201 Works

Data from: Detection of tephra layers in Antarctic sediment cores with hyperspectral imaging

Ismael F. Aymerich, Marc Oliva, Santiago Giralt & Julio Martín-Herrero
Tephrochronology uses recognizable volcanic ash layers (from airborne pyroclastic deposits, or tephras) in geological strata to set unique time references for paleoenvironmental events across wide geographic areas. This involves the detection of tephra layers which sometimes are not evident to the naked eye, including the so-called cryptotephras. Tests that are expensive, time-consuming, and/or destructive are often required. Destructive testing for tephra layers of cores from difficult regions, such as Antarctica, which are useful sources of...

Data from: \"Transcriptome sequences for Campanula gentilis\" in Genomic Resources Notes accepted 1 April 2015 – 31 May 2015

Töre Demet, Federico Luebert, Guilhem Mansion, Ludo A. H. Muller, M. Vidotto, E. Boscari, L. Congiu, A. Grapputo, L. Zane, Vera Maria Fonseca Almeida-Val, Maria Manuela Coelho, Tiago Filipe Jesus & Demet Töre
In this report, we present the transcriptome of a single accession of Campanula gentilis Kovanda, obtained through the sequencing of both a normalized and a non-normalized cDNA library generated from stem and leaf tissue. The resources we provide include the raw sequence reads, the assembled contigs, the putative open reading frames, the contig/ORF annotations and the normalized as well as non-normalized expression levels.

Data from: Natural history and survival in stage 1 Val30Met transthyretin familial amyloid polyneuropathy

Teresa Coelho, Mónica Inês, Isabel Conceiçao, Marta Soares, Mamede De Carvalho & João Costa
Objectives: To assess natural history and treatment effect on survival among transthyretin-associated familial amyloid polyneuropathy (TTR-FAP) Val30Met patients. Methods: Multi-institutional, hospital-based study of TTR-FAP Val30Met patients prospectively followed-up until December 2016, grouped into untreated (n = 1,771), liver transplant (LTx) (n = 957) or tafamidis-treated (n = 432) cohorts. Standardized mortality ratios (SMR), Kaplan-Meier and Cox methods were used to estimate excess mortality, survival probabilities and adjusted hazard ratios (HR) for all-cause mortality, respectively. Results:...

Data from: Climate modifies response of non-native and native species richness to nutrient enrichment

Habacuc Flores-Moreno, Peter B. Reich, Eric M. Lind, Lauren L. Sullivan, Eric W. Seabloom, Laura Yahdjian, Andrew S. MacDougall, Lara G. Reichmann, Juan Alberti, Selene Báez, Jonathan D. Bakker, Marc W. Cadotte, Maria C. Caldeira, Enrique J. Chaneton, Carla M. D'Antonio, Philip A. Fay, Jennifer Firn, Nicole Hagenah, W. Stanley Harpole, Oscar Iribarne, Kevin P. Kirkman, Johannes M. H. Knops, Kimberly J. La Pierre, Ramesh Laungani, Andrew D. B. Leakey … & Elizabeth T. Borer
Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of...

Data from: Wing trait-inversion associations in Drosophila subobscura can be generalized within continents, but may change through time

Pedro Simoes, Inês Fragata, Miguel Lopes-Cunha, Margarida Lima, Bárbara Kellen, Margarida Bárbaro, Mauro Santos & Margarida Matos
Clinal variation is one of the most emblematic examples of the action of natural selection at a wide geographical range. In Drosophila subobscura parallel clines in body size and inversions, but not in wing shape, were found in Europe and South and North America. Previous work has shown that a bottleneck effect might be largely responsible for differences in wing trait-inversions association between one European and one South American population. One question still unaddressed is...

Data from: Spatial patterns of self-recruitment of a coral reef fish in relation to island-scale retention mechanisms

Ricardo Beldade, Sally J. Holbrook, Russell J. Schmitt, Serge Planes & Giacomo Bernardi
Oceanographic features influence the transport and delivery of marine larvae, and physical retention mechanisms, such as eddies, can enhance self-recruitment (i.e. the return of larvae to their natal population). Knowledge of exact locations of hatching (origin) and settlement (arrival) of larvae of reef animals provides a means to compare observed patterns of self-recruitment ‘connectivity’ with those expected from water circulation patterns. Using parentage inference based on multiple sampling years in Moorea, French Polynesia, we describe...

Data from: Influence of plant-pollinator interactions on the assembly of plant and hummingbird communities

Marina Wolowski, Luísa G. Carvalheiro & Leandro Freitas
Understanding how ecological processes structure species assemblages is a central issue in community ecology. While the influence of plant–pollinator interactions on each other's evolution is well recognized, their role in the assembly of interdependent communities of plants and pollinators is still unclear. Using data from seven communities of hummingbirds and plants that they pollinate from two tropical rain forest types (lowland and montane), we evaluated phylogenetic relationships and signal of functional traits, over space and...

Data from: Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

Pauline Charruau, Carlos Fernandes, Pablo Orozco-TerWengel, Joris Peters, Luke Hunter, H. Ziaie, A. Jourabchian, H. Jowkar, Georges Schaller, Stephane Ostrowski, Paul Vercammen, Thierry Grange, Christian Schlötterer, Antoinette Kotze, Eva-Maria Geigl, Chris Walzer & Pamela A. Burger
The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between...

Data from: Structure and functioning of intertidal food webs along an avian flyway: a comparative approach using stable isotopes

Teresa Catry, Pedro M. Lourenço, Ricardo J. Lopes, Camilo Carneiro, José A. Alves, Joana Costa, Hamid Rguibi-Idrissi, Stuart Bearhop, Theunis Piersma & José P. Granadeiro
Food webs and trophic dynamics of coastal systems have been the focus of intense research throughout the world, as they prove to be critical in understanding ecosystem processes and functions. However, very few studies have undertaken a quantitative comparison of entire food webs from a key consumer perspective across a broad geographical area, limiting relevant comparisons among systems with distinct biotic and abiotic components. We investigate the structure and functioning of food webs in four...

Data from: An expanded molecular phylogeny of Plumbaginaceae, with emphasis on Limonium (sea lavenders): taxonomic implications and biogeographic considerations

Konstantina Koutroumpa, Spyros Theodoridis, Ben H. Warren, Ares Jiménez, Ferhat Celep, Musa Doğan, Maria M. Romeiras, Arnoldo Santos-Guerra, José María Fernández-Palacios, Juli Caujapé-Castells, Mónica Moura, Miguel M. Sequeira, Elena Conti & Miguel Menezes De Sequeira
Plumbaginaceae is characterized by a history of multiple taxonomic rearrangements and lacks a broad molecular phylogenetic framework. Limonium is the most species‐rich genus of the family with ca. 600 species and cosmopolitan distribution. Its center of diversity is the Mediterranean region, where ca. 70% of all Limonium species are endemic. In this study, we sample 201 Limonium species covering all described infrageneric entities and spanning its wide geographic range, along with 64 species of other...

Data from: Changes in melanocyte RNA and DNA methylation favor pheomelanin synthesis and may avoid systemic oxidative stress after dietary cysteine supplementation in birds

Sol Rodríguez-Martínez, Rafael Márquez, Ângela Inácio & Ismael Galván
Cysteine plays essential biological roles, but excessive amounts produce cellular oxidative stress. Cysteine metabolism is mainly mediated by the enzymes cysteine dioxygenase and γ-glutamylcysteine synthetase, respectively coded by the genes CDO1 and GCLC. Here we test a new hypothesis posing that the synthesis of the pigment pheomelanin also contributes to cysteine homeostasis in melanocytes, where cysteine can enter the pheomelanogenesis pathway. We conducted a experiment in the Eurasian nuthatch Sitta europaea, a bird producing large...

Data from: How much starvation, desiccation and oxygen depletion can Drosophila melanogaster tolerate before its upper thermal limits are affected?

Tommaso Manenti, Tomás Rocha Cunha, Jesper Givskov Sørensen & Volker Loeschcke
Heat tolerance is commonly assessed as the critical thermal maximum (CTmax) using the dynamic method exposing organisms to a gradually increasing (ramping) temperature until organisms fall into a coma. The CTmax estimate is dependent on the ramping rate, with decreased rates leading to longer treatments and ultimately lower CTmax estimates. There is a current discussion surrounding the physiological dynamics of the effect of the time of exposure by temperature interaction on these estimates. Besides temperature...

Data from: Does sex matter? Gender-specific responses to forest fragmentation in Neotropical bats

Ricardo Rocha, Diogo F. Ferreira, Adrià López-Baucells, Fabio Z. Farneda, Joao M.B. Carreiras, Jorge M. Palmeirim & Christoph F. J. Meyer
Understanding the consequences of habitat modification on wildlife communities is central to the development of conservation strategies. However, albeit male and female individuals of numerous species are known to exhibit differences in habitat use, sex-specific responses to habitat modification remain little explored. Here, we used a landscape-scale fragmentation experiment to assess, separately for males and females, the effects of fragmentation on the abundance of Carollia perspicillata and Rhinophylla pumilio, two widespread Neotropical frugivorous bats. We...

Data from: Dispersal and group formation dynamics in a rare and endangered temperate forest bat (Nyctalus lasiopterus, Chiroptera: Vespertilionidae)

João D. Santos & Christoph F. J. Meyer
For elusive mammals like bats, colonization of new areas and colony formation are poorly understood, as is their relationship with the genetic structure of populations. Understanding dispersal and group formation behaviors is critical not only for a better comprehension of mammalian social dynamics, but also for guiding conservation efforts of rare and endangered species. Using nuclear and mitochondrial markers, we studied patterns of genetic diversity and differentiation among and within breeding colonies of giant noctule...

Data from: Evolution of mating behaviour between two populations adapting to common environmental conditions

Margarida Bárbaro, Mário S. Mira, Inês Fragata, Pedro Simões, Margarida Lima, Miguel Lopes-Cunha, Bárbara Kellen, Josiane Santos, Susana A. M. Varela, Margarida Matos & Sara Magalhães
Populations from the same species may be differentiated across contrasting environments, potentially affecting reproductive isolation among them. When such populations meet in a novel common environment, this isolation may be modified by biotic or abiotic factors. Curiously, the latter have been overlooked. We filled this gap by performing experimental evolution of three replicates of two populations of Drosophila subobscura adapting to a common laboratorial environment, and simulated encounters at three time points during this process....

Data from: Incipient allochronic speciation in the pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

Helena Santos, Christian Burban, Jerome Rousselet, Jean-Pierre Rossi, Manuela Branco & Carole Kerdelhué
A plausible case of allochronic differentiation, where barrier to gene flow is primarily due to a phenological shift, was recently discovered in Portugal for the pine processionary moth Thaumetopoea pityocampa. Previous results suggested that the observed "summer population" (SP) originated from the sympatric winter population (WP). Our objectives were to finely analyse these patterns and test their stability in time, through field monitoring and genetic analyses of larvae and adults across different years. Reproductive activity...

Data from: Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs

Jennifer Firn, James M. McGree, Eric Harvey, Habacuc Flores-Moreno, Martin Schütz, Yvonne M. Buckley, Elizabeth T. Borer, Eric W. Seabloom, Kimberly J. La Pierre, Andrew M. MacDougall, Suzanne M. Prober, Carly J. Stevens, Lauren L. Sullivan, Erica Porter, Emma Ladouceur, Charlotte Allen, Karine H. Moromizato, John W. Morgan, W. Stanley Harpole, Yann Hautier, Nico Eisenhauer, Justin P. Wright, Peter B. Adler, Carlos Alberto Arnillas, Jonathan D. Bakker … & Anita C. Risch
Leaf traits are frequently measured in ecology to provide a ‘common currency’ for predicting how anthropogenic pressures impact ecosystem function. Here, we test whether leaf traits consistently respond to experimental treatments across 27 globally distributed grassland sites across 4 continents. We find that specific leaf area (leaf area per unit mass)—a commonly measured morphological trait inferring shifts between plant growth strategies—did not respond to up to four years of soil nutrient additions. Leaf nitrogen, phosphorus...

Data from: Drivers of power line use by white storks: a case study of birds nesting on anthropogenic structures

Francisco Moreira, Ricardo C. Martins, Ines Catry & Marcello D'Amico
1. Anthropogenic structures are mainly known to have negative impacts on wildlife populations but sometimes arethey can be beneficial. Power lines are a main driver of bird mortality through collision or electrocution, but electricity pylons are also commonly used for nest building by some species. Birds and nests cause power outages that need to be tackled by electricity companies. However, the use of pylons by threatened species provides an opportunity for conservation purposes. 2. In...

Data from: Selection on structural allelic variation biases plasticity estimates

Mauro Santos, Margarida Matos, Sheng Pei Wang & David M Althoff
Wang and Althoff (2019) explored the capacity of Drosophila melanogaster to exhibit adaptive plasticity in a novel environment. In a full-sib, half-sib design, they scored the activity of the enzyme alcohol dehydrogenase (ADH) and plastic responses, measured as changes in ADH activity across ethanol concentrations in the range of 0-10% (natural variation) and 16% (the novel environment). ADH activity increased with alcohol concentration, and there was a positive association between larval viability and ADH activity...

Data from: An holistic ecological analysis of the diet of Cory’s shearwaters using prey morphological characters and DNA barcoding

Hany Alonso, José Pedro Granadeiro, Silke Waap, José Xavier, William O. C. Symondson, Jaime A. Ramos & Paulo Catry
Knowledge of the dietary choices and trophic niches of organisms is the key to understanding their roles in ecosystems. In seabird diet studies, prey identification is a difficult challenge, often yielding results with technique-specific biases. Additionally, sampling efforts are often not extensive enough to reveal intra-populational variation. Immature animals, which may constitute up to 50% of a population, may occupy a significantly different trophic niche to more-experienced birds, but this remains largely unexplored. We investigated...

Data from: Semi-permeable species boundaries in Iberian barbels (Barbus and Luciobarbus, Cyprinidae)

Hugo F. Gante, Ignacio Doadrio, Maria Judite Alves & Thomas E. Dowling
Background: The evolution of species boundaries and the relative impact of selection and gene flow on genomic divergence are best studied in populations and species pairs exhibiting various levels of divergence along the speciation continuum. We studied species boundaries in Iberian barbels, Barbus and Luciobarbus, a system of populations and species spanning a wide degree of genetic relatedness, as well as geographic distribution and range overlap. We jointly analyze multiple types of molecular markers and...

Data from: Mauritius on fire: tracking historical human impacts on biodiversity loss

William D. Gosling, Jona De Kruif, Sietze J. Norder, Erik J. De Boer, Henry Hooghiemstra, Kenneth F. Rijsdijk, Crystal N.H. McMichael & Crystal N. H. McMichael
Fire was rare on Mauritius prior to human arrival (AD 1598); subsequently three phases of elevated fire activity occurred: c. 1630-1747, 1787-1833, and 1950-modern. Elevated fire frequency coincided with periods of high human impact evidenced from the historical record, and is linked to the extinction of island endemics.

European Database of Seismogenic Faults (EDSF)

Roberto Basili, Vanja Kastelic, Mine Betül Demircioglu, David Garcia Moreno, Eliza S. Nemser, Patrizio Petricca, Sotiris P. Sboras, Glenda M. Besana-Ostman, João Cabral, Thierry Camelbeeck, Riccardo Caputo, Laurentiu Danciu, Hilal Domaç, João Filipe de Barros Duarte Fonseca, Julián García-Mayordomo, Domenico Giardini, Branislav Glavatovic, Levent Gulen, Yigit Ince, Spyros Pavlides, Karin Sesetyan, Gabriele Tarabusi, Mara Monica Tiberti, Murat Utkucu, Gianluca Valensise … & Jochen Wössner
The European Database of Seismogenic Faults (EDSF) was compiled in the framework of the EU Project SHARE, Work Package 3, Task 3.2. EDSF includes only faults that are deemed to be capable of generating earthquakes of magnitude equal to or larger than 5.5 and aims at ensuring a homogenous input for use in ground-shaking hazard assessment in the Euro-Mediterranean area. Several research institutions participated in this effort with the contribution of many scientists (see the...

Data from: Temperature niche shift observed in a Lepidoptera population under allochronic divergence

Helena Santos, Maria Rosa Paiva, Catarina Tavares, Carole Kerdelhué & Manuela Branco
A process of adaptive divergence for tolerance to high temperatures was identified by using a rare model-system, consisting of two sympatric populations of a Lepidoptera (Thaumetopoea pityocampa) with different life-cycle timings, a "mutant" population with summer larval development, Leiria SP, and the founder natural population, having winter larval development, Leiria WP. A third, allopatric population (Bordeaux WP) was also studied. First and second instar larvae were experimentally exposed to daily-cycles of heat treatment reaching maximum...

Data from: Population divergence with or without admixture: selecting models using an ABC approach

Vitor C. Sousa, Mark A. Beaumont, Pedro Fernandes, Maria M. Coelho, Lounès Chikhi, M A Beaumont, P Fernandes, V C Sousa, L Chikhi & M M Coelho
Genetic data have been widely used to reconstruct the demographic history of populations, including the estimation of migration rates, divergence times and relative admixture contribution from different populations. Recently, increasing interest has been given to the ability of genetic data to distinguish alternative models. One of the issues that has plagued this kind of inference is that ancestral shared polymorphism is often difficult to separate from admixture or gene flow. Here, we applied an Approximate...

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