107 Works

Data from: ITS1 versus ITS2 as DNA metabarcodes for fungi

Rakel Blaalid, Surendra Kumar, R. Henrik Nilsson, Kessy Abarenkov, Paul M. Kirk & Håvard Kauserud
The nuclear ribosomal Internal Transcribed Spacer ITS region is widely used as a DNA metabarcoding marker to characterize the diversity and composition of fungal communities. In amplicon pyrosequencing studies of fungal diversity, one of the spacers ITS1 or ITS2 of the ITS region is normally used. In this methodological study we evaluate the usability of ITS1 vs. ITS2 as a DNA metabarcoding marker for fungi. We analyse three data sets: two comprising ITS1 and ITS2...

Areal interpolation of spatial interaction data

Jan Šimbera & Anto Aasa

Data from: High ecosystem service delivery potential of small woodlands in agricultural landscapes

Alicia Valdés, Jonathan Lenoir, Pieter De Frenne, Emilie Andrieu, Jorg Brunet, Olivier Chabrerie, Sara Cousins, Marc Deconchat, Pallieter De Smedt, Martin Diekmann, Steffen Ehrmann, Emilie Gallet-Moron, Stefanie Gaertner, Brice Giffard, Karin Hansen, Martin Hermy, Annette Kolb, Vincent Leroux, Jaan Liira, Jessica Lindgren, Ludmilla Martin, Tobias Naaf, Taavi Paal, Willem Proesmans, Michael Scherer-Lorenzen … & Guillaume Decocq
Global forest loss and fragmentation have strongly increased the frequency of forest patches smaller than a few hectares. Little is known about the biodiversity and ecosystem service supply potential of such small woodlands in comparison to larger forests. As it is widely recognized that high biodiversity levels increase ecosystem functionality and the delivery of multiple ecosystem services, small, isolated woodlands are expected to have a lower potential for ecosystem service delivery than large forests hosting...

A probable oligochaete from an Early Triassic Lagerstätte of the southern Cis-Urals and its evolutionary implications

Andrey Zhuravlev, Dmitry Shcherbakov, Tarmo Timm, Alexander Tzetlin & Olev Vinn
Oligochaetes, despite their important role in terrestrial ecosystems and a tremendous biomass, are extremely rare fossils. The palaeontological record of these worms is restricted to some cocoons, presumable trace fossils and a few body fossils the most convincing of which are discovered in Mesozoic and Cenozoic strata. The Olenekian (Lower Triassic) siliciclastic lacustrine Petropavlovka Lagerstätte of the southern Cis-Urals yields a number of extraordinary freshwater fossils including an annelid. The segmented body with a secondary...

Data from: Patterns of modern pollen and plant richness across northern Europe

Triin Reitalu, Anne E. Bjune, Ansis Blaus, Thomas Giesecke, Aveliina Helm, Isabelle Matthias, Sylvia H. Peglar, J. Sakari Salonen, Heikki Seppa, Vivika Väli & H. John B. Birks
1. Sedimentary pollen offers excellent opportunities to reconstruct vegetation changes over past millennia. Number of different pollen taxa or pollen richness is used to characterise past plant richness. To improve the interpretation of sedimentary pollen richness, it is essential to understand the relationship between pollen and plant richness in contemporary landscapes. This study presents a regional-scale comparison of pollen and plant richness from northern Europe and evaluates the importance of environmental variables on pollen and...

Data from: Weak and inconsistent associations between melanic darkness and fitness related traits in an insect

Siiri-Lii Sandre, Tanel Kaart, Nathan Morehouse & Toomas Tammaru
The idea that the fitness value of body colouration may be affected by biochemically mediated trade-offs has received much research attention. For example, melanisation is believed to interact with other fitness-related traits via competition for substrates, costs associated with the synthesis of melanin, or pleiotropic effects of the involved genes. However, genetic correlations between colouration and fitness-related traits remain poorly understood. Here we present a quantitative genetic study of a colouration trait correlated to melanin-based...

Data from: Plant diversity in oceanic archipelagos: realistic patterns emulated by an agent‐based computer simulation

Madli Jõks & Meelis Pärtel
Although islands as natural laboratories have held the attention of scientists for centuries, they continue to offer new study questions, especially in the context of the current biodiversity crisis. To date, habitat diversity on islands and spatial configuration of archipelagos have received less attention than classical island area and isolation. Moreover, in the field where experiments are impossible, correlative methods have dominated, despite the call for more mechanistic approaches. We developed an agent‐based computer simulation...

Data from: A small badge of longevity: opposing survival selection on the size of white and black wing markings

Tuul Sepp, Kalev Rattiste, Lauri Saks, Richard Meitern, Janek Urvik, Ants Kaasik & Peeter Hõrak
According to handicap principle, exaggerated ornamental traits are supposed to exert costs on their bearers. However, there is much less theoretical and practical consensus about whether and under which conditions ornament expression should positively correlate with survival. We measured age-related variation and survival selection on the size of white wing patches and black wing tips in a long-lived monogamous seabird, the common gull Larus canus. Males had larger white patches than females but patch size...

Data from: Community assembly and drivers of phytoplankton functional structure

Riina Klais, Veera Norros, Sirpa Lehtinen, Timo Tamminen & Kalle Olli
We analysed the functional composition of coastal phytoplankton communities (n = 7941) along the gradient from marine to brackish waters of the Baltic Sea, using species-specific morphological and ecological functional traits (ability to fix atmospheric nitrogen, mixotrophy, use of silica in cell walls, formation of chains or colonies, motility, accessory pigment composition, and size), to describe and measure the functional differences between species. Mean pairwise functional distance of phytoplankton communities increased from spring to mid-...

Multiscale drivers of carabid beetle (Coleoptera: Carabidae) assemblages in small European woodlands

Ronan Marrec, Vincent Le Roux, Ludmilla Martin, Jonathan Lenoir, Jörg Brunet, Sara Cousins, Pallieter De Smedt, Marc Deconchat, Martin Diekmann, Steffen Ehrmann, Emilie Gallet-Moron, Brice Giffard, Jaan Liira, Jessica Lindgren, Alicia Valdés, Kris Verheyen, Monika Wulf & Guillaume Decocq
Aim The spatiotemporal connectivity of forest patches in lowland agricultural landscapes and their age matter to explain current biodiversity patterns across regional as well as biogeographical extents, to the point that it exceeds the contribution of macroclimate for plant diversity in the understory of temperate forests. Whether this holds true for other taxonomic groups remains largely unknown. Yet, it has important consequences for ecosystem functioning and the delivery of ecosystem services. Focusing on carabid beetle...

Data from: Elucidating mechanisms for insect body size: partial support for the oxygen-dependent induction of moulting hypothesis

Sami Mikael Kivelä, Sonja Viinamäki, Netta Keret, Karl Gotthard, Esa Hohtola & Panu Välimäki
Body size is a key life history trait and knowledge of its mechanistic basis is crucial in life history biology. Such knowledge is accumulating in holometabolous insects, whose growth is characterised and body size affected by moulting. According to the oxygen-dependent induction of moulting (ODIM) hypothesis, moult is induced at a critical mass where oxygen demand of growing tissues overrides the supply that principally grows only at moults. Support for the ODIM hypothesis is controversial...

Data from: Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians

Brandon L. Pierce, Lin Tong, Lin S. Chen, Ronald Rahaman, Maria Argos, Farzana Jasmine, Shantanu Roy, Rachelle Paul-Brutus, Harm-Jan Westra, Lude Franke, Tonu Esko, Rakibuz Zaman, Tariqul Islam, Mahfuzar Rahman, John A. Baron, Muhammad G. Kibriya & Habibul Ahsan
A large fraction of human genes are regulated by genetic variation near the transcribed sequence (cis-eQTL, expression quantitative trait locus), and many cis-eQTLs have implications for human disease. Less is known regarding the effects of genetic variation on expression of distant genes (trans-eQTLs) and their biological mechanisms. In this work, we use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis-...

Data from: Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic

Sunil Mundra, Rune Halvorsen, Håvard Kauserud, Mohammad Bahram, Leho Tedersoo, Bo Elberling, Elisabeth J. Cooper & Pernille Bronken Eidesen
Changing climate is expected to alter precipitation patterns in the Arctic, with consequences for subsurface temperature and moisture conditions, community structure, and nutrient mobilization through microbial belowground processes. Here, we address the effect of increased snow depth on the variation in species richness and community structure of ectomycorrhizal (ECM) and saprotrophic fungi. Soil samples were collected weekly from mid-July to mid-September in both control and deep snow plots. Richness of ECM fungi was lower, while...

Data from: Insulin-like growth factor 1 and life-history evolution of passerine birds

Jaanis Lodjak, Raivo Mand & Marko Mägi
1. Natural selection has generated a diversity of ways in which vertebrates allocate their resources between fundamental life-history traits. The availability of possible evolutionary trajectories of these traits is limited by various genetic, physiological, and phylogenetic constraints. This causes trade-offs due to shared resource pools for, or genetic linkage of, competing traits. The majority of these trade-offs are mediated by hormones and create the variability of phenotypes that can be observed in nature. 2. Insulin-like...

Data from: Metabolic rate associates with, but does not generate covariation between, behaviours in western stutter-trilling crickets, Gryllus integer

Indrikis A. Krams, Petri T. Niemelä, Giedrius Trakimas, Ronalds Krams, Gordon M. Burghardt, Tatjana Krama, Aare Kuusik, Marika Mand, Markus J. Rantala, Raivo Mand, Jukka Kekäläinen, Ilkka Sirkka, Severi Luoto, Raine Kortet & Indrikis Krams
The causes and consequences of among-individual variation and covariation in behaviours are of substantial interest to behavioural ecology, but the proximate mechanisms underpinning this (co)variation are still unclear. Previous research suggests metabolic rate as a potential proximate mechanism to explain behavioural covariation. We measured the resting metabolic rate (RMR), boldness and exploration in western stutter-trilling crickets, Gryllus integer, selected differentially for short and fast development over two generations. After applying mixed-effects models to reveal the...

Parental age does not influence offspring telomeres during early life in common gulls (Larus canus)

Tuul Sepp, Richard Meitern, Britt Heidinger, Kristina Noreikiene, Kalev Rattiste, Peeter Hõrak, Lauri Saks, Jeffrey Kittilson, Janek Urvik & Mathieu Giraudeau
Parental age can affect offspring telomere length through heritable and epigenetic-like effects, but at what stage during development these effects are established is not well known. To address this, we conducted a cross-fostering experiment in common gulls (Larus canus) that enabled us distinguish between pre- and post-natal parental age effects on offspring telomere length. Whole clutches were exchanged after clutch completion within and between parental age classes (young and old) and blood samples were collected...

Data from: Wintering bird communities are tracking climate change faster than breeding communities

Aleksi Lehikoinen, Åke Lindström, Andrea Santangeli, Päivi Sirkiä, Lluis Brotons, Vincent Devictor, Jaanus Elts, Ruud P. B. Fobben, Henning Heldbjerg, Sergi Herrando, Marc Herremans, Marie-Anne R. Hudson, Frederic Jiguet, Alison Johnston, Romain Lorrilliere, Emma-Liina Marjakangas, Nicole L. Michel, Charlotte M. Moshøj, Renno Nellis, Jean-Yves Paquet, Adam C. Smith, Tibor Szep & Chris Van Turnhout
1. Global climate change is driving species’ distributions towards the poles and mountain tops during both non-breeding and breeding seasons, leading to changes in the composition of natural communities. However, the degree of season differences in climate-driven community shifts has not been thoroughly investigated at large spatial scales. 2. We compared the rates of change in the community composition during both winter (non-breeding season) and summer (breeding) and their relation to temperature changes. 3. Based...

Data from: Higher predation risk for insect prey at low latitudes and elevations

Tomas Roslin, Bess Hardwick, Vojtech Novotny, William K. Petry, Nigel R. Andrew, Ashley Asmus, Isabel C. Barrio, Yves Basset, Andrea Larissa Boesing, Timothy C. Bonebrake, Erin K. Cameron, Wesley Dáttilo, David A. Donoso, Pavel Drozd, Claudia L. Gray, David S. Hik, Sarah J. Hill, Tapani Hopkins, Shuyin Huang, Bonny Koane, Benita Laird-Hopkins, Liisa Laukkanen, Owen T. Lewis, Sol Milne, Isaiah Mwesige … & Eleanor M. Slade
Biotic interactions underlie ecosystem structure and function, but predicting interaction outcomes is difficult. We tested the hypothesis that biotic interaction strength increases toward the equator, using a global experiment with model caterpillars to measure predation risk. Across an 11,660-kilometer latitudinal gradient spanning six continents, we found increasing predation toward the equator, with a parallel pattern of increasing predation toward lower elevations. Patterns across both latitude and elevation were driven by arthropod predators, with no systematic...

Data from: Co-introduction of native mycorrhizal fungi and plant seeds accelerates restoration of post-mining landscapes

Tanel Vahter, C. Bueno, John Davison, Koit Herodes, Inga Hiiesalu, Liis Kasari-Toussaint, Jane Oja, Pal Olsson, Siim Sepp, Martin Zobel, Martti Vasar & Maarja Öpik
1. Grasslands are among the most threatened terrestrial biomes, and habitat conservation alone will be insufficient to meet biodiversity goals. While restoration of indigenous grasslands is a priority, conflict with economic objectives means that incorporation of alternative habitats is necessary to offset grassland loss. With up to 800,000 km² of land affected by mining globally, there is an opportunity to create additional grassland habitat in post-mining landscapes. 2. We aimed to assess whether co-introduction of...

Data from: The bacterial community structure and functional profile in the heavy metal contaminated paddy soils,surrounding a nonferrous smelter in South Korea

Sherlyn C. Tipayno, Jaak Truu, Sandipan Samaddar, Marika Truu, Jens-Konrad Preem, Kristjan Oopkaup, Mikk Espenberg, Poulami Chatterjee, Yeongyeong Kang, Kiyoon Kim & Tongmin Sa
The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. The present study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the...

Not a melting pot: plant species aggregate in their non-native range

Gisela C. Stotz, James F. Cahill, Jonathan A. Bennett, Cameron N. Carlyle, Edward W. Bork, Diana Askarizadeh, Sandor Bartha, Carl Beierkuhnlein, Bazartseren Boldgiv, Leslie Brown, Marcelo Cabido, Giandiego Campetella, Stefano Chelli, Ofer Cohen, Sandra Díaz, Lucas Enrico, David Ensing, Batdelger Erdenetsetseg, Alessandra Fidelis, Heath W. Garris, Hugh A.L. Henry, Anke Jentsch, Mohammad Hassan Jouri, Kadri Koorem, Peter Manning … & Lauchlan H. Fraser
Aim: Plant species continue to be moved outside of their native range by human activities. Here, we aim at determining whether, once introduced, plants assimilate into native communities, or whether they aggregate, thus forming mosaics of native- and alien-rich communities. Alien species may aggregate in their non-native range due to shared habitat preferences, such as their tendency to establish in high-biomass, species-poor areas. Location: 22 herbaceous grasslands in 14 countries, mainly in the temperate zone....

Data from: Estimating dark diversity and species pools: an empirical assessment of two methods

Rob J. Lewis, Robert Szava-Kovats & Meelis Pärtel
1. Species absent from a community, but with the potential to establish (dark diversity) are an important, yet rarely considered, component of habitat specific species pools. However, quantifying this component remains a challenge as dark diversity cannot be observed directly, and must be estimated. Here, we empirically test whether species ecological requirements or species co-occurrences provide accurate estimates of dark diversity. 2. We used two spatially nested independent datasets, one comprising 3033 samples of coastal...

Data from: Is telomere length a molecular marker of past thermal stress in wild fish?

Paul V. Debes, Marko Visse, Bineet Panda, Petteri Ilmonen & Anti Vasemägi
Telomeres protect eukaryotic chromosomes; variation in telomere length has been linked (primarily in homoeothermic animals) to variation in stress, cellular ageing and disease risk. Moreover, telomeres have been suggested to function as biomarker for quantifying past environmental stress, but studies in wild animals remain rare. Environmental stress, such as extreme environmental temperatures in poikilothermic animals, may result in oxidative stress that accelerates telomere attrition. However, growth, which may depend on temperature, can also contribute to...

Data from: Multi-level patterns in population genetics: variogram series detects a hidden isolation-by- distance- dominated structure of Scandinavian brown bears Ursus arctos

Julia Schregel, Jaanus Remm, Hans Geir Eiken, Jon E. Swenson, Urmas Saarma & Snorre B. Hagen
1. Large-scale pattern-oriented approaches are useful to understand the multi-level processes that shape the genetic structure of a population. Matching the scales of patterns and putative processes is both a key to success and a challenge. 2. We have developed a simple statistical approach, based on variogram analysis, that identifies multiple spatial scales where the population pattern, in this case genetic structure, have highest expression (i.e. the spatial scales at which the strength of patterning...

Data from: Outlier loci detect intraspecific biodiversity amongst spring and autumn spawning herring across local scales

Riho Gross, Dorte Bekkevold, Sarah J. Helyar, Timo Arula & Henn Ojaveer
Herring, Clupea harengus, is one of the ecologically and commercially most important species in European northern seas, where two distinct ecotypes have been described based on spawning time; spring and autumn. To date, it is unknown if these spring and autumn spawning herring constitute genetically distinct units. We assessed levels of genetic divergence between spring and autumn spawning herring in the Baltic Sea using two types of DNA markers, microsatellites and Single Nucleotide Polymorphisms, and...

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