Data from: In silico phylogenomics using complete genomes: a case study on the evolution of hominoidsIgor Rodrigues Costa, Francisco Prosdocimi & W. Bryan Jennings
The increasing availability of complete genome data is facilitating the acquisition of phylogenomic datasets, but the process of obtaining orthologous sequences from other genomes and assembling multiple sequence alignments remains piecemeal and arduous. We designed software that performs these tasks and outputs anonymous loci (AL) or anchor loci (AE/UCE) datasets in ready-to-analyze formats. We demonstrate our program by applying it to the hominoids. Starting with human, chimpanzee, gorilla, and orangutan genomes, our software generated an...
Two billion ha have been identified globally for forest restoration. Our meta-analysis encompassing 221 study landscapes worldwide reveals forest restoration enhances biodiversity by 15–84% and vegetation structure by 36–77%, compared with degraded ecosystems. For the first time, we identify the main ecological drivers of forest restoration success (defined as a return to a reference condition, that is, old-growth forest) at both the local and landscape scale. These are as follows: the time elapsed since restoration...
Data from: Is there a correlation between abundance and environmental suitability derived from ecological niche modelling? A meta-analysisMarcelo M. Weber, Richard D. Stevens, José Alexandre F. Diniz-Filho & Carlos Eduardo V. Grelle
It is thought that species abundance is correlated with environmental suitability and that environmental variables, scale, and type of model fitting can confound this relationship. We performed a meta-analysis to (i) test whether species abundance is positively correlated with environmental suitability derived from correlative ecological niche models (ENM), (ii) test whether studies encompassing large areas within a species range (>50%) exhibited higher AS correlations than studies encompassing small areas within a species range (<50%), (iii)...
Data from: Metaproteomics reveals metabolic transitions between healthy and diseased stony coral Mussismilia braziliensisGizele D. Garcia, Eidy De O. Santos, Gabriele V. Sousa, Russolina B. Zingali, Cristiane C. Thompson & Fabiano L. Thompson
Infectious diseases such as white plague syndrome (WPS) and black band disease (BBD) have caused massive coral loss worldwide. We performed a metaproteomic study on the Abrolhos coral Mussismilia braziliensis to define the types of proteins expressed in healthy corals compared to WPS- and BBD-affected corals. A total of 6363 MS/MS spectra were identified as 361 different proteins. Healthy corals had a set of proteins that may be considered markers of holobiont homoeostasis, including tubulin,...
Collectively, reservoirs created by dams are thought to be an important source of greenhouse gases (GHGs) to the atmosphere. So far, efforts to quantify, model, and manage these emissions have been limited by data availability and inconsistencies in methodological approach. Here, we synthesize reservoir CH4, CO2, and N2O emission data with three main objectives: (1) to generate a global estimate of GHG emissions from reservoirs, (2) to identify the best predictors of these emissions, and...
Data from: A quantitative framework to estimate the relative importance of environment, spatial variation and patch connectivity in driving community compositionViviane F. Monteiro, Paulo C. Paiva & Pedro R. Peres-Neto
Perhaps the most widely used quantitative approach in metacommunity ecology is the estimation of the importance of local environment vs. spatial structuring using the variation partitioning framework. Contrary to metapopulation models, however, current empirical studies of metacommunity structure using variation partitioning assume a space-for-dispersal substitution due to the lack of analytical frameworks that incorporate patch connectivity predictors of dispersal dynamics. Here, a method is presented that allows estimating the relative importance of environment, spatial variation...
Regions in the Amazon Basin have been associated with specific biogeochemical processes, but a detailed chemical classification of the abundant and ubiquitous dissolved organic matter (DOM), beyond specific indicator compounds and bulk measurements, has not yet been established. We sampled water from different locations in the Negro, Madeira/Jamari and Tapajós River areas to characterize the molecular DOM composition and distribution. Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) combined with excitation emission matrix (EEM)...
Data from: Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant cladeBrad R. Ruhfel, Claudia P. Bove, C. Thomas Philbrick & Charles C. Davis
PREMISE OF THE STUDY: The clusioid clade (Malpighiales) has an ancient fossil record (∼90 Ma) and extant representatives exhibit a pantropical distribution represented on all former Gondwanan landmasses (Africa, Australia, India, Madagascar, and South America) except Antarctica. Several biogeographers have hypothesized that the clusioid distribution is an example of Gondwanan vicariance. Our aim is to test the hypothesis that the modern distribution of the clusioid clade is largely explained by Gondwanan fragmentation. METHODS: Using a...
Parasites play a role in the control of transient algal blooms, but it is not known whether parasite-mediated selection results in coevolution of the host and the parasites over this short time span. We investigated the presence of coevolution between the toxic dinoflagellate Alexandrium minutum and two naturally occurring endoparasites during blooms lasting a month in two river estuaries, using cross-inoculation experiments across time and space. Higher parasite abundance was associated with a large daily...
Data from: Comparative leaf anatomy of wild Manihot Mill. species (Euphorbiaceae) from Chapada Diamantina, Bahia, BrazilIsrael Lopes Da Cunha Neto, Fabiano Machado Martins, Márcio Lacerda Lopes Martins & Lucimara Reis De Oliveira Silva
The leaf anatomy of nine species of Manihot Mill. were studied with the objective of finding anatomical features that contribute to understanding the taxonomy of the genus. Leaf samples were collected in the field and from herbarium specimens, and standardized methods were used for both light and scanning electron microscopy. The following species were studied: M. bellidifolia P. Carvalho & M. Martins, M. brachyandra Pax & K. Hoffm., M. caerulescens Pohl, M. diamantinensis Allem, M....
Federal University of Rio de Janeiro10
University of Quebec at Montreal1
Universidade Federal de Goiás1
Eastern Kentucky University1
Western Connecticut State University1
Universidade Federal de Minas Gerais1
Australian National University1
French National Centre for Scientific Research1
Technical University Munich1