172 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...

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: 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-...

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...

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: 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: 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: 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: 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: 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...

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...

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: Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of Primula veris

Iris Reinula, Sabrina Träger, Ignacio M. Hernández-Agramonte, Aveliina Helm & Tsipe Aavik
This dataset contains genetic and landscape data of 19 Primula veris populations in Muhu and Saaremaa islands in Estonia. Genetic samples were collected in 2015 and 2016. Landscape data was extracted from maps dated 2016 and 2017 for current data and 1930s for historical data. Data is divided to node- and link-based data. Node-based data contains genetic diversity data of the P. veris populations and landscape data in circular buffers surrounding the populations. Link-based data...

Competitiveness prediction for nodule colonization in Sinorhizobium meliloti through combined in vitro tagged strain characterization and genome-wide association analysis

Agnese Bellabarba, G. Bacci, F. Decorosi, E. Aun, E. Azzarello, M. Remm, L. Giovannetti, C. Viti, A. Mengoni & F. Pini
Associations between leguminous plants and symbiotic nitrogen-fixing rhizobia are a classic example of mutualism between a eukaryotic host and a specific group of prokaryotic microbes. Although this symbiosis is in part species-specific, different rhizobial strains may colonise the same nodule. Some rhizobial strains are commonly known as better competitors than others, but detailed analyses that aim to predict rhizobial competitive abilities based on genomes are still scarce. Here, we performed a bacterial genome-wide association (GWAS)...

Saprotrophic fungal diversity predicts ectomycorrhizal fungal diversity along the timberline in the framework of island biogeography theory

Teng Yang, Leho Tedersoo, Xiao Fu, Chang Zhao, Xu Liu, Guifeng Gao, Liang Cheng, Jonathan M. Adams & Haiyan Chu
In the context of a timberline tree species (Betula ermanii) as “virtual island”, we surveyed ectomycorrhizal (EcM) fungal diversity along a 430-m vertical gradient on the top of Changbai Mountain, China, sampling fine roots and neighboring soils of B. ermanii. Besides elevation, soil properties and plant functional traits, endophytic and saprotrophic fungal diversity were assessed as candidate predictors to construct integrative models. EcM fungal diversity decreased with increasing elevation, and exhibited positive diversity to diameter...

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...

Intraspecific trait changes in response to drought lead to trait convergence between- but not within species

Slendy Julieth Rodriguez Alarcon, Riin Tamme & Carlos Perez Carmona
Drought is expected to increase in future climate scenarios. Although responses to drought of individual functional traits are relatively well-known, simultaneous changes across multiple traits in response to water scarcity remain poorly understood despite its importance to understand alternative strategies to resist drought. We grew 52 herbaceous species in monocultures under drought and control treatments and characterized the functional space using seven measured above- and belowground traits: plant height, leaf area, specific leaf area, leaf...

Bird migration in space and time: chain migration by Eurasian curlew (Numenius arquata arquata) along the East Atlantic Flyway

Rebecca Pederson, Pierrick Bocher, Stefan Garthe, Jérôme Fort, Moritz Mercker, Verena Auernhammer, Martin Boschert, Philippe Delaporte, Jaanus Elts, Wolfgang Fiedler, Michał Korniluk, Dominik Krupiński, Riho Marja, Pierre Rousseau, Lukas Thiess & Philipp Schwemmer
Migration patterns in birds vary in space and time. Spatial patterns include chain, leap frog, and telescopic migration. Temporal patterns such as migration duration, number and duration of stopovers may vary according to breeding latitude, sex and season. This study aimed to verify these patterns in a long-distance migrant, the Eurasian curlew (Numenius arquata arquata), and to provide a synopsis of spatio-temporal migration patterns in this species of concern throughout the East Atlantic Flyway. We...

Fruit-feeding butterfly populations respond to variation in adult food availability: evidence from longitudinal body mass and abundance data

Freerk Molleman, Jorge Granados-Tello, Colin Chapman & Toomas Tammaru
The degree to which variation in adult food availability affects the population dynamics of a species depends on its position on the capital-income breeding continuum. The long-lived butterflies that feed on fruits as adults constitute an example of Lepidoptera with a high degree of income breeding. For three species of fruit-feeding butterflies in Uganda, we assessed the contribution of the income to breeding in the wild, and the consequences of variation in fruit availability for...

Additional file 2 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 2: Supplementary Table S2. Significance of differences between each pipeline in the reproducibility of beta diversity between the technical replicates. Significance of differences in Bray-Curtis distance between the pipelines were calculated based on the Tukey’s HSD test.

Additional file 14 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 14: Supplementary information.

Additional file 8 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 8: Supplementary Figure S4. Data usage efficiency of different amplicon sequence data analysis pipelines. Data usage efficiency on gut 16S rRNA (gut- 16S) and soil 16S rRNA (soil-16S) amplicons tested with different pipelines at different read truncation lengths (170, 200, and 230 & 170, 200, and 220 bases for the gut and soil datasets, respectively), by comparing the number of sequence clusters (ASVs /OTUs) to retrieved read counts in the final output matrix...

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  • University of Tartu
  • Swedish University of Agricultural Sciences
  • Earlham Institute
  • Quadram Institute
  • University of Turku
  • Estonian University of Life Sciences
  • Lund University
  • Stockholm University
  • Tartu University Hospital
  • University of Groningen