128 Works

Data from: Bayesian tests of topology hypotheses with an example from diving beetles

Johannes Bergsten, Anders N. Nilsson & Fredrik Ronquist
We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important...

Data from: Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata

Baosheng Wang, Jian-Feng Mao, Jie Gao, Wei Zhao & Xiao-Ru Wang
Pinus densata is an intriguingly successful homoploid hybrid species that occupies vast areas of the southeastern Tibetan Plateau in which neither of its parental species are present, but the colonization processes involved are poorly understood. To shed light on how this species colonized and became established on the plateau, we surveyed paternally inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA variation within and among 54 populations of P. densata and its putative parental species...

Data from: Time for recovery of riparian plants in restored northern Swedish streams: a chronosequence study

Eliza Maher Hasselquist, Christer Nilsson, Joakim Hjältén, Dolly Jørgensen, Lovisa Lind & Lina E. Polvi
A lack of ecological responses in stream restoration projects has been prevalent throughout recent literature with many studies reporting insufficient time for recovery. We assessed the relative importance of time, site variables, and landscape setting for understanding how plant species richness and understory productivity recover over time in riparian zones of northern Swedish streams. We used a space-for-time substitution consisting of 13 stream reaches restored 5–25 years ago, as well as five unrestored channelized reference...

Data from: Long telomeres are associated with clonality in wild populations of the fissiparous starfish Coscinasterias tenuispina

Alex Garcia-Cisneros, Rocío Pérez-Portela, Bethanie C. Almroth, Sofie Degerman, Creu Palacín & Helen Nilsson Sköld
TelTelomeres usually shorten during an organism’s lifespan and have thus been used as an aging and health marker. When telomeres become sufficiently short, senescence is induced. The most common method of restoring telomere length is via telomerase reverse transcriptase activity, highly expressed during embryogenesis. However, although asexual reproduction from adult tissues has an important role in the life cycles of certain species, its effect on the aging and fitness of wild populations, as well as...

Presence-absence sampling for estimating plant density using survey data with variable plot size

Göran Ståhl, Magnus Ekström, Jonas Dahlgren, Per-Anders Esseen, Anton Grafström & Bengt Jonsson
1. Presence-absence sampling is an important method for monitoring state and change of both individual plant species and communities. With this method only the presence or absence of the target species is recorded on plots and thus the method is straightforward to apply and less prone to surveyor judgment compared to other vegetation monitoring methods. However, in the basic setting all plots must be equally large or otherwise it is unclear how data should be...

Differential nutrient limitation and tree height control leaf physiology, supporting niche partitioning in tropical dipterocarp forests

David Bartholomew, Lindsay Banin, Paulo Bittencourt, Mohammed Aminur Bin Suis, Lina Mercado, Reuben Nilus, David Burslem & Lucy Rowland
Revealing the mechanisms of environmental niche partitioning within lowland tropical forests is important for understanding the drivers of current species distributions and potential vulnerability to environmental change. Tropical forest structure and species composition change across edaphic gradients in Borneo over short distances. However, our understanding of how edaphic conditions affect tree physiology and whether these relationships drive niche partitioning within Bornean forests remains incomplete. This study evaluated how leaf physiological function changes with nutrient availability...

Return to work following diagnosis of low-grade glioma: A nationwide matched cohort study

Isabelle Rydén, Louise Carstam, Sasha Gulati, Anja Smits, Katharina S. Sunnerhagen, Per Hellström, Roger Henriksson, , Øyvind Salvesen & Asgeir Jakola
Objective: Return-to-work (RTW) following diagnosis of infiltrative low-grade gliomas (LGG) is unknown. Methods: Swedish patients with histopathological verified WHO grade II diffuse glioma diagnosed between 2005-2015 were included. Data were acquired from several Swedish registries. A total of 381 patients aged 18-60 were eligible. A matched control population (n=1900) was acquired. Individual data on sick leave, compensations, comorbidity, and treatments assigned were assessed. Predictors were explored using multivariable logistic regression. Results: One year before surgery/index...

Data from: Reindeer control over subarctic treeline alters soil fungal communities with potential consequences for soil carbon storage

Henni Ylänne, Rieke L. Madsen, Carles Castaño, Daniel B. Metcalfe & Karina E. Clemmensen
Here we present the data and R script from “Reindeer control over subarctic treeline alters soil fungal communities with potential consequences for soil carbon storage” by Henni Ylänne, Rieke L. Madsen, Carles Castaño, Daniel B. Metcalfe and Karina E. Clemmensen (Global Change Biology, 2021). In this study we reported the impacts of grazing regime and mountain birch vicinity on the abundance, diversity and community composition of the soil fungal community, and explored how the soil...

Predator-prey overlap in three dimensions: cod benefit from capelin coming near the seafloor

Johanna Fall, Edda Johannesen, Göran Englund, Geir Odd Johansen & Øyvind Fiksen
Spatial overlap between predator and prey is a prerequisite for predation, but the degree of overlap is not necessarily proportional to prey consumption. This is because many of the behavioural processes that precede ingestion are non-linear and depend on local prey densities. In aquatic environments, predators and prey distribute not only across a surface, but also vertically in the water column, adding another dimension to the interaction. Integrating and simplifying behavioural processes across space and...

Stable water isotopes in Western Siberian inland waters

P. Ala-Aho, C. Soulsby, O.S. Pokrovsky, S.N. Kirpotin, J. Karlsson, S. Serikova, R. Manasypov, A. Lim, I. Krickov, S.N. Vorobyev, L.G. Kolesnichenko, S. Loiko & D. Tetzlaff
The data consist of stable water isotope composition in the rivers , lakes, soils and flooded areas in the Western Siberia Lowlands (WSL). Sampling area encompassed a 1700 km south-north transect spanning from approx. 56°N to 68°N in latitude and 74°E to 84°E in longitude. Samples were collected during multiple field campaigns between February 2014 and November 2016. The dataset in produced as a part of the JPI/NERC funded SIWA project "Climate impact on the...

Data from: Urine is an important nitrogen source for plants irrespective of vegetation composition in an Arctic tundra: insights from a 15N-enriched urea tracer experiment

Hélène Barthelemy, Sari Stark, Anders Michelsen & Johan Olofsson
1. Mammalian herbivores can strongly influence nitrogen (N) cycling and herbivore urine could be a central component of the N cycle in grazed ecosystems. Despite its potential role for ecosystem productivity and functioning, the fate of N derived from urine has rarely been investigated in grazed ecosystems. 2. This study explored the fate of 15N-enriched urea in tundra sites that have been either lightly or intensively grazed by reindeer for more than 50 years. We...

Data from: The mechanics of predator-prey interactions: first principles of physics predict predator-prey size ratios

Sebastien Portalier, Gregor Fussmann, Michel Loreau & Mehdi Cherif
1. Robust predictions of predator-prey interactions are fundamental for the understanding of food webs, their structure, dynamics, resistance to species loss, response to invasions and ecosystem function. Most current food web models measure parameters at the food web level to predict patterns at the same level. Thus, they are sensitive to the quality of the data, and may be ineffective in predicting non-observed interactions and disturbed food webs. There is a need for mechanistic models...

Data from: Informative plot sizes in presence-absence sampling of forest floor vegetation

Göran Ståhl, Magnus Ekström, Jonas Dahlgren, Per-Anders Esseen, Anton Grafström & Bengt-Gunnar Jonsson
1. Plant communities are attracting increased interest in connection with forest and landscape inventories due to society’s interest in ecosystem services. However, the acquisition of accurate information about plant communities poses several methodological challenges. Here we investigate the use of presence-absence sampling with the aim to monitor state and change of plant density. We study what plot sizes are informative, i.e. the estimators should have as high precision as possible. 2. Plant occurrences were modeled...

Data from: Increased dopamine release after working-memory updating training: neurochemical correlates of transfer

Lars Bäckman, Otto Waris, Jarkko Johansson, Micael Andersson, Juha O. Rinne, Kati Alakurtti, Anna Soveri, Matti Laine & Lars Nyberg
Previous work demonstrates that working-memory (WM) updating training results in improved performance on a letter-memory criterion task, transfers to an untrained n-back task, and increases striatal dopamine (DA) activity during the criterion task. Here, we sought to replicate and extend these findings by also examining neurochemical correlates of transfer. Four positron emission tomography (PET) scans using the radioligand raclopride were performed. Two of these assessed DAD2 binding (letter memory; n-back) before 5 weeks of updating...

Data from: Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive Virginia rail

Auriel M. V. Fournier, Alexis R. Sullivan, Joseph K. Bump, Marie Perkins, Mark C. Shieldcastle & Sammy L. King
Stable hydrogen isotope (δD) methods for tracking animal movement are widely used yet often produce low resolution assignments. Incorporating prior knowledge of abundance, distribution or movement patterns can ameliorate this limitation, but data are lacking for most species. We demonstrate how observations reported by citizen scientists can be used to develop robust estimates of species distributions and to constrain δD assignments. We developed a Bayesian framework to refine isotopic estimates of migrant animal origins conditional...

Data from: Testing the role of phenotypic plasticity for local adaptation: growth and development in time-constrained Rana temporaria populations

Martin I Lind & Frank Johansson
Phenotypic plasticity can be important for local adaptation, since it enables individuals to survive in a novel environment until genetic changes have been accumulated by genetic accommodation. By analyzing the relationship between development rate and growth rate, it can be determined if plasticity in life history traits is caused by changed physiology or behaviour. We extended this to examine if plasticity had been aiding local adaptation, by investigating if the plastic response had been fixed...

Data from: 28 year temporal sequence of epidemic dynamics in a natural rust – host plant metapopulation

Lars Ericson, Warren J. Müller & Jeremy J. Burdon
A long-term study of disease dynamics caused by the rust Uromyces valerianae in 31 discrete populations of Valeriana salina provides a rare opportunity to explore extended temporal patterns in the epidemiology of a natural host-pathogen metapopulation. Over a 28-year period, pathogen population dynamics varied across the metapopulation with disease incidence (presence/absence), prevalence (% plants infected) and severity (% leaf area covered by lesions) all showing strong population and year effects, indicative of heterogeneity among years...

Data from: Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers

Jin Pan, Baosheng Wang, Zhi-Yong Pei, Wei Zhao, Jie Gao, Jian-Feng Mao & Xiao-Ru Wang
Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing...

Data from: Genome-wide admixture and ecological niche modeling reveal the maintenance of species boundaries despite long history of interspecific gene flow

Amanda R. De La Torre, David R. Roberts & Sally N. Aitken
1.The maintenance of species boundaries despite interspecific gene flow has been a continuous source of interest in evolutionary biology. Many hybridizing species have porous genomes with regions impermeable to introgression, conferring reproductive barriers between species. 2.We used ecological niche modeling to study the glacial and postglacial recolonization patterns between the widely hybridizing spruce species Picea glauca and P. engelmannii in western North America. 3.Genome-wide estimates of admixture based on a panel of 311 candidate gene...

Data from \"Removal of grazers alters the response of tundra soil carbon to warming and enhanced nitrogen availability\", Ecological Monograps in October 2019

Henni Ylänne, Elina Kaarlejärvi, Maria Väisänen, Minna K Männistö, Saija H. K. Ahonen, Johan Olofsson & Sari Stark
Here we present the data used in the manuscript "Removal of grazers alters the response of tundra soil carbon to warming and enhanced nitrogen availability", Ecological Monograps, Early view in October 2019 by H. Ylänne, E. Kaarlejärvi, M. Väisänen, M. K. Männistö, S. H. K. Ahonen, J. Olofsson & S. Stark. In this paper we studied, how five years of experimental warming and increased soil nitrogen availability interact with both long- and short-term differences in...

Data from: Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study

Lina Cai, Eleanor Wheeler, Nicola D. Kerrison, Jian'an Luan, Panos Deloukas, Paul W. Franks, Pilar Amiano, Eva Ardanaz, Catalina Bonet, Guy Fagherazzi, Leif C. Groop, Rudolf Kaaks, José María Huerta, Giovanna Masala, Peter M. Nilsson, Kim Overvad, Valeria Pala, Salvatore Panico, Miguel Rodriguez-Barranco, Olov Rolandsson, Carlotta Sacerdote, Matthias B. Schulze, Annemieke M.W. Spijkeman, Anne Tjonneland, Rosario Tumino … & Nicholas J. Wareham
Type 2 diabetes (T2D) is a global public health challenge. Whilst the advent of genome-wide association studies has identified >400 genetic variants associated with T2D, our understanding of its biological mechanisms and translational insights is still limited. The EPIC-InterAct project, centred in 8 countries in the European Prospective Investigations into Cancer and Nutrition study, is one of the largest prospective studies of T2D. Established as a nested case-cohort study to investigate the interplay between genetic...

Temporal and spatial changes in benthic invertebrate trophic networks along a taxonomic richness gradient

Julie Garrison, Marie Nordström, Jan Albertsson & Francisco Nascimento
Species interactions underlie most ecosystem functions and are important for understanding ecosystem changes. Representing one type of species interaction, trophic networks were constructed from biodiversity monitoring data and known trophic links to assess how ecosystems have changed over time. The Baltic Sea is subject to many anthropogenic pressures, and low species diversity makes it an ideal candidate for determining how pressures change food webs. In this study, we used benthic monitoring data from 20 years...

Experimentally increased snow depth affects High Arctic microarthropods inconsistently over two consecutive winters

Eveline Krab, Erik Lundin, Stephen Coulson, Ellen Dorrepaal & Elisabeth Cooper
Climate change induced alterations to winter conditions may affect decomposer organisms controlling the vast carbon stores in northern soils. Soil microarthropods are abundant decomposers in Arctic ecosystems affecting soil carbon release through their activities. We studied whether increased snow depth affected microarthropods, and if effects were consistent over two consecutive winters. We sampled Collembola and soil mites from a snow accumulation experiment at Svalbard in early summer and used soil microclimatic data to explore to...

Data from: How bird clades diversify in response to climatic and geographic factors

Genoveva Rodriguez-Castaneda, Anouschka R. Hof & Roland Jansson
While the environmental correlates of global patterns in standing species richness are well understood, it is poorly known which environmental factors promote diversification (speciation minus extinction) in clades. We tested several hypotheses for how geographic and climatic variables should affect diversification using a large dataset of bird sister genera endemic to the New World. We found support for the area, evolutionary speed, environmental predictability and climatic stability hypotheses, but productivity and topographic complexity were rejected...

Data from: Edge influence on vegetation at natural and anthropogenic edges of boreal forests in Canada and Fennoscandia

Karen A. Harper, S. Ellen Macdonald, Michael S. Mayerhofer, Shekhar R. Biswas, Per-Anders Esseen, Kristoffer Hylander, Katherine J. Stewart, Azim U. Mallik, Pierre Drapeau, Bengt-Gunnar Jonsson, Daniel Lesieur, Jari Kouki & Yves Bergeron
1. Although anthropogenic edges are an important consequence of timber harvesting, edges due to natural disturbances or landscape heterogeneity are also common. Forest edges have been well-studied in temperate and tropical forests, but less so in less productive, disturbance-adapted boreal forests. 2. We synthesized data on forest vegetation at edges of boreal forests and compared edge influence among edge types (fire, cut, lake/wetland; old vs. young), forest types (broadleaf vs. coniferous) and geographic regions. Our...

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