46 Works

Data from: Recovery of native genetic background in admixed Populations Using haplotypes, phenotypes, and pedigree information – using Cika cattle as a case breed

Mojca Simčič, Anamarija Smetko, Johann Sölkner, Doris Seichter, Gregor Gorjanc, Dragomir Kompan & Ivica Medugorac
The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning...

Data from: Recovery of large carnivores in Europe’s modern human-dominated landscapes

Guillaume Chapron, Petra Kaczensky, John D. C. Linnell, Manuela Von Arx, Djuro Huber, Henrik Andrén, José Vicente López-Bao, Michal Adamec, Francisco Álvares, Ole Anders, Linas Balčiauskas, Vaidas Balys, Péter Bedő, Ferdinand Bego, Juan Carlos Blanco, Urs Breitenmoser, Henrik Brøseth, Luděk Bufka, Raimonda Bunikyte, Paolo Ciucci, Alexander Dutsov, Thomas Engleder, Christian Fuxjäger, Claudio Groff, Katja Holmala … & Luigi Boitani
The conservation of large carnivores is a formidable challenge for biodiversity conservation. Using a data set on the past and current status of brown bears (Ursus arctos), Eurasian lynx (Lynx lynx), gray wolves (Canis lupus), and wolverines (Gulo gulo) in European countries, we show that roughly one-third of mainland Europe hosts at least one large carnivore species, with stable or increasing abundance in most cases in 21st-century records. The reasons for this overall conservation success...

Data from: Niches within a niche: ecological differentiation of subterranean amphipods across Europe’s interstitial waters

Cene Fiser, Teo Delić, Roman Luštrik, Maja Zagmajster & Florian Altermatt
Species that successfully colonized subterranean environments are subject to two opposing selection processes. Stringent abiotic factors select for convergent adaptations, such as loss of eyes and pigments, while interspecific competition drives between-species divergence. Subterranean species can resolve opposing selection by adaptation to physically different microhabitats. Yet, species frequently co-occur in physically homogeneous subterranean habitats, like interstitial. These co-occurrences in such a narrow ecological context can be explained either by equalizing mechanisms, in which neither of...

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...

Simple and complex, sexually dimorphic retinal mosaic of fritillary butterflies

Gregor Belušič, Kentaro Arikawa, Marko Ilić, Primož Pirih, Pei-Ju Chen, Andrej Meglič, Jošt Prevc & Masaya Yago
Butterflies have variable sets of spectral photoreceptors that underlie colour vision. The photoreceptor organization may be optimised for the detection of body colouration. Fritillaries (Argynnini) are nymphalid butterflies exhibiting varying degrees of sexual dimorphism in wing colouration. In two sister species, the females have orange (Argynnis paphia) and dark wings (A. sagana), respectively, while the males of both species have orange wings with large patches of pheromone-producing androconia. In spite of the differences in female...

The awareness, visibility and support for young carers across Europe: a Delphi study

Henk Herman Nap, Renske Hoefman, Nynke De Jong, Lieke Lovink, Ludo Glimmerveen, Feylyn Lewis, Sara Santini, Barbara D’Amen, Marco Socci, Licia Boccaletti, Giulia Casu, Alessandra Manattini, Rosita Brolin, Karina Sirk, Valentina Hlebec, Tatjana Rakar, Tjasa Hudobivnik, Agnes Leu, Fabian Berger, Lennart Magnusson & Elizabeth Hanson
Across Europe, young carers (YCs) and their need for support receive limited attention in the media, policy and empirical research, even though, similar to adult carers, they also provide care to ill family members. The Delphi study, a qualitative research methodology, which provides the focus for this article, had the overall aim of exploring existing successful strategies to support YCs. Compared to YCs, even less is known about adolescent young carers (AYCs), a group that...

A hotspot of groundwater amphipod diversity on a crossroad of evolutionary radiations

Špela Borko, Florian Altermatt, Maja Zagmajster & Cene Fišer
Supplementary data to article entitled A hotspot of groundwater amphipod diversity on a crossroad of evolutionary radiations Groundwater harbours an exceptional fauna and provides invaluable ecosystem services, yet is among the least explored and consequently least protected ecosystems. Successful protection of its biodiversity depends on complete species inventories, knowledge of species spatial distribution, and quantification of biodiversity patterns, as well as disentanglement of the processes that shaped biodiversity patterns. We studied the hyper-speciose amphipod genus...

Data from: Genome-wide SNP data unveils the globalization of domesticated pigs

Bin Yang, Leilei Cui, Miguel Perez-Enciso, Aleksei Traspov, Richard P. M. A. Crooijmans, Natalia Zinovieva, Lawrence B. Schook, Alan Archibald, Kesinee Gatphayak, Christophe Knorr, Alex Triantafyllidis, Panoraia Alexandri, Gono Semiadi, Olivier Hanotte, Deodália Dias, Peter Dovč, Pekka Uimari, Laura Iacolina, Massimo Scandura, Martien A. M. Groenen, Lusheng Huang & Hendrik-Jan Megens
Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global...

Data from: Towards a common methodology for developing logistic tree mortality models based on ring-width data

Maxime Cailleret, Christof Bigler, Harald Bugmann, J. Julio Camarero, Katarina Cufar, Hendrik Davi, Ilona Mészáros, Francesco Minunno, Mikko Peltoniemi, Elisabeth Robert, María-Laura Suarez, Roberto Tognetti & Jordi Martinez-Vilalta
Tree mortality is a key process shaping forest dynamics. Thus, there is a growing need for indicators of the likelihood of tree death. During the last decades, an increasing number of tree-ring based studies have aimed to derive growth–mortality functions, mostly using logistic models. The results of these studies, however, are difficult to compare and synthesize due to the diversity of approaches used for the sampling strategy (number and characteristics of alive and death observations),...

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: Top predators constrain mesopredator distributions

Thomas M. Newsome, Aaron C. Greenville, Duško Ćirović, Christopher R. Dickman, Chris N. Johnson, Miha Krofel, Mike Letnic, William J. Ripple, Euan G. Ritchie, Stoyan Stoyanov & Aaron J. Wirsing
Top predators can suppress mesopredators by killing them, competing for resources and instilling fear, but it is unclear how suppression of mesopredators varies with the distribution and abundance of top predators at large spatial scales and among different ecological contexts. We suggest that suppression of mesopredators will be strongest where top predators occur at high densities over large areas. These conditions are more likely to occur in the core than on the margins of top...

Data from: Conservation of a domestic metapopulation structured into related and partly admixed strains

Jelena Ramljak, Gjoko Bunevski, Hysen Bytyqi, Božidarka Marković, Muhamed Brka, Ante Ivanković, Kristaq Kume, Srđan Stojanović, Vasil Nikolov, Mojca Simčič, Johann Soelkner, Elisabeth Kunz, Sophie Rothammer, Doris Seichter, Hans-Peter Grünenfelder, Elli T. Broxham, Waltraud Kugler & Ivica Medugorac
Preservation of genetic diversity is one of the most pressing challenges in the planetary boundaries concept. Within this context, we focused on genetic diversity in a native, unselected and highly admixed domesticated metapopulation. A set of 1828 individuals from 60 different cattle breeds was analysed using a medium density SNP chip. Among these breeds, 14 Buša strains formed a metapopulation represented by 350 individuals, while the remaining 46 breeds represented the global cattle population. Genetic...

Data from: Patterns and correlates of claims for brown bear damage on a continental scale

Carlos Bautista, Javier Naves, Eloy Revilla, Néstor Fernández, Jörg Albrecht, Anne K. Scharf, Robin Rigg, Alexandros A. Karamanlidis, Klemen Jerina, Djuro Huber, Santiago Palazón, Raido Kont, Paolo Ciucci, Claudio Groff, Aleksandar Dutsov, Juan Seijas, Pierre-Ives Quenette, Agnieszka Olszańska, Maryna Shkvyria, Michal Adamec, Janis Ozolins, Marko Jonozovič & Nuria Selva
Wildlife damage to human property threatens human–wildlife coexistence. Conflicts arising from wildlife damage in intensively managed landscapes often undermine conservation efforts, making damage mitigation and compensation of special concern for wildlife conservation. However, the mechanisms underlying the occurrence of damage and claims at large scales are still poorly understood. Here, we investigated the patterns of damage caused by brown bears Ursus arctos and its ecological and socio-economic correlates at a continental scale. We compiled information...

Data from: Disturbance history is a key driver of tree lifespan in temperate primary forests

Jakob Pavlin, Thomas A. Nagel, Marek Svitok, Joseph L. Pettit, Krešimir Begović, Stjepan Mikac, Abdulla Dikku, Elvin Toromani, Momchil Panayotov, Tzvetan Zlatanov, Ovidiu Haruta, Sorin Dorog, Oleh Chaskovskyy, Martin Mikoláš, Pavel Janda, Michal Frankovič, Ruffy Rodrigo, Ondřej Vostarek, Michal Synek, Martin Dušátko, Tomáš Kníř, Daniel Kozák, Ondrej Kameniar, Radek Bače, Vojtěch Čada … & Miroslav Svoboda
AIMS We examined differences in lifespan among the dominant tree species (spruce (Picea abies (L.) H. Karst.), fir (Abies alba Mill.), beech (Fagus sylvatica L.), and maple (Acer pseudoplatanus L.)) across primary mountain forests of Europe. We ask how disturbance history, lifetime growth patterns, and environmental factors influence lifespan. LOCATIONS Balkan mountains, Carpathian mountains, Dinaric mountains. METHODS Annual ring widths from 20,600 cores from primary forests were used to estimate tree life spans, growth trends,...

Data from: Miniaturization, genome size, and biological size in a diverse clade of salamanders

Sean Rovito, Louis Paul Decena-Segarra, Lilijana Bizjak-Mali, Ales Kladnik & Stanley Sessions
Genome size (C-value) can affect organismal traits across levels of biological organization, from tissue complexity to metabolism. Neotropical salamanders show wide variation in genome and body sizes, including several clades with miniature species. Because miniaturization imposes strong constraints on morphology and development, and genome size is strongly correlated with cell size, we hypothesize that body size has played an important role in the evolution of genome size in bolitoglossine salamanders. If this hypothesis is correct,...

Data from: Is foraging innovation lost following colonisation of a less variable environment? a case study in surface- vs. cave-dwelling Asellus aquaticus

Gábor Herczeg, Viktória Priszcilla Hafenscher, Gergely Balázs, Žiga Fišer, Simona Kralj-Fišer & Gergely Horváth
Behavioural innovation is a key process for successful colonisation of new habitat types. However, it is costly due to the necessary cognitive and neural demands and typically connected to ecological generalism. Therefore, loss of behavioural innovativeness is predicted following colonisation of new, simple and invariable environments. We tested this prediction by studying foraging innovativeness in the freshwater isopod Asellus aquaticus. We sampled its populations along the route of colonising a thermokarstic water-filled cave (simple, stable...

How did subterranean amphipods cross the Adriatic Sea? Phylogenetic evidence for the dispersal-vicariance interplay mediated by marine regression-transgression cycles

Teo Delić, Fabio Stoch, Spela Borko, Jean-Francois Flot & Cene Fišer
Aim: We tested the hypothesis that historical marine regression-transgression cycles shaped the distribution patterns of subterranean amphipods through repeated cycles of dispersal and vicariance against the hypothesis that subterranean amphipods colonized both sides of the Adriatic Sea independently. Location: Western Balkan Peninsula, Adriatic Sea Islands and Apennine Peninsula, Europe Taxon: A clade of freshwater subterranean amphipods, genus Niphargus (Crustacea: Amphipoda). Methods: The taxonomic structure of the studied clade was revised using unilocus species delimitations. Timeframe...

Data from: Taxonomic, phylogenetic and ecological diversity of Niphargus (Amphipoda: Crustacea) in the Hölloch cave system (Switzerland)

Cene Fišer, Marjeta Konec, Roman Alther, Vid Švara & Florian Altermatt
Groundwater belongs to the spatially most extensive, but least explored freshwater systems. On a global scale, the species richness of several subterranean invertebrate taxa parallels species richness found in surface waters, while on a local scale species richness hardly exceeds 20 species. This results in a high contribution of groundwater ecosystems to regional β- and γ-diversity, and to a smaller degree to α-diversity, and deserves focused attention. In general, more species are to be found...

Data from: A population genomics insight into the Mediterranean origins of wine yeast domestication

Pedro Almeida, Raquel Barbosa, Polona Zalar, Yumi Imanishi, Kiminori Shimizu, Benedetta Turchetti, Jean-Luc Legras, Marta Serra, Sylvie Dequin, Arnaud Couloux, Julie Guy, Douda Bensasson, Paula Gonçalves & José Paulo Sampaio
The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and...

Morphological measurements of six cave and nine surface Asellus aquaticus populations

Gergely Balázs, Anna Biró, Žiga Fišer, Cene Fišer & Gábor Herczeg
The dataset contains data of 17 functional morphological traits measured on 656 individuals from the Asellus aquaticus species complex from six cave and nine surface populations from four countries. The measured traits are covering a wide range of functionalities including locomotion, fecundity and sensing. By including individuals from both sex, and from surface and cave habitats questions concerning troglomorphic adaptation and sexual dimorphism and their interaction can be addressed.

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...

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