92 Works

Data from: Genetic diversity in widespread species is not congruent with species richness in alpine plant communities

Pierre Taberlet, Niklaus E. Zimmermann, Thorsten Englisch, Andreas Tribsch, Rolf Holderegger, Nadir Alvarez, Harald Niklfeld, Zbigniew Mirek, Atte Moilanen, Wolfgang Ahlmer, Paolo Ajmone Marsan, Enzo Bona, Maurizio Bovio, Philippe Choler, Elżbieta Cieślak, Gheorghe Coldea, Licia Colli, Vasile Cristea, Jean-Pierre Dalmas, Božo Frajman, Luc Garraud, Myriam Gaudeul, Ludovic Gielly, Walter Gutermann, Nejc Jogan … & Karol Marhold
The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, i.e. ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesized to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning,...

Data from: The importance of naming cryptic species and the conservation of endemic subterranean amphipods

Teo Delić, Peter Trontelj, Michal Rendoš & Cene Fišer
Molecular taxonomy often uncovers cryptic species, reminding us that taxonomic incompleteness is even more severe than previous thought. The importance of cryptic species for conservation is poorly understood. Although some cryptic species may be seriously threatened or otherwise important, they are rarely included in conservation programs as most of them remain undescribed. We analysed the importance of cryptic species in conservation by scrutinizing the South European cryptic complex of the subterranean amphipod Niphargus stygius sensu...

Information-Seeking Behaviour of Slovenian Researchers: Implications for information services

Polona Vilar, Primož Južnič & Tomaz Bartol
The paper present one part of a survey of information behaviour of Slovenian researchers. Results show that Slovenian researchers in most areas show usual traits of scholarly information behaviour. Exceptions are the non-use of Web 2.0 tools for research purposes and low use of open-access materials. Survey confirmed that ICT is influential in preferences regarding resource formats, access, means for information exchange, organization of resources, writing, reading, etc. The use of grey literature is quite...

The interplay between habitat use, morphology and locomotion in subterranean crustaceans of the genus Niphargus

Simona Kralj-Fišer, Žiga Fišer, Ester Premate, Teja Vovk, Gabor Herczeg, Gergely Balázs, Denis Copilas-Ciocianu, Teo Delić & Cene Fišer
Locomotion is an important, fitness-related functional trait. Environment selects for type of locomotion and shapes the morphology of locomotion-related traits such as body size and appendages. In subterranean aquatic arthropods, these traits are subjected to multiple, at times opposing selection pressures. Darkness selects for enhanced mechano- and chemosensory systems and hence elongation of appendages. Conversely, water currents have been shown to favor short appendages. However, no study has addressed the variation in locomotion of invertebrates...

Red-green opponency in the long visual fibre photoreceptors of brushfoot butterflies (Nymphalidae)

Gregor Belušič, Marko Ilić, Primoz Pirih & Andrej Meglic
In many butterflies, the ancestral trichromatic insect colour vision, based on UV-, blue- and green-sensitive photoreceptors, is extended with red-sensitive cells. Physiological evidence for red receptors has been missing in Nymphalid butterflies, although some species can discriminate red hues well. In eight species from genera Archaeoprepona, Argynnis, Charaxes, Danaus, Melitaea, Morpho, Heliconius and Speyeria we found a novel class of green-sensitive photoreceptors that have hyperpolarising responses to stimulation with red light. These green-positive, red-negative (G+R–)...

Cross-continental comparison of parasite communities in a wide-ranging carnivore suggests associations with prey diversity and host density

Astrid Stronen, Barbara Molnar, Paolo Ciucci, Chris Darimont, Lorenza Grottoli, Paul Paquet, Tim Sallows, Judit Smits & Heather Bryan
Parasites are integral to ecosystem functioning yet often overlooked. Improved understanding of host-parasite associations is important, particularly for wide-ranging species for which host range shifts and climate change could alter host-parasite interactions and their effects on ecosystem function. Among the most widely distributed mammals with diverse diets, grey wolves (Canis lupus) host parasites that are transmitted among canids and via prey species. Grey wolf-parasite associations may therefore influence the population dynamics and ecological functions of...

Additional file 3 of Isolation and characterization of extracellular vesicles from biotechnologically important fungus Aureobasidium pullulans

Anja Černoša, Cene Gostinčar, Teja Lavrin, Rok Kostanjšek, Metka Lenassi & Nina Gunde-Cimerman
Additional file 3: The information of mil-RNAs apu-miR-1 and apu-miR-2 by miRDeep2.

Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study

Yan Liu, Polonca Štefanič, Youzhi Miao, Yansheng Xue, Weibing Xun, Nan Zhang, Qirong Shen, Ruifu Zhang, Zhihui Xu & Ines Mandic-Mulec
Abstract Bacillus is a genus of microorganisms (bacteria) and contains many important commercial species used in industry, agriculture and healthcare. Many different Bacilli are relatively well understood at the single-cell level; however, molecular tools that determine the diversity and ecology of Bacillus community are limited, which limits our understanding of how the Bacillus community works. In the present study, we investigated the potential of the housekeeping gene gyrA as a molecular marker for determining the...

Dissertations and Data

Joachim Schopfel, Primož Južnič, Helene Prost, Cécile Malleret, Ana Češarek & Teja Koler-Povh

Additional file 1 of Pan-cancer analysis of pre-diagnostic blood metabolite concentrations in the European Prospective Investigation into Cancer and Nutrition

Marie Breeur, Pietro Ferrari, Laure Dossus, Mazda Jenab, Mattias Johansson, Sabina Rinaldi, Ruth C. Travis, Mathilde His, Tim J. Key, Julie A. Schmidt, Kim Overvad, Anne Tjønneland, Cecilie Kyrø, Joseph A. Rothwell, Nasser Laouali, Gianluca Severi, Rudolf Kaaks, Verena Katzke, Matthias B. Schulze, Fabian Eichelmann, Domenico Palli, Sara Grioni, Salvatore Panico, Rosario Tumino, Carlotta Sacerdote … & Vivian Viallon
Additional file 1. Supplementary material regarding (i) the definition of cancer cases for HCC, GBC, Adv.PrC and Loc.PrC; (ii) the definition and implementation of the data-shared lasso; (iii) the models used to derive point estimates and confidence intervals from the model selected by the data-shared lasso; and (iv) the univariate analysis conducted for comparison.

Data from: Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches

Tomaž Skrbinšek, Maja Jelenčič, Lisette Waits, Ivan Kos, Klemen Jerina & Peter Trontelj
The effective population size (Ne) could be the ideal parameter for monitoring populations of conservation concern as it conveniently summarizes both the evolutionary potential of the population and its sensitivity to genetic stochasticity. However, tracing its change through time is difficult in natural populations. We applied four new methods for estimating Ne from a single sample of genotypes to trace temporal change in Ne for bears in the Northern Dinaric Mountains. We genotyped 510 bears...

Data from: Future ecosystem services from European mountain forests under climate change

Marco Mina, Harald Bugmann, Thomas Cordonnier, Florian Irauschek, Matija Klopcic, Marta Pardos & Maxime Cailleret
Ecosystem services (ES) from mountain forests are highly relevant for human societies. ES with a direct economic support function (e.g. timber production), regulatory services (e.g. protection from natural hazards) and cultural services (e.g. recreation) are likely to be affected strongly by a rapidly changing climate. To evaluate whether adverse climate change effects on ES can be counteracted by adapting management, dynamic models and indicator-based assessments are needed. We applied a forest dynamic model in case...

Data from: Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants

David Eme, Maja Zagmajster, Teo Delić, Cene Fiser, Jean-François Flot, Lara Konecny-Dupré, Snaebjorn Palsson, Fabio Stoch, Valerija Zakšek, Christophe J. Douady & Florian Malard
Ecologists increasingly rely on molecular delimitation methods (MMs) to identify species boundaries, thereby potentially increasing the number of putative species because of the presence of morphologically cryptic species. It has been argued that cryptic species could challenge our understanding of what determine large-scale biodiversity patterns which have traditionally been documented from morphology alone. Here, we used morphology and three MMs to derive four different sets of putative species among the European groundwater crustaceans. Then, we...

Data from: Quantifying natural disturbances using a large-scale dendrochronological reconstruction to guide forest management

Vojtěch Čada, Volodymyr Trotsiuk, Pavel Janda, Martin Mikolas, Radek Bace, Thomas Nagel, Robert Morrissey, Alan Tepley, Ondřej Vostarek, Krešimir Begović, Oleh Chaskovskyy, Martin Dušátko, Ondrej Kameniar, Daniel Kozák, Jana Lábusová, Jakub Málek, Peter Meyer, Joseph Pettit, Jonathan Schurman, Kristýna Svobodová, Michal Synek, Marius Teodosiu, Karol Ujházy & Miroslav Svoboda
Estimates of historical disturbance patterns are essential to guide forest management aimed at ensuring the sustainability of ecosystem functions and biodiversity. However, quantitative estimates of various disturbance characteristics required in management applications are rare in longer-term historical studies. Thus, our objectives were to: (1) quantify past disturbance severity, patch size, and stand proportion disturbed, and (2) test for temporal and sub-regional differences in these characteristics. We developed a comprehensive dendrochronological method to evaluate an approximately...

Grey Literature in Slovenia – Traditional is solved, what's next?

Primož Južnic
This paper presents the research done on the special libraries of institutions that are the biggest producers of grey literature in Slovenia. They were defined as the one that do not belong to the formal information and publishing industry (organisations (or individuals working for them) in industry, research institutes, museums and governmental agencies. The results of the research show how the long-term use and collaboration to the National Union bibliographic system prepared librarians and other...

Large carnivore expansion in Europe is associated with human population density and land cover changes

Marta Cimatti, Nathan Ranc, Ana Ana Benítez-López, Luigi Maiorano, Luigi Boitani, Francesca Cagnacci, Mirza Čengić, Paolo Ciucci, Mark Huijbregts, Miha Krofel, José López Bao, Nuria Selva, Henrik Andren, Carlos Bautista, Duško Cirovic, Heather Hemmingmoore, Ilka Reinhardt, Miha Marenče, Yorgos Mertzanis, Luca Pedrotti, Igor Trbojević, Andreas Zetterberg, Tomasz Zwijacz-Kozica & Luca Santini
Aim: The recent recovery of large carnivores in Europe has been explained as resulting from a decrease in human persecution driven by widespread rural land abandonment, paralleled by forest cover increase and the consequent increase in availability of shelter and prey. We investigated whether land cover and human population density changes are related to the relative probability of occurrence of three European large carnivores: the grey wolf (Canis lupus), the Eurasian lynx (Lynx lynx) and...

Data from: Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

Jenni Harmoinen, Alina Von Thaden, Jouni Aspi, Laura Kvist, Berardino Cocchiararo, Anne Jarausch, Andrea Gazzola, Teodora Sin, Hannes Lohi, Marjo Hytönen, Ilpo Kojola, Astrid Vik Stronen, Romolo Caniglia, Federica Mattucci, Marco Galaverni, Raquel Godinho, Aritz Ruiz-González, Ettore Randi, Violeta Muñoz-Fuentes & Carsten Nowak
Background: Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected...

Additional file 1 of Pan-cancer analysis of pre-diagnostic blood metabolite concentrations in the European Prospective Investigation into Cancer and Nutrition

Marie Breeur, Pietro Ferrari, Laure Dossus, Mazda Jenab, Mattias Johansson, Sabina Rinaldi, Ruth C. Travis, Mathilde His, Tim J. Key, Julie A. Schmidt, Kim Overvad, Anne Tjønneland, Cecilie Kyrø, Joseph A. Rothwell, Nasser Laouali, Gianluca Severi, Rudolf Kaaks, Verena Katzke, Matthias B. Schulze, Fabian Eichelmann, Domenico Palli, Sara Grioni, Salvatore Panico, Rosario Tumino, Carlotta Sacerdote … & Vivian Viallon
Additional file 1. Supplementary material regarding (i) the definition of cancer cases for HCC, GBC, Adv.PrC and Loc.PrC; (ii) the definition and implementation of the data-shared lasso; (iii) the models used to derive point estimates and confidence intervals from the model selected by the data-shared lasso; and (iv) the univariate analysis conducted for comparison.

Pan-cancer analysis of pre-diagnostic blood metabolite concentrations in the European Prospective Investigation into Cancer and Nutrition

Marie Breeur, Pietro Ferrari, Laure Dossus, Mazda Jenab, Mattias Johansson, Sabina Rinaldi, Ruth C. Travis, Mathilde His, Tim J. Key, Julie A. Schmidt, Kim Overvad, Anne Tjønneland, Cecilie Kyrø, Joseph A. Rothwell, Nasser Laouali, Gianluca Severi, Rudolf Kaaks, Verena Katzke, Matthias B. Schulze, Fabian Eichelmann, Domenico Palli, Sara Grioni, Salvatore Panico, Rosario Tumino, Carlotta Sacerdote … & Vivian Viallon
Abstract Background Epidemiological studies of associations between metabolites and cancer risk have typically focused on specific cancer types separately. Here, we designed a multivariate pan-cancer analysis to identify metabolites potentially associated with multiple cancer types, while also allowing the investigation of cancer type-specific associations. Methods We analysed targeted metabolomics data available for 5828 matched case-control pairs from cancer-specific case-control studies on breast, colorectal, endometrial, gallbladder, kidney, localized and advanced prostate cancer, and hepatocellular carcinoma nested...

Additional file 2 of Pan-cancer analysis of pre-diagnostic blood metabolite concentrations in the European Prospective Investigation into Cancer and Nutrition

Marie Breeur, Pietro Ferrari, Laure Dossus, Mazda Jenab, Mattias Johansson, Sabina Rinaldi, Ruth C. Travis, Mathilde His, Tim J. Key, Julie A. Schmidt, Kim Overvad, Anne Tjønneland, Cecilie Kyrø, Joseph A. Rothwell, Nasser Laouali, Gianluca Severi, Rudolf Kaaks, Verena Katzke, Matthias B. Schulze, Fabian Eichelmann, Domenico Palli, Sara Grioni, Salvatore Panico, Rosario Tumino, Carlotta Sacerdote … & Vivian Viallon
Additional file 2: Supplementary tables and figures. Figure S1. Pearson correlation between the 117 original metabolites. Figure S2. Sensitivity analyses of mutually adjusted ORs for the overall associations and cancer type-specific deviations. Figure S3. Sensitivity analysis of mutually adjusted ORs for the overall associations and cancer type-specific deviations with or without excluding hormone users. Figure S4. p-values of tests for departure from linearity and effect modification by BMI. Figure S5. ORs for the overall associations...

Tree growth response to drought partially explains regional-scale growth and mortality patterns in Iberian forests

Antonio Gazol, J. Julio Camarero, Raúl Sánchez-Salguero, Miguel A. Zavala, Xavier Serra-Maluquer, Emilia Gutiérrez, Martín De Luis, Gabriel Sangüesa-Barreda, Klemen Novak, Vicente Rozas, Pedro A. Tíscar, Juan C. Linares, Edurne Martínez Del Castillo, Montse Ribas, Ignacio García-González, Fernando Silla, Álvaro Camison, Mar Génova, José M. Olano, Ana-Maria Hereş, Jorge Curiel Yuste, Luis A. Longares, Andrea Hevia, J. Diego Galván & Paloma Ruiz-Benito
To quantify responses to drought from different data sources we take advantage of an extensive network of cross-dated tree-ring data with increment cores from 16 tree species sampled across the Spanish Iberian Peninsula (hereafter abbreviated as RWI-net), and of the Spanish National Forest Inventory (hereafter abbreviated as NFI) sampling tree and plot level data each km in forested areas. We selected the five most severe droughts that have affected each selected RWI-net population in the...

Opponent processing in the retinal mosaic of nymphalid butterflies

Gregor Belušič, Primož Pirih, Marko Ilić & Andrej Meglič
The eyes of nymphalid butterflies, investigated with incident illumination, show colourful facet reflection patterns, the eye shine, which is uniform or heterogeneous, dependent on the species. Facet colours suggest that the ommatidia contain different sets of photoreceptors and screening pigments, but how the colours and the cell characteristics are associated has not been clearly established. Here we analyse the retinae of two nymphalids, Apatura ilia, which has a uniform eyeshine, and Charaxes jasius, a species...

Timing and synchrony of birth in Eurasian lynx across Europe

Jenny Mattisson, John D.C. Linnell, Ole Anders, Elisa Belotti, Christine Breitenmoser-Würsten, Ludek Bufka, Christian Fuxjäger, Marco Heurich, Gjorge Ivanov, Włodzimierz Jędrzejewski, Radio Kont, Rafał Kowalczyk, Miha Krofel, Dime Melovski, Deniz Mengüllüoğlu, Tomma Lilli Middelhoff, Anja Molinari-Jobin, John Odden, Jānis Ozoliņš, Henryk Okarma, Jens Persson, Krzysztof Schmidt, Kristina Vogt, Fridolin Zimmermann & Henrik Andrén
The ecology and evolution of reproductive timing and synchrony has been a topic of great interest in evolutionary ecology for decades. Originally motivated by questions related to behavioural and reproductive adaptation to environmental conditions, the topic has acquired new relevance in the face of climate change. However, there has been relatively little research on reproductive phenology in mammalian carnivores. The Eurasian lynx (Lynx lynx) occurs across the Eurasian continent, covering three of the four main...

Additional file 2 of The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation

Haowei Du, Angad Jolly, Christopher M. Grochowski, Bo Yuan, Moez Dawood, Shalini N. Jhangiani, He Li, Donna Muzny, Jawid M. Fatih, Zeynep Coban-Akdemir, Mary Esther Carlin, Angela E. Scheuerle, Karin Witzl, Jennifer E. Posey, Matthew Pendleton, Eoghan Harrington, Sissel Juul, P. J. Hastings, Weimin Bi, Richard A. Gibbs, Fritz J. Sedlazeck, James R. Lupski, Claudia M. B. Carvalho & Pengfei Liu
Additional file 2: Table S2.

Additional file 1 of Hospitals with and without neurosurgery: a comparative study evaluating the outcome of patients with traumatic brain injury

Aimone Giugni, Lorenzo Gamberini, Greta Carrara, Luca Antiga, Obou Brissy, Virginia Buldini, Italo Calamai, Akos Csomos, Alessandra De Luca, Enrico Ferri, Joanne M. Fleming, Primoz Gradisek, Rafael Kaps, Theodoros Kyprianou, Silvia Lagomarsino, Isaac Lazar, Costanza Martino, Malgorzata Mikaszewska-Sokolewicz, Andrea Montis, Gabor Nardai, Giovanni Nattino, Giuseppe Nattino, Giulia Paci, Laila Portolani, Nektaria Xirouchaki … & Guido Bertolini
Additional file 1. The additional file provides supplementary tables and figures that could not fit in the paper.

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