44 Works

Data from: Scale-dependent adaptive evolution and morphological convergence to climatic niche in Californian eriogonoids (Polygonaceae)

Anna Kostikova, Nicolas Salamin, Peter B. Pearman, Glenn Litsios, Sarah Burgy & Laura Milani
Aim: Macroevolutionary patterns and processes change substantially depending on levels of taxonomic and ecological organization, and the resolution of environmental and spatial variability. In comparative methods, the resolution of environmental and spatial variability often defines the number of selective regimes used to test whether phenotypic characteristics are adaptively correlated with the environment. Here, we examine how investigator choice of the number of selective regimes, determined by varying the resolution of among-species variability in the species...

Data from: Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing

Gregory Neils Puncher, Alessia Cariani, Gregory E. Maes, Jeroen Van Houdt, Koen Herten, Rita Cannas, Naiara Rodriguez-Ezpeleta, Aitor Albaina, M. Andone Estonba, Molly Lutcavage, Alex Hanke, Jay Rooker, James S. Franks, Joseph M. Quattro, Gualtiero Basilone, Igaratza Fraile, Urtzi Laconcha, Nicolas Goñi, Ai Kimoto, A. David Macías, Francisco Alemany, Simeon Deguara, Salem W. Zgozi, Fulvio Garibaldi, Isik K. Oray … & Fausto Tinti
The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species’ stock dynamics, a genome-wide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly...

Data from: Does functional soil microbial diversity contribute to explain within-site plant β-diversity in an alpine grassland and a dehesa meadow in Spain?

Yoseph N. Araya, Maik Bartelheimer, Cipriano J. Valle, Rosa M. Crujeiras & Gonzalo García-Baquero
Questions Once effects of hydrological and chemical soil properties have been accounted for, does soil microbial diversity contribute to explain change in plant community structure (i.e. within-site β-diversity)? If so, at what spatial scale does microbial diversity operate? Location La Mina in Moscosa Farm, Salamanca, western Spain (dehesa community) and Laguna Larga in the Urbión Peaks, Soria, central-northern Spain (alpine grassland). Methods The abundance of vascular plant species, soil Gram-negative microbial functional types and soil...

Data from: Genetic uniqueness of the Waorani tribe from the Ecuadorian Amazon

Laura Valverde, Maria Teresa Zarrabeitia, Adrian Odriozola, Marian Martínez De Pancorbo, Sergio Cardoso, Miguel Angel Alfonso-Sánchez, Dora Sánchez & Begoña Martínez-Jarreta
South America and especially the Amazon basin is known to be home to some of the most isolated human groups in the world. Here we report on a study of mitochondrial DNA (mtDNA) in the Waorani from Ecuador, probably the most warlike human population known to date. Seeking to look in more depth at the characterization of the genetic diversity of this Native American tribe, molecular markers from the X and Y chromosomes were also...

Data from: \"Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)\" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

Iratxe Montes, Jorge Langa, César Vilas, Sarah J. Helyar, Paula Álvarez, Darrell Conklin & Andone Estonba
This paper reports on SNP discovery in the Atlantic mackerel transcriptome, using next generation sequencing technologies and applying developed methodology already proven successful for the European anchovy. A total of 9,966 high quality transcriptome contigs were assembled, from which 951 putative SNPs were discovered. In all, 479 putative SNPs and 1,624 simple sequence repeats (SSRs) suitable for genotyping were identified. A subset of 96 was selected for genotyping; from these, 80 SNPs were considered polymorphic...

Data from: Determining diet from faeces: selection of metabarcoding primers for the insectivore Pyrenean desman (Galemys pyrenaicus)

Amaiur Esnaola, Aitor Arrizabalaga-Escudero, Jorge Gonzalez-Esteban, Arturo Elosegi & Joxerra Aihartza
Molecular techniques allow non-invasive dietary studies from faeces, providing an invaluable tool to unveil ecological requirements of endangered or elusive species. They contribute to progress on important issues such as genomics, population genetics, dietary studies or reproductive analyses, essential knowledge for conservation biology. Nevertheless, these techniques require general methods to be tailored to the specific research objectives, as well as to substrate- and species-specific constraints. In this pilot study we test a range of available...

Controls of chlorophyll fluorescence spectra vary among leaves in a boreal forest and over a spring recovery of photosynthesis

Paulina Rajewicz, Chao Zhang, Jon Atherton, Shari Van Wittenberghe, Anu Riikonen, Troy Magney, Beatriz Fernandez-Marin, Jose Ignacio Garcia Plazaola & Albert Porcar-Castell
Chlorophyll fluorescence can be used to track to seasonal dynamics of photosynthesis in boreal forests. However, the relationship between chlorophyll fluorescence and photosynthesis is affected by biochemical and morphological factors, which vary across time and space as a function of light environment, species, and environmental conditions. We investigated how various factors, and their spatio-temporal dynamics during spring recovery of photosynthesis in a boreal forest, affect spatio-temporal variation in chlorophyll fluorescence spectra. The factors under consideration...

Data from: Effects of spring temperatures on the strength of selection on timing of reproduction in a long-distance migratory bird

Marcel E. Visser, Phillip Gienapp, Arild Husby, Michael Morrisey, Iván De La Hera, Francisco Pulido & Christiaan Both
Climate change has differentially affected the timing of seasonal events for interacting trophic levels, and this has often led to increased selection on seasonal timing. Yet, the environmental variables driving this selection have rarely been identified, limiting our ability to predict future ecological impacts of climate change. Using a dataset spanning 31 years from a natural population of pied flycatchers (Ficedula hypoleuca), we show that directional selection on timing of reproduction intensified in the first...

Data from: Grazing exclusion unleashes competitive plant responses in Iberian Atlantic mountain grasslands

Iñaki Odriozola, Gonzalo García-Baquero, Marie-Josée Fortin, Nere Amaia Laskurain & Arantza Aldezabal
Questions: Does the absence of equalizing mechanisms after cessation of grazing unleash strong aboveground competitors to create large patches in the community? Do these competitive intraspecific aggregations displace and exclude other species, thereby reducing species diversity? Location: Atlantic grasslands in the Aralar Natural Park, Basque Country, Northern Iberian Peninsula. Methods: Large herbivores were experimentally excluded from three sites (50 m × 50 m exclusion fences) during nine years in a productive semi-natural grassland system with...

Data from: \"Diagnostic SNPs for inferring population structure in American mink (Neovison vison) identified through RAD sequencing\" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014

Janne Pia Thirstrup, Aritz Ruiz-Gonzalez, Jose Martin Pujolar, Peter Foged Larsen, Rasmus O. Nielsen, Ettore Randi, Andrzej Zalewski, Cino Pertoldi, Mariella Baratti, Tiziana Di Lorenzo, Alessio Iannucci, Diana Maria Paola Galassi, Valentina Iannilli, Just Jensen, Dragos Postolache & Giovanni Giuseppe Vendramin
The article documents the public availability of RAD sequencing data and generated SNPs for the American mink (Neovison vison). 224,095 polymorphic loci were identified from 14 mink from which primers were designed for a subset of 380 SNPs. The panel was tested on 211 mink. Fisher’s F-statistics (Fis, FIT and FST) as well as observed (HO), expected (HE) and unbiased expected (uHE) heterozygosity was calculated for the SNPs and 194 SNPs was validated as being...

Data from: The effects of pastoral intensification on the feeding interactions of generalist predators in streams

Caitlin E. Pearson, William O.C. Symondson, Elizabeth L. Clare, Steve J. Ormerod, Esther Iparraguirre Bolaños & Ian P. Vaughan
Land use change can alter trophic interactions with wide-ranging functional consequences, yet the consequences for aquatic food webs have been little-studied. In part, this may reflect the challenges of resolving the diets of aquatic organisms using classical gut contents analysis, especially for soft-bodied prey. We used next generation sequencing to resolve prey use in nearly 400 individuals of two predatory invertebrates (the Caddisfly, Rhyacophila dorsalis, and the Stonefly Dinocras cephalotes) in streams draining land with...

Data from: \"De novo assembled transcriptome of organs involved in reproduction in an endangered endemic Iberian cyprinid fish (Squalius pyrenaicus)\" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

Miguel P. Machado, Joana Pinho, Ana R. Grosso, Manfred Schartl, Maria M. Coelho, C. Vilas, Wolfgang Arthofer, Alexander Rief, Birgit C. Schlick-Steiner, Julia Seeber, Florian M. Steiner, D. Conklin, A. Estonba, J. Langa & I. Montes
Sex determination systems are diverse, especially among fish, and include genetic and/or environmental components. Unexpectedly for such a basic aspect of development, sex determination systems change rapidly during evolution and gonadal fate is not ultimate, being actively maintained lifelong. Here, sequences of expressed genes involved in maintenance of gonad identity and reproduction processes were obtained through transcriptome assembly of the brain-gonadal axis tissues of a freshwater fish inhabiting highly variable environments, the gonochoristic Iberian fish...

Data from: Wood-inhabiting fungi with tight associations with other species have declined as a response to forest management

Nerea Abrego, David Dunson, Panu Halme, Isabel Salcedo & Otso Ovaskainen
Research on mutualistic and antagonistic networks, such as plant–pollinator and host–parasite networks, has shown that species interactions can influence and be influenced by the responses of species to environmental perturbations. Here we examine whether results obtained for directly observable networks generalize to more complex networks in which species interactions cannot be observed directly. As a case study, we consider data on the occurrences of 98 wood-inhabiting fungal species in managed and natural forests. We specifically...

Physiology and acclimation potential are tuned with phenology in larvae of a prolonged breeder amphibian

Urtzi Enriquez-Urzelai, Alfredo G. Nicieza, Albert Montori, Gustavo A. Llorente & Miren Bego Urrutia
Due to the speed of climate changes, rapid buffering mechanisms such as phenotypic plasticity – which may depend on breeding phenology – could be key to avoid extinction. The links between phenology and plasticity, however, remain understudied. Here we explored the matching between phenology and the thermal sensitivity of standard (SMR) and routine metabolic rates (RMR), metabolic scope (i.e. the difference between RMR and SMR), survival and growth-development trajectories in larvae of a prolonged breeder...

Data from: Isolation by distance, resistance and/or clusters? Lessons learned from a forest-dwelling carnivore inhabiting a heterogeneous landscape

Aritz Ruiz-González, Samuel A. Cushman, María José Madeira, Benjamín J. Gómez-Moliner & Ettore Randi
Landscape genetics provides a valuable framework to understand how landscape features influence gene flow and to disentangle the factors that lead to discrete and/or clinal population structure. Here, we attempt to differentiate between these processes in a forest-dwelling small carnivore [European pine marten (Martes martes)]. Specifically, we used complementary analytical approaches to quantify the spatially explicit genetic structure and diversity and analyse patterns of gene flow for 140 individuals genotyped at 15 microsatellite loci. We...

Data from: A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo

Aiko Higashi, Satoshi Nagai, Sergio Seone & Shoko Ueki
Geographic distributions of phytoplankton species can be defined by events on both evolutionary time and shorter scales, e.g., recent climate changes. Additionally, modern industrial activity, including the transport of live fish and spat for aquaculture and aquatic microorganisms in ship ballast water, may aid the spread of phytoplankton. Obtaining a reliable marker is key to gaining insight into the phylogeographic history of a species. Here, we report a hypervariable mitochondrial gene in the cosmopolitan bloom-forming...

Data from: Morphological variation as a tool for monitoring bird populations: a review

José Luis Tellería, Iván De La Hera & Javier Perez-Tris
This paper shows how our knowledge of the evolution, ecology and conservation of birds can be improved through the analysis of external morphological traits. After giving a short history of morphological studies of birds, we discuss the pros and cons of such data in exploring within-species variation and describe the main patterns and hypotheses related to the factors affecting bird size and shape. We describe the usefulness of external measurements (including body mass and feather...

Data from: Assessing niche partitioning of co-occurring sibling bat species by DNA metabarcoding

Aitor Arrizabalaga-Escudero, Elizabeth L. Clare, Egoitz Salsamendi, Antton Alberdi, Inazio Garin, Joxerra Aihartza & Urtzi Goiti
Niche partitioning through foraging is a mechanism likely involved in facilitating the coexistence of ecologically similar and co-occurring animal species by separating their use of resources. Yet, this mechanism is not well understood in flying insectivorous animals. This is particularly true of bats, where many ecologically similar or cryptic species coexist. The detailed analysis of the foraging niche in sympatric, cryptic sibling species provides an excellent framework to disentangle the role of specific niche factors...

Data from: The leaf economic and plant size spectra of European forest understory vegetation

Josep Padullés Cubino, Idoia Biurrun, Gianmaria Bonari, Tatiana Braslavskaya, Xavier Font, Ute Jandt, Florian Jansen, Valerijus Rašomavičius, Wolfgang Willner & Milan Chytrý
Forest understories play a vital role in ecosystem functioning and the provision of ecosystem services. However, the extent to which environmental conditions drive dominant ecological strategies in forest understories at the continental scale remains understudied. Here, we used ~29,500 forest vegetation plots sampled across Europe and classified into 25 forest types to explore the relative role of macroclimate, soil pH, and tree canopy cover in driving abundance-weighted patterns in the leaf economic spectrum (LES) and...

Data from: Testing macroecological abundance patterns: the relationship between local abundance and range size, range position and climatic suitability among European vascular plants

Maria Sporbert, Petr Keil, Gunnar Seidler, Helge Bruelheide, Ute Jandt, Svetlana Aćić, Idoia Biurrun, Juan Antonio Campos, Andraž Čarni, Milan Chytrý, Renata Custerevska, Jürgen Dengler, Valentin Golub, Florian Jansen, Anna Kuzemko, Jonathan Lenoir, Corrado Marcenò, Jesper Erenskjold Moeslund, Aaron Pérez-Haase, Solvita Rūsiņa, Urban Šilc, Ioannis Tsiripidis, Vigdis Vandvik, Kiril Vassilev, Risto Virtanen … & Erik Welk
Aim: A fundamental question in macroecology centres around understanding the relationship between species’ local abundance and their distribution in geographic and climatic space (i.e. the multi-dimensional climatic space or climatic niche). Here, we tested three macroecological hypotheses that link local abundance to the following range properties: (1) the abundance-range size relationship, (2) the abundance-range centre relationship, and (3) the abundance-suitability relationship. Location: Europe Taxon: Vascular plants Methods: Distribution range maps were extracted from the Chorological...

Type of broadleaf forest matters most for ptyctimous mite communities (Acari, Oribatida) in Norway

Anna Seniczak, Wojciech Niedbała, J. Carlos Iturrondobeitia, Stanisław Seniczak, Steffen Roth & Bjarte H. Jordal
We studied ptyctimous moss mites, which are characteristic of forest habitats, in Norwegian broadleaf forests considered as biodiversity hotspot areas in Fennoscandia. The study aimed to evaluate the effect of different factors (regional locality, annual precipitation, mean annual temperature, forest type, forest wetness and microhabitat) on the ptyctimous mites and on discovering their richness in broadleaf forests. Samples were collected from nine broadleaf forests in western, southern and eastern Norway, in different climatic conditions, six...

Dataset for estimation of the biotic and climatic niche breadths and geographic range size of beech (Fagus) species worldwide

Qiong Cai, Erik Welk, Chengjun Ji, Wenjing Fang, Francesco Maria Sabatini, Jianxiao Zhu, Jiangling Zhu, Zhiyao Tang, Fabio Attorre, Juan Antonio Campos, Andraž Čarni, Milan Chytrý, Süleyman Çoban, Jürgen Dengler, Jiri Dolezal, Richard Field, József Pál Frink, Hamid Gholizadeh, Adrian Indreica, Ute Jandt, Dirk Nikolaus Karger, Jonathan Lenoir, Robert K. Peet, Remigiusz Pielech, Michele De Sanctis … & Helge Bruelheide
This dataset could be used to test whether the commonly observed positive range size–niche breadth relationship, as posited by the “niche breadth hypothesis”, exists for Fagus, one of the most dominant and widespread broad‐leaved deciduous tree genera in temperate forests of the Northern Hemisphere. There are many ways to estimate niche breadth. Here, we estimated biotic and climatic niche breadths per species using plot‐based co‐occurrence data and climate data, respectively. The range sizes of the...

Exposure to the Covid-19 pandemic and generosity in Spain

Diego Andrés Jorrat, Pablo Brañas-Garza, Antonio Alfonso, Teresa García Muñoz, Jaromir Kovarik & Antonio Espín
We report data from an online experiment, which allow us to study how generosity has changed during the initial explosive growth of the Covid-19 pandemic in Spain. We have gathered data from over a six-day period in which Covid-19-associated deaths in Spain, one of the most affected countries in the corresponding period, increased fourfold. In our experiment, participants could donate a fraction of a €100 prize to a charity. Our data are particularly rich in...

Data from: Dissecting the hydrological niche: soil moisture, space and lifespan

Gonzalo García-Baquero, Jonathan Silvertown, David J. Gowing & Cipriano J. Valle
Questions: Are communities structured on a hydrological (soil moisture) gradient? Is there spatial segregation into hydrological niches? What is the shape of the hydrological niches of individual species? Controlling for spatial autocorrelation, how much of the spatial structure in the community is due to variation in hydrology? Do annuals and perennials behave alike with respect to the above questions? Locations: La Mina in Moscosa Farm, Salamanca, western Spain (dehesa community) and Laguna Larga in the...

Data from: Patterns of species relatedness created by competitive exclusion depend on species niche differences: evidence from Iberian Atlantic grasslands

Iñaki Odriozola, Gonzalo Garcia-Baquero, Ana Etxeberria & Arantza Aldezabal
It is commonly assumed that closely related species share more similar niches than do distantly related species, thus limiting their ability to coexist and leading to patterns of phylogenetic over-dispersion. On the contrary, recent theoretical developments argue that competitive exclusion may lead to patterns of either over-dispersion, clustering or randomness, depending on the relative importance of niche differences and interspecific competitive ability differences. In this study, we utilized semi-natural grassland communities to test the hypothesis...

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  • 2012

Resource Types

  • Dataset


  • University of the Basque Country
  • Aarhus University
  • Ikerbasque
  • University of Picardie Jules Verne
  • University of Barcelona
  • Masaryk University
  • University of Helsinki
  • Martin Luther University Halle-Wittenberg
  • Swiss Institute of Bioinformatics
  • University of Sussex