29 Works

Data from Reis et al (2020) Causes and consequences of liana infestation in Southern Amazonia. Journal of Ecology DOI: 10.1111/1365-2745.13470

Simone Matias Reis, Beatriz Schwantes Marimon, Paulo S. Morandi, Fernando Elias, Adriane Esquivel‐Muelbert, Ben Hur Marimon Junior, Sophie Fauset, Edmar Almeida de Oliveira, Geertje M.F. van der Heijden, David Galbraith, Ted R. Feldpausch & Oliver L. Phillips

A “Dirty” Footprint: Soil macrofauna biodiversity and fertility in Amazonian Dark Earths and adjacent soils

Wilian C. Demetrio, Ana C. Conrado, Agno N. S. Acioli, Alexandre C. Ferreira, Marie L. C. Bartz, Samuel W. James, Elodie Silva, Lilianne S. Maia, Gilvan C. Martins, Rodrigo S. Macedo, David W. G. Stanton, Patrick Lavelle, Elena Velasquez, Anne Zangerlé, Rafaella Barbosa, Sandra C. Tapia‐Coral, Aleksander W. Muniz, Alessandra Santos, Talita Ferreira, Rodrigo F. Segalla, Thibaud Decaëns, Herlon S. Nadolny, Clara P. Peña‐Venegas, Cláudia M. B. F. Maia, Amarildo Pasini … & George G. Brown
Amazonian rainforests once thought to hold an innate pristine wilderness, are increasingly known to have been densely inhabited by populations showing a diverse and complex cultural background prior to European arrival. To what extent these societies impacted their landscape is unclear. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies as a result of more sedentary habits. Much is known of the chemistry of these soils, yet their...

Data from: Genetic switches designed for eukaryotic cells and controlled by serine integrases

Mayna Gomide, Thais Sales, Luciana Barros, Cintia Limia, Marco Antônio Oliveira, Lilian Florentino, Leila Barros, Maria Laura Robledo, Gustavo José, Mariana Almeida, Rayane Lima, Stevens Rehen, Cristiano Lacorte, Eduardo Melo, André Murad, Martín Bonamino, Cintia Coelho & Elibio Rech
Recently, new serine integrases have been identified, increasing the possibility of scaling up genomic modulation tools. Here, we describe the use of unidirectional genetic switches to evaluate the functionality of six serine integrases in different eukaryotic systems: the HEK 293T cell lineage, bovine fibroblasts and plant protoplasts. Moreover, integrase activity was also tested in human cell types of therapeutic interest: peripheral blood mononuclear cells (PBMCs), neural stem cells (NSCs) and undifferentiated embryonic stem (ES) cells....

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....

Data from: The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Angelique D'Hont, France Denoeud, Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel, Stéphanie Bocs, Gaëtan Droc, Mathieu Rouard, Corinne Da Silva, Jabbari Kamel, Céline Cardi, Julie Poulain, Marlène Souquet, Karine Labadie, Cyril Jourda, Juliette Lengellé, Marguerite Rodier-Goud, Adriana Alberti, Maria Bernard, Margot Correa, Saravanaraj Ayyampalayam, Michael R. McKain, Jim Leebens-Mack … & Patrick Wincker
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid...

A worldwide assessment of soil macroinvertebrate communities

Patrick Lavelle, Jerome Mathieu, Alister Spain, George Brown, Carlos Fragoso, Emmanuel Lapied, Adriana De Aquino, Isabelle Barois, Edmundo Barrios, Eleusa Barros, Juan Camilo Bedano, Eric Blanchart, Mark Caulfield, Yamileth Chagueza, Jun Dai, Thibaud Decaens, Anahi Domninquez, Yamileth Dominquez, Alex Feijoo, Patricia Folgaraiti, Steven Fonte, Norma Gorosito, Esperanza Huerta, Juan Jose Jimenez, Courtland Kelly … & Cesar Botero
Soil macroinvertebrate communities have been assessed worldwide using the standard ISO/TSBF sampling procedure. The Macrofauna database currently comprises 3694 sites distributed throughout 41 countries, from 55º S latitude to 57ºN, sea level to over 4000m in elevation, in total annual total rainfall regimes between 500 and >3000mm and 5 to 32ºC mean temperature. These communities are significantly influenced by climatic parameters, soil texture and vegetation cover. Abundance and diversity were highest in tropical rain forests...

Surveys of crocodilians in the hydroelectric dam, Brazilian Amazonia

Zilca Campos, Fábio Muniz, Guilherme Mourão & William Magnusson
We counts caimans in the Madeira River, before (2010-2011) and after (2012-2014, 2016-2019) hydroelectric dam.

Data from: Recommendations for assessing earthworm populations in Brazilian ecosystems

Herlon Nadolny, Alessandra Santos, Wilian Demetrio, Talita Ferreira, Lilianne Dos Santos Maia, Ana Caroline Conrado, Marie Bartz, Marilice Garrastazu, Elodie Da Silva, Dilmar Baretta, Amarildo Pasini, Fabiane Vezzani, José Paulo Sousa, Luis Cunha, Jerome Mathieu, Patrick Lavelle, Jörg Römbke & George Brown
Earthworms are often related to fertile soils and frequently used as environmental quality indicators. However, to optimize their use as bioindicators, their populations must be evaluated together with environmental and anthropogenic variables regulating earthworm communities. In this review we identify the earthworm, soil chemical, physical, environmental and management-related variables evaluated in 124 published studies that quantified earthworm abundance (>7300 samples) in 765 sites with different types of climate, soils, land use and management systems in...

Development and uncertainty assessment of pedotransfer functions for predicting water contents at specific pressure heads

Ali Mehmandoostkotlar, Quirijn De Jong Van Lier, Bo V Iversen, Alexandre Barros & Harry Vereecken
There has been much effort to improve the performance of pedotransfer functions (PTFs) using intelligent algorithms, but the issue of covariate shift, i.e. different probability distributions in training and testing datasets, and its impact on prediction uncertainty of PTFs has been rarely addressed. The common practice in PTF generation is to randomly separate the dataset in training and testing subsets, and outcomes of this random selection may be different if the process is subject to...

Reliably predicting pollinator abundance: challenges of calibrating process-based ecological models

Emma Gardner, Tom Breeze, Yann Clough, Henrik Smith, Katherine Baldock, Alistair Campbell, Michael Garratt, Mark Gillespie, William Kunin, Megan McKerchar, Jane Memmott, Simon Potts, Deepa Senapathi, Graham Stone, Felix Wäckers, Duncan Westbury, Andrew Wilby & Thomas Oliver
1. Pollination is a key ecosystem service for global agriculture but evidence of pollinator population declines is growing. Reliable spatial modelling of pollinator abundance is essential if we are to identify areas at risk of pollination service deficit and effectively target resources to support pollinator populations. Many models exist which predict pollinator abundance but few have been calibrated against observational data from multiple habitats to ensure their predictions are accurate. 2. We selected the most...

The response of carbon assimilation and storage to long-term drought in tropical trees is dependent on light availability

Lucy Rowland, Antonio Da Costa, Rafael Oliveira, Paulo Bittencourt, André Giles, Ingrid Coughlin, David Bartholomew, Tomas Ferreira Domingues, Raquel Miatto, Leandro Ferreira, Steel Vasconcelos, Joao Junior, Alex Oliveira, Maurizio Mencuccini & Patrick Meir
1) Whether tropical trees acclimate to long-term drought stress remains unclear. This uncertainty is amplified if drought stress is accompanied by changes in other drivers such as the increases in canopy light exposure that might be induced by tree mortality or other disturbances. 2) Photosynthetic capacity, leaf respiration, non-structural carbohydrate (NSC) storage and stomatal conductance were measured on 162 trees at the world’s longest running (15 yr) tropical forest drought experiment. We test whether surviving...

Genomic prediction applied to multiple traits and environments in second season maize hybrids

Amanda Avelar De Oliveira, , Luís Felipe Ventorim Ferrão, Rodrigo Rampazo Amadeu, Lauro José Moreira Guimarães, Claudia Teixeira Guimarães, Maria Marta Pastina & Gabriel Rodrigues Alves Margarido
Genomic selection has become a reality in plant breeding programs with the reduction in genotyping costs. Especially in maize breeding programs, it emerges as a promising tool for predicting hybrid performance. The dynamics of a commercial breeding program involve the evaluation of several traits simultaneously in a large set of target environments. Therefore, multi-trait multi-environment (MTME) genomic prediction models can leverage these data sets by exploring the correlation between traits and Genotype-by-Environment (G×E) interaction. Herein,...

Interviews from field research in Rio de Janeiro State - Brazil

Nádia Aun & Renato Linhares De Assis
This paper presents a case study on organic agriculture at Região Serrana Fluminense, Rio de Janeiro State, Brazil. We sought to understand what was the role of organic farming, and if it can be considered as an aggregating element between different kind of people or groups who were located in the same region. The methodology used to carry out this investigation was based on the concept of the Rural Network, which enabled us to comprehend...

Traits data from trees exposed to a 50% reduction in canopy throughfall for 14 years in Caxiuanã, Brazil, September to October 2016

L. Rowland, R.S. Oliveira, P.R.L. Bittencourt, A.L. Giles, I. Coughlin, P. De Britto Costa, T. Domingues, L.V. Ferreira, S.S. Vasconcelos, J.A.S. Junior, A.A.R. Oliveira, A.C.L. Da Costa, P. Meir & M. Mencuccini
Data comprise tree trait data collected during September and October 2016 (the peak dry season), in the Caxiuanã National Forest Reserve, eastern Amazon, Brazil. 17 traits (including plot type, tree species name, diameter at breast height, tree light score, carboxylation capacity, electron transport capacity, leaf respiration in the dark, stomatal conductance, stem CO2 efflux, leaf mass per area, leaf nitrogen and phosphorus content, branch wood density, leaf water potential, xylem pressure, lumen conductance, percentage loss...

Data and scripts from: Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava

Marcelo F. Simon, J. Moises Mendoza F., Márcio Lacerda Lopes Martins, Sergei V. Drovetski, Natalia A. S. Przelomska, Hope Loiselle, Taciana B. Cavalcanti, Peter W. Inglis, Natalie G. Mueller, Robin G. Allaby, Fábio De Oliveira Freitas & Logan Kistler
The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only ~6Mya have significantly complicated previous phylogenetic analyses. Several basic elements of Manihot evolutionary history therefore remain unresolved. Here, we conduct a comprehensive phylogenomic analysis of Manihot, focusing on exhaustive sampling of South American taxa. We find that two recently described species from northeast...

Precipitation, water level and descriptive statistics

Marcelo Medeiros, Marcelo Simon, Washington Oliveira & Pamela Moser
Extreme weather events and the presence of mega-hydroelectric dams, when combined, present an emerging threat to natural habitats in the Amazon region. To understand the magnitude of these impacts, we used remote sensing data to assess forest loss in areas affected by the extreme 2014 flood in the entire Madeira River basin, the location of two mega-dams. In addition, forest plots (26 ha) were monitored between 2011 and 2015 (14,328 trees) in order to evaluate...

Data from: Selection of early soybean inbred lines using multiple indices

Gabriel De Siqueira Gesteira, Adriano Teodoro Bruzi, Roberto Kazuhiko Zito, Vanoli Fronza & Neylson Eustáquio Arantes
Soybean [Glycine max (L.) Merr.] has been studied and enhanced for most of its economically important traits. Previous research has studied the association among them and the effect of the genotype × environment interaction; however, less is known about their correlation considering absolute maturity, as well as the use of multiple selection indices to study the genotype × environment interaction and select superior cultivars. Regarding this, the aim of the present study was to identify...

Data from: Incorporating animal spatial memory in step selection functions

Luiz Gustavo R. Oliveira-Santos, James D. Forester, Ubiratan Piovezan, Walfrido M. Tomas & Fernando A. S. Fernandez
Memory is among the most important and neglected forces that shapes animal movement patterns. Research on the movement-memory interface is crucial to understand how animals use spatial learning to navigate across space because memory-biased navigation is directly linked to animals’ space use and home range behaviour; however, because memory cannot be measured directly, it is difficult to account for. Here, we incorporated spatial memory into Step Selection Functions (SSF) to understand how resource selection and...

Data from: Repeat variants for the SbMATE transporter protect sorghum roots from aluminum toxicity by transcriptional interplay in cis and trans

Janaina O. Melo, Laura G. C. Martins, Beatriz A. Barros, Maiana R. Pimenta, Ubiraci G. P. Lana, Christiane E. M. Duarte, Maria M. Pastina, C. T. Guimaraes, Robert E. Schaffert, Leon V. Kochian, Elizabeth P. B. Fontes & Jurandir Vieira Magalhaes
Acidic soils, where aluminum (Al) toxicity is a major agricultural constraint, are globally widespread and are prevalent in developing countries. In sorghum, the root citrate transporter SbMATE confers Al tolerance by protecting root apices from toxic Al3+, but can exhibit reduced expression when introgressed into different lines. We show that allele-specific SbMATE transactivation occurs and is caused by factors located away from SbMATE. Using expression-QTL mapping and -GWAS, we establish that SbMATE transcription is controlled...

Data from: Assessing the expected response to genomic selection of individuals and families in Eucalyptus breeding with an additive-dominant model

Rafael T. Resende, Marcos D.V. Resende, Fabyano F. Silva, Camila F. Azevedo, Elizabete K. Takahashi, Orzenil B. Silva-Junior & Dario Grattapaglia
We report a genomic selection (GS) study of growth and wood quality traits in an outbred F2 hybrid Eucalyptus population (n=768) using high-density single-nucleotide polymorphism (SNP) genotyping. Going beyond previous reports in forest trees, models were developed for different selection targets, namely, families, individuals within families and individuals across the entire population using a genomic model including dominance. To provide a more breeder-intelligible assessment of the performance of GS we calculated the expected response as...

Predation on sentinel prey increases with increasing latitude in Brassica-dominated agroecosystems

Hannah Gray, Hannah Gray, Juliano Farias, Madelaine Venzon, Jorge Braz Torres, Lucas Machado Souza, Rafael Carlesso Aita & David Andow
In natural ecosystems, arthropod predation on herbivore prey is higher at lower latitudes, mirroring the latitudinal diversity gradient observed across many taxa. This pattern has not been systematically examined in human-dominated ecosystems, where frequent disturbances can shift the identity and abundance of local predators, altering predation rates from those observed in natural ecosystems. We investigated the how latitude, biogeographical, and local ecological factors influenced arthropod predation in Brassica oleracea dominated agroecosystems in 55 plots spread...

Aproveitamento sustentável de coprodutos da agroindústria amazônica: estratégias para o fortalecimento da piscicultura

Leonardo Takahashi
Na região Norte, o peixe é a base da dieta das populações amazônicas, no entanto, a escassez de pescado imposta pela sobrepesca, tem impulsionado o crescimento da piscicultura como atividade estratégica para garantir a segurança alimentar e renda dessas populações, além do abastecimento de mercados locais. Neste cenário, a complexa logística de transporte entre o Norte e as demais regiões do país, tem um reflexo negativo no custo de produção da piscicultura, sobretudo no preço...

Data from: Are Brazil nut populations threatened by fruit harvest?

Todd D. Bertwell, Karen A. Kainer, , Christina L. Staudhammer, Lúcia H. De Oliveira Wadt & Wendell P. Cropper
Harvest of Brazil nuts from the large, iconic tree Bertholletia excelsa generates substantial income for smallholders, providing a strong incentive to conserve the mature forests where it grows. Although much previous work has focused on the impact of nut harvest on new seedling recruits into B. excelsa populations, the connection between harvest rates and long-term population stability is still unclear. Moreover, there is additional uncertainty for Brazil nut management in terms of population response to...

Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient Neotropical mountains

Thais Vasconcelos, Suzana Alcantara, Caroline Andrino, Félix Forest, Marcelo Reginato, Marcelo Simon & José Pirani
Mountains are among the most biodiverse areas on the globe. In young mountain ranges, exceptional plant species-richness is often associated to recent and rapid radiations linked to the mountain uplift itself. In ancient mountains, however, orogeny vastly precedes the evolution of vascular plants, so species-richness has been explained by species accumulation during long periods of low extinction rates. Here we evaluate these assumptions by analyzing plant diversification dynamicsin thecampo rupestre, an ecosystem associated to pre-Cambrian...

Data from: Evolutionary diversity in tropical tree communities peaks at intermediate precipitation

Danilo M. Neves, Kyle G. Dexter, Timothy R. Baker, Fernanda Coelho De Souza, Ary T. Oliveira-Filho, Luciano P. Queiroz, Haroldo C. Lima, Marcelo F. Simon, Gwilym P. Lewis, Ricardo A. Segovia, Luzmila Arroyo, Carlos Reynel, José L. Marcelo-Peña, Isau Huamantupa-Chuquimaco, Daniel Villarroel, G. Alexander Parada, Aniceto Daza, Reynaldo Linares-Palomino, Leandro V. Ferreira, Rafael P. Salomão, Geovane S. Siqueira, Marcelo T. Nascimento, Claudio N. Fraga & R. Toby Pennington
Global patterns of species and evolutionary diversity in plants are primarily determined by a temperature gradient, but precipitation gradients may be more important within the tropics, where plant species richness is positively associated with the amount of rainfall. The impact of precipitation on the distribution of evolutionary diversity, however, is largely unexplored. Here we detail how evolutionary diversity varies along precipitation gradients by bringing together a comprehensive database on the composition of angiosperm tree communities...

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