate historical versus contemporary drivers of phylogeographic endemism in a tropical system, we analyse the effects of current...

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: 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...

Questão 04 - Tarefa 01 - PPGEE Poli USP - Aerosois e Radiometria

Wesley Barbosa
Derivado: Médias horárias de propriedades intensivas em aerossóis de AOS, Delene e Ogren.Medição da radiação superficial Teste de controle de qualidade, incluindo limites climatologicamente configuráveis

pcs5031-lista1

Rodrigo Carvalho
Amostra de dataset para a disciplina PCS5031

Projeto Final - Introdução à Ciência dos Dados - Mestrado em Engenharia de Computação - Poli USP

Wesley Lourenco Barbosa
Dados gerados no desenvolvimento do trabalho final da disciplina.

Data from: Improving accuracies of genomic predictions for drought tolerance in maize by joint modeling of additive and dominance effects in multi-environment trials

Kaio Olímpio Das Graças Dias, Salvador Alejandro Gezan, Claudia Teixeira Guimarães, Alireza Nazarian, Luciano Da Costa E Silva, Sidney Netto Parentoni, Paulo Evaristo De Oliveira Guimarães, Carina De Oliveira Anoni, José Maria Villela Pádua, Marcos De Oliveira Pinto, Roberto Willians Noda, Carlos Alexandre Gomes Ribeiro, Jurandir Vieira De Magalhães, Antonio Augusto Franco Garcia, João Cândido De Souza, Lauro José Moreira Guimarães & Maria Marta Pastina
Breeding for drought tolerance is a challenging task that requires costly, extensive and precise phenotyping. Genomic selection (GS) can be used to maximize selection efficiency and the genetic gains in maize (Zea mays L.) breeding programs for drought tolerance. Here we evaluated the accuracy of genomic selection of additive (A) against additive+dominance (AD) models to predict the performance of untested maize single-cross hybrids for drought tolerance in multi-environment trials. Phenotypic data of five drought-tolerance traits...

Data from: Are there general laws for digit evolution in squamates? The loss and re-evolution of digits in a clade of fossorial lizards (Brachymeles, Scincinae)

Günter P. Wagner, Oliver W. Griffith, Philip J. Bergmann, Gaelle Bello-Hellegouarch, Tiana Kohlsdorf, Anjan Bhullar & Cameron D. Siler
Evolutionary simplification of autopodial structures is a major theme in studies of body‐form evolution. Previous studies on amniotes have supported Morse's law, that is, that the first digit reduced is Digit I, followed by Digit V. Furthermore, the question of reversibility for evolutionary digit loss and its implications for “Dollo's law” remains controversial. Here, we provide an analysis of limb and digit evolution for the skink genus Brachymeles. Employing phylogenetic, morphological, osteological, and myological data,...

Data from: Personality-matching habitat choice, rather than behavioural plasticity, is a likely driver of a phenotype–environment covariance

Benedikt Holtmann, Eduardo S.A. Santos, Carlos E. Lara, Shinichi Nakagawa & Eduardo S. A. Santos
An emerging hypothesis of animal personality posits that animals choose the habitat that best fits their personality, and that the match between habitat and personality can facilitate population differentiation, and eventually speciation. However, behavioural plasticity and the adjustment of behaviours to new environments have been a classical explanation for such matching patterns. Using a population of dunnocks (Prunella modularis), we empirically tested whether personality or behavioural plasticity is responsible for the non-random distribution of shy...

Data from: A model of urban scaling laws based on distance dependent interactions

Fabiano L. Ribeiro, João Miranda, Fernando F. Ferreira & Camilo Rodrigues Neto
Socio-economic related properties of a city grow faster than a linear relationship with the population, in a log–log plot, the so-called superlinear scaling. Conversely, the larger a city, the more efficient it is in the use of its infrastructure, leading to a sublinear scaling on these variables. In this work, we addressed a simple explanation for those scaling laws in cities based on the interaction range between the citizens and on the fractal properties of...

Data from: Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

Alison G. Nazareno, Jordan B. Bemmels, Christopher W. Dick & Lúcia G. Lohmann
High throughput DNA sequencing facilitates the analysis of large portions of the genome in non-model organisms, ensuring high accuracy of population genetic parameters. However, empirical studies evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double digest restriction associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a non-model plant species for which no...

Data from: Mating system and effective population size of the overexploited Neotropical tree (Myroxylon peruiferum L.f.) and their impact on seedling production

Ellida De Aguiar Silvestre, Kaiser Dias Schwarcz, Carolina Grando, Jaqueline Bueno De Campos, Patricia Sanae Sujii, Evandro Vagner Tambarussi, Camila Menezes Trindade Macrini, José Baldin Pinheiro, Pedro Henrique Santin Brancalion & Maria Imaculada Zucchi
The reproductive system of a tree species has substantial impact on genetic diversity and structure within and among natural populations. Such information, should be considered when planning tree planting for forest restoration. Here, we describe the mating system and genetic diversity of an overexploited Neotropical tree, Myroxylon peruiferum L.f. (Fabaceae) sampled from a forest remnant (10 seed trees and 200 seeds) and assess whether the effective population size of nursery-grown seedlings (148 seedlings) is sufficient...

Data from: Land use type, forest cover, and forest edges modulate avian cross-habitat spillover

Andrea Larissa Boesing, Elizabeth Nichols & Jean-Paul Metzger
1.Natural habitats adjacent to agricultural areas are often considered sources of species that provide beneficial regulating ecosystem services through cross-habitat spillover. Both inter-habitat matrix and landscape configuration can influence spillover by controlling organismal ability to disperse through landscapes, and affecting the provision of additional or supplementary resources that impact organism survival. 2.To understand how landscape structure in terms of matrix land use type, forest cover, and edge density might facilitate avian cross-habitat spillover, we sampled...

Data from: Evolution of a complex phenotype with biphasic ontogeny: contribution of development versus function and climatic variation to skull modularity in toads

Monique Nouailhetas Simon & Gabriel Marroig
The theory of morphological integration and modularity predicts that if functional correlations among traits are relevant to mean population fitness, the genetic basis of development will be molded by stabilizing selection to match functional patterns. Yet, how much functional interactions actually shape the fitness landscape is still an open question. We used the anuran skull as a model of a complex phenotype for which we can separate developmental and functional modularity. We hypothesized that functional...

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