15 Works

Negative impacts of dominance on bee communities: Does the influence of invasive honey bees differ from native bees?

Lucas Alejandro Garibaldi, Lucas Garibaldi, Néstor Pérez-Méndez, Guaraci Cordeiro, Alice Hughes, Michael Orr, Isabel Alves Dos Santos, Breno Freitas, Favízia Freitas De Oliveira, Gretchen Lebuhn, Ignasi Bartomeus, Marcelo Aizen, Patricia Andrade, Betina Blochtein, Danilo Boscolo, Patricia Drumond, Maria Gaglianone, Barbara Gemmill-Herren, Rosana Halinski, Cristiane Krug, Marcia Maues, Lucia Piedade Kiill, Mardiore Pinheiro, Carmen Pires & Blandina Felipe Viana
Invasive species can reach high abundances and dominate native environments. One of the most impressive examples of ecological invasions is the spread of the African sub-species of the honey bee throughout the Americas, starting from its introduction in a single locality in Brazil. The invasive honey bee is expected to more negatively impact bee community abundance and diversity than native dominant species, but this has not been tested previously. We developed a comprehensive and systematic...

Data from: The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity

E. Bianco, H. W. Soto, L. Vargas & M. Perez-Enciso
The history of domestic species and of their wild ancestors is not a simple one, and feral processes can clarify key aspects of this history, including the adaptive processes triggered by new environments. Here, we provide a comprehensive genomic study of Isla del Coco (Costa Rica) feral pigs, a unique population that was allegedly founded by two individuals and has remained isolated since 1793. Using SNP arrays and genome sequencing, we show that Cocos pigs...

Data from: Characterization of stress coping style in Senegalese sole (Solea senegalensis) juveniles and breeders for aquaculture

Z. Ibarra-Zatarain, Elvira Fatsini, Sonia Rey, Olvido Chereguini, Ignacio Martin, Inmaculada Rasines, Carles Alcaraz & Neil Duncan
The aim of this work was to characterize stress coping styles of Senegalese sole (Solea senegalensis) juveniles and breeders and to select an operational behavioural screening test (OBST) that can be used by the aquaculture industry to classify and select between behavioural phenotypes in order to improve production indicators. A total of 61 juveniles and 59 breeders were subjected to five individual behavioural tests and two grouping tests. At the end of the individual tests,...

Data from: Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods

Josep Piñol, Gisela Mir, Priscila Gomez-Polo & Nuria Agusti
The quantification of the biological diversity in environmental samples using high-throughput DNA sequencing is hindered by the PCR bias caused by variable primer–template mismatches of the individual species. In some dietary studies, there is the added problem that samples are enriched with predator DNA, so often a predator-specific blocking oligonucleotide is used to alleviate the problem. However, specific blocking oligonucleotides could coblock nontarget species to some degree. Here, we accurately estimate the extent of the...

Fruit abundance and trait matching determine diet type and body condition across frugivorous bird populations

Juan P. González-Varo, Alejandro Onrubia, Néstor Pérez-Méndez, Rubén Tarifa & Juan C. Illera
Research on seed-dispersal mutualisms has been highly unbalanced towards the plants, largely overlooking the fitness effects of fruit resources on frugivorous animals. Moreover, despite morphological mismatches like gape limitation may reduce the abundance of fruits that are actually accessible to a frugivore species, there is very little evidence on the trait-matching implications from a frugivore’s perspective. Here, we refine recent resource-provisioning models to comprehensively test the joint effects of fruit abundance and trait matching on...

Tropical South America Diatom Database (TSADB)

Xavier Benito
Determining the mechanisms of community assembly forms the foundation of biogeography and community ecology. Studies of the biodiversity and distribution of Neotropical macro-organisms have revealed the roles of environmental, spatial, and historical factors in structuring communities at different spatial and temporal scales, but the role of these factors play for species and communities on microorganisms are still poorly known. Diatoms are a very species-rich group of algae, disperse widely, and sensitive to environmental variation due...

Data from: A collection of European sweet cherry phenology data for assessing climate change

Bénédicte Wenden, José Antonio Campoy, Julien Lecourt, Gregorio López Ortega, Michael Blanke, Sanja Radičević, Elisabeth Schüller, Andreas Spornberger, Danilo Christen, Hugo Magein, Daniela Giovannini, Carlos Campillo, Svetoslav Malchev, José Miguel Peris, Mekjell Meland, Rolf Stehr, Gérard Charlot & José Quero-García
Professional and scientific networks built around the production of sweet cherry (Prunus avium L.) led to the collection of phenology data for a wide range of cultivars grown in experimental sites characterized by highly contrasted climatic conditions. We present a dataset of flowering and maturity dates, recorded each year for one tree when available, or the average of several trees for each cultivar, over a period of 37 years (1978 - 2015). Such dataset is...

Data from: Impacts of urbanization on insect herbivory and plant defences in oak trees

Xoaquín Moreira, Luis Abdala-Roberts, Jorge Berny Mier C. Y Terán, Felisa Covelo, Raúl De La Mata, Marta Francisco, Bess Hardwick, Ricardo M. Pires, Tomas Roslin, Dmitry S. Schigel, Jan P.J.G. Ten Hoopen, Bart G.H. Timmermans, Laura J.A. Van Dijk, Bastien Castagneyrol, Ayco J.M. Tack, Jorge C. Berny Mier Y Teran, Laura J. A. Van Dijk & Ayco J. M. Tack
Systematic comparisons of species interactions in urban vs. rural environments can improve our understanding of shifts in ecological processes due to urbanization. However, such studies are relatively uncommon and the mechanisms driving urbanization effects on species interactions (e.g., between plants and insect herbivores) remain elusive. Here we investigated the effects of urbanization on leaf herbivory by insect chewers and miners associated with the English oak (Quercus robur) by sampling trees in rural and urban areas...

Data from: Herbivore control in connected seascapes: habitat determines when population regulation occurs in the life history of a key herbivore

Jordi Boada, Simone Farina, Rohan Arthur, Javier Romero, Patricia Prado & Teresa Alcoverro
Herbivore outbreaks often trigger catastrophic overgrazing events in marine macrophyte ecosystems. The sea urchin Paracentrotus lividus, the dominant herbivore of shallow Mediterranean seascapes, is capable of precipitating shifts to barrens when its populations explode. P. lividus is found ubiquitously in rocky macroalgal communities and in sandy seagrass meadows of Posidonia oceanica, two of the most important subtidal habitats in the Mediterranean. We explored if habitat-specific regulation across the principal stages of the urchin life cycle...

Hazelnut SSR database: genetic profiles of the accessions, list of synonyms, and true-to-type genotypes

Paolo Boccacci, Maria Aramini, Matthew Ordidge, Theo Van Hintum, Daniela Torello Marinoni, Nadia Valentini, Jean-Paul Sarraquigne, Anita Solar, Mercè Rovira, Loretta Bacchetta & Roberto Botta
Hazelnut (Corylus avellana L.) is one of the most important tree nut crops in Europe. Germplasm accessions are conserved in ex situ repositories, located in countries where hazelnut production occurs. In this work, we used ten simple sequence repeat (SSR) markers as the basis to establish a core collection representative of the hazelnut genetic diversity conserved in different European collections. A total of 480 accessions were used: 430 from ex situ collections and 50 landraces...

Data from: Molecular and morphological diversity of on-farm hazelnut (Corylus avellana L.) landraces from southern Europe and their role in the origin and diffusion of cultivated germplasm

P. Boccacci, M. Aramini, N. Valentini, L. Bacchetta, M. Rovira, P. Drogoudi, A. P. Silva, A. Solar, F. Calizzano, V. Erdoğan, V. Cristofori, L. F. Ciarmiello, C. Contessa, J. J. Ferreira, F. P. Marra & R. Botta
Hazelnut (Corylus avellana L.) is a traditional nut crop in southern Europe. Germplasm exploration conducted on-farm in five countries (Portugal, Spain, Italy, Slovenia, and Greece) identified 77 landraces. The present work describes phenotypic variation in nut and husk traits and investigates genetic relationships using 10 simple sequence repeat (SSR) markers among these landraces, 57 well-known references cultivars, and 19 wild accessions. Among the 77 landraces, 42 had unique fingerprints while 35 showed a SSR profile...

Data from: Soil microclimate changes affect soil fungal communities in a Mediterranean pine forest

Carles Castaño, Björn D. Lindahl, Josu G. Alday, Andreas Hagenbo, Juan Martínez De Aragón, Javier Parladé, Joan Pera & José Antonio Bonet
• Soil microclimate is a potentially important regulator of the composition of plant-associated fungal communities in climates with significant drought periods. Here, we investigated spatio-temporal dynamics of soil fungal communities in a Mediterranean Pinus pinaster forest in relation to soil moisture and temperature. • Fungal communities in 336 soil samples collected monthly during a year from 28 long-term experimental plots were assessed by PacBio sequencing of ITS2 amplicons. Total fungal biomass was estimated by analysing...

Data from: Urbanization affects oak–pathogen interactions across spatial scales

Laura Van Dijk, Xoaquin Moreira, Anna Barr, Luis Abdala-Roberts, Bastien Castagneyrol, Maria Faticov, Bess Hardwick, Jan Ten Hoopen, Raul De La Mata, Ricardo Matheus Pires, Tomas Roslin, Dmitry Schigel, Bart Timmermans & Ayco Tack
The world is rapidly urbanizing, thereby transforming natural landscapes and changing the abundance and distribution of organisms. However, insights into the effects of urbanization on species interactions, and plant-pathogen interactions in particular, are lacking. We investigated the effects of urbanization on powdery mildew infection on Quercus robur at continental and within-city scales. At the continental scale, we compared infection levels between urban and rural areas of different-sized cities in Europe, and investigated whether plant traits,...

Guidelines to apply for ethical approval of animal experiments

Jan Langbein, Mette Herskin, Frédéric Dehareng, Emer Kennedy, Kenny Rutherford, Antonio Velarde, Véronique Deiss & Isabelle Veissier
This chapter presents common aspects applying in all EU Member States and in the UK (since Directive 2010/63/EU was transposed into British law before Brexit), and gives the specifications that apply in each research institute of the SmartCow project.

Validation of eating duration using an automatic feeding system

Emma Ternman, Marta Terré, Matthieu Bouchon, Bruno Meunier, Lene Munksgaard & Isabelle Veissier
Feed intake is important to consider when studying welfare, productivity and efficiency in ruminants, particularly cattle. Over the last decade, several methods for automatic intake recording have been developed. These methods have been described in the chapter on feed and water intake of the present book of methods. Automatic feed bins do not only record feed intake, but also feeding behaviour. The duration of feed bin visits estimated by the Insentec Roughage Intake Control system...

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