Rune Halvorsen - Academia.edu (original) (raw)

Papers by Rune Halvorsen

Applied Vegetation Science, 2002

Boreal coniferous forests have been impacted by long distance airborne pollutant deposition for m... more Boreal coniferous forests have been impacted by long distance airborne pollutant deposition for most of the 20th century. Changes in forest understorey vegetation attributable to N-deposition have been observed in southern Sweden, but not so far in southern Norway. We recorded the quantity of all species of vascular plants, bryophytes and lichens in 144 plots in a fertilization experiment in

Global Ecology and Biogeography

Many habitats and species of conservation concern are too rare to be adequately represented in a ... more Many habitats and species of conservation concern are too rare to be adequately represented in a simple random sample of observation units, e.g., for monitoring purposes. Here, we explore possibilities and limitations of a promising alternative approach, probability-based sampling, by which the probability of being sampled is a function of the predicted probability of occurrence in a potential sampling unit. We compare probability-based vs. random sampling for rare and common target phenomena by simulating variables at three nested sample levels allowing investigation of, e.g., presence or absence of a habitat, presence or abundance of a species in the habitat, and properties of this species, and by deriving theoretical limits for the different sampling designs based on a priori knowledge of the properties of the system. We show that the lower limit for target prevalence, allowing for reliable estimation of its properties, can be expressed as a function of the acceptable precision, ...

Nature Communications

Thermal melanism theory states that dark-colored ectotherm organisms are at an advantage at low t... more Thermal melanism theory states that dark-colored ectotherm organisms are at an advantage at low temperature due to increased warming. This theory is generally supported for ectotherm animals, however, the function of colors in the fungal kingdom is largely unknown. Here, we test whether the color lightness of mushroom assemblages is related to climate using a dataset of 3.2 million observations of 3,054 species across Europe. Consistent with the thermal melanism theory, mushroom assemblages are significantly darker in areas with cold climates. We further show differences in color phenotype between fungal lifestyles and a lifestyle differentiated response to seasonality. These results indicate a more complex ecological role of mushroom colors and suggest functions beyond thermal adaption. Because fungi play a crucial role in terrestrial carbon and nutrient cycles, understanding the links between the thermal environment, functional coloration and species' geographical distributions will be critical in predicting ecosystem responses to global warming.

Land Use Policy

Due to the multidisciplinary nature of landscape research, many different systems and methods for... more Due to the multidisciplinary nature of landscape research, many different systems and methods for landscape identification and classification exist. This paper provides a systematic review of 54 contemporary landscape characterisation approaches from all over the world, with the aim of identifying major methodological strategies. Multivariate statistical analyses revealed segregation of the approaches according to the landscape concept applied, the degree of observer independence and various other factors involved in the landscape characterisation process. Our review confirmed a major distinction between approaches rooted in the natural sciences and approaches rooted in the arts and the humanities. Three substantially different methodological approaches or strategies were identified: 1) 'holistic' landscape character assessment approaches, by which visual perception and socio-cultural aspects of the landscape are emphasised; 2) landscape characterisation methods based on a priori selection of geo-ecological and land-use-related properties of the landscape; and 3) biophysical landscape characterisation approaches which rely strongly on statistical analyses in order to identify gradients of variation in the presence and/or abundance of landscape elements and properties. Assessment of landform and the composition of natural and human landscape elements was a central part of all of the reviewed methods. A trend towards increasing observer-independence over time was identified.

Ecography

Sets of presence records used to model species' distributions typically consist of observations c... more Sets of presence records used to model species' distributions typically consist of observations collected opportunistically rather than systematically. As a result, sampling probability is geographically uneven, which may confound the model's characterization of the species' distribution. Modelers frequently address sampling bias by manipulating training data: either subsampling presence data or creating a similar spatial bias in non-presence background data. We tested a new method, which we call 'background thickening', in the latter category. Background thickening entails concentrating background locations around presence locations in proportion to presence location density. We compared background thickening to two established sampling bias correction methods-target group background selection and presence thinning-using simulated data and data from a case study. In the case study, background thickening and presence thinning performed similarly well, both producing better model discrimination than target group background selection, and better model calibration than models without correction. In the simulation, background thickening performed better than presence thinning when the number of simulated presence locations was low, and vice versa. We discuss drawbacks to target group background selection, why background thickening and presence thinning are conservative but robust sampling bias correction methods, and why background thickening is better than presence thinning for small sample sizes. Particularly, background thickening is advantageous for treating sampling bias when data are scarce because it avoids discarding presence records.

Frontiers in Ecology and Evolution

Biological specimens in natural history collections worldwide are increasingly being used in biog... more Biological specimens in natural history collections worldwide are increasingly being used in biogeographical, environmental, and taxonomic studies. For their meaningful use, correct species identification is crucial. For example, clarifying if a species is new to science requires an overview of what has already been described. This includes comparisons with existing authoritative specimens (types). Most type specimens are rather old and their DNA expected to be degraded to various extents. Comparative DNA sequence analysis is in regular use in taxonomic research of today and is essential for identifying and delimiting species. In this study, we focus on lichenized fungi (lichens), in which many species groups are highly inconspicuous and impossible to identify to species based on morphology alone. Our aim was to test the non-mutually exclusive hypotheses that DNA quality of lichens depends on (1) time since collection, (2) taxonomic affinity, and/or (3) habitat/ecology. We included two species from each of four different lichen genera (i.e., Cladonia, Nephroma, Peltigera, and Ramalina), each species pair with a different autecology. For each species, we included samples from approximately every 25 years from present to about 150 years back in time. We used a two-step PCR-based approach followed by sequencing on an Ion Torrent PGM to produce target sequences (mtSSU) of degraded DNA. We received satisfactory DNA sequence information for 54 of 56 specimens. We recovered full-length sequences for several more than 100-years-old specimens, including a 127-years-old specimen, and retrieved enough sequence information for species identification of a 150-years-old specimen. As expected, sequencing success was negatively correlated with age of the specimens. It also varied with taxonomic affinity. We found no significant correlation between sequencing success and habitat ecology of the investigated specimens. The herein tested Ion Torrent sequencing approach outperformed Sanger sequencing with regard to sequencing success and efficiency. We find the protocol used herein highly suitable for obtaining sequences from both young and old lichen specimens and discuss potential improvements to it.

Soil Biology and Biochemistry

Journal of Biogeography

Aim Macroecological scales of species compositional trends are well documented for a variety of p... more Aim Macroecological scales of species compositional trends are well documented for a variety of plant and animal groups, but remain sparse for fungi, despite their ecological 53 importance in carbon and nutrient cycling. It is, thus, essential to understand the composition 54 of fungal assemblages across broad geographical scales, and the underlying drivers. Our 55 overall aim was to describe these patterns for fungi across two nutritional modes 56 (saprotrophic and ectomycorrhizal). Furthermore, we aimed to elucidate the temporal 57 component of fruiting patterns and to relate these to soil carbon and nitrogen deposition. 58 Location Central and northern Europe 59 Methods 4.9 million fungal fruit body observations throughout Europe, collected between 60 1970-2010, were analyzed to determine the two main environmental and geographical 61 gradients structuring fungal assemblages for two main nutritional modes, saprotrophic and 62 ectomycorrhizal fungi. 63 Results Two main gradients explaining the geography of compositional patterns were 64 identified, for each nutritional mode. Mean annual temperature (and related collinear, 65 seasonal measures) correlated most strongly with the first gradient for both nutritional modes. 66 Soil organic carbon was the highest correlate of the second compositional gradient for 67 ectomycorrhizal fungi, suspected as an indicator of vegetation-and pH-related covariates. In 68 contrast, nitrogen deposition constituted a second gradient for saprotrophic fungi, likely a 69 proxy for anthropogenic pollution. Compositional gradients and environmental conditions 70 correlated similarly when the data were divided into two time intervals of 1970-1990 and 71 1991-2010. Evidence of compositional temporal change was highest with increasing altitude 72 and latitude. 73 Main conclusions Fungal assemblage patterns demonstrate clear biogeographical patterns 74 that relate the nutritional modes to their main environmental correlates of temperature, soil

Sommerfeltia

This paper provides a theoretical understanding of sampling bias in presence-only data in the con... more This paper provides a theoretical understanding of sampling bias in presence-only data in the context of species distribution modelling. This understanding forms the basis for two integrated frameworks, one for detecting sampling bias of different kinds in presence-only data (the bias assessment framework) and one for assessing potential effects of sampling bias on species distribution models (the bias effects framework). We exemplify the use of these frameworks to museum data for nine insect species in Norway, for which the distribution along the two main bioclimatic gradients (related to oceanicity and temperatures) are modelled using the MaxEnt method. Models of different complexity (achieved by use of two different model selection procedures that represent spatial prediction or ecological response modelling purposes, respectively) were generated with different types of background data (uninformed and background-target-group [BTG]). The bias assessment framework made use of compa...

Molecular ecology resources, Jan 19, 2018

Analysis of microbial community structure by multivariate ordination methods, using data obtained... more Analysis of microbial community structure by multivariate ordination methods, using data obtained by high-throughput sequencing of amplified markers (i.e., DNA metabarcoding), often requires clustering of DNA sequences into operational taxonomic units (OTUs). Parameters for the clustering procedure tend not to be justified but are set by tradition rather than being based on explicit knowledge. In this study, we explore the extent to which ordination results are affected by variation in parameter settings for the clustering procedure. Amplicon sequence data from nine microbial community studies, representing different sampling designs, spatial scales and ecosystems, were subjected to clustering into OTUs at seven different similarity thresholds (clustering thresholds) ranging from 87% to 99% sequence similarity. The 63 data sets thus obtained were subjected to parallel DCA and GNMDS ordinations. The resulting community structures were highly similar across all clustering thresholds. ...

The Open Marine Biology Journal

The biological reason for a species' presence under given environmental conditions is that the sp... more The biological reason for a species' presence under given environmental conditions is that the species possesses traits that make establishment and survival, usually also reproduction, possible under these conditions. Biological traits analysis (BTA), when coupled with environmental variables, can provide information regarding which traits are to be expected for a given environmental state. As such, BTA provides complementary information to multivariate analysis of community data based on species composition. In this study, BTA was conducted on a data set of sediment macrofauna collected from a temperate fjord system and related to a wide range of environmental variables. The biological traits were analysed in a multiple parallel ordination framework, which can enhance the reliability of the extracted gradient structure and evaluate the importance of weight given to abundance. Two traitclines, gradients in functional attributes of the species, were found in the study area. The first traitcline was related to bottom currents and sediment constituents while the second traitcline was related to current strength and particle deposition on the bottom. Together with a companion study of gradients in species composition (coenoclines), this study of functional features (traitclines) illustrates that the species composition may consist of taxonomically different, but functionally similar species, giving rise to strong gradients in species composition but weak gradients in trait category composition when subjected to ordination analyses.

Molecular Ecology, 2016

Human activity has more than doubled the amount of nitrogen entering the global nitrogen cycle, a... more Human activity has more than doubled the amount of nitrogen entering the global nitrogen cycle, and the boreal forest biome is a nitrogen-limited ecosystem sensitive to nitrogen load perturbation. Although bryophyte-associated microbes contribute significantly to boreal forest ecosystem function, particularly in carbon and nitrogen cycling, little is known about their responses to anthropogenic global change. Amplicon pyrosequencing of the ITS2 region of rDNA was used to investigate how fungal communities associated with three bryophyte species responded to increased nitrogen loads in a long-term fertilization experiment in a boreal Picea abies forest in southern Norway. Overall, OTU richness, community composition and the relative abundance of specific ecological guilds were primarily influenced by host species identity and tissue type. Although not the primary factor affecting fungal communities, nitrogen addition did impact the abundance of specific guilds of fungi and the resulting overall community composition. Increased nitrogen loads decreased ectomycorrhizal abundance, with Amphinema, Cortinarius, Russula and Tylospora OTUs responding negatively to fertilization. Pathogen abundance increased with fertilization, particularly in the moss pathogen Eocronartium. Saprophytic fungi were both positively and negatively impacted by the nitrogen addition, indicating a complex community level response. The overshadowing of the effects of increased nitrogen loads by variation related to host and tissue type highlights the complexity of bryophyte-associated microbial communities and the intricate nature of their responses to anthropogenic global change.

MicrobiologyOpen, Jan 2, 2016

Changing climate is expected to alter precipitation patterns in the Arctic, with consequences for... more 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 higher, while saprotrophic fungi was lower in increased snow depth plots relative to controls. ECM fungal richness was related to soil NO3 -N, NH4 -N, and K; and saprotrophic fungi to NO3 -N and pH. Small but significant changes in the composition of saprotrophic fungi could be attributed to snow treatment and sampling time, but not so for the ECM fungi. Delayed snow melt did not influence the temporal variation in fungal communities between the treatments. Results su...

Microbial Ecology, 2016

High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the... more High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the rough and saline environment. Fungi have adapted to the extremely cold and saline conditions which driftwood faces in the high north. For the first time, we applied high-throughput sequencing to fungi residing in driftwood to reveal their taxonomic richness, community composition, and ecology in the North Atlantic. Using pyrosequencing of ITS2 amplicons obtained from 49 marine logs, we found 807 fungal operational taxonomic units (OTUs) based on clustering at 97 % sequence similarity cut-off level. The phylum Ascomycota comprised 74 % of the OTUs and 20 % belonged to Basidiomycota. The richness of basidiomycetes decreased with prolonged submersion in the sea, supporting the general view of ascomycetes being more extremotolerant. However, more than one fourth of the fungal OTUs remained unassigned to any fungal class, emphasising the need for better DNA reference data from the marine habitat. Different fungal communities were detected in coniferous and deciduous logs. Our results highlight that driftwood hosts a considerably higher fungal diversity than currently known. The driftwood fungal community is not a terrestrial relic but a speciose assemblage of fungi adapted to the stressful marine environment and different kinds of wooden substrates found in it.

Molecular Ecology, 2015

Ectomycorrhizal (ECM) fungi are important for efficient nutrient uptake of several widespread arc... more Ectomycorrhizal (ECM) fungi are important for efficient nutrient uptake of several widespread arctic plant species. Knowledge of temporal variation of ECM fungi, and the relationship of these patterns to environmental variables, is essential to understand energy and nutrient cycling in Arctic ecosystems. We sampled roots of Bistorta vivipara ten times over two years; three times during the growing-season (June, July and September) and twice during winter (November and April) of both years. We found 668 ECM OTUs belonging to 25 different ECM lineages, whereof 157 OTUs persisted throughout all sampling time-points. Overall, ECM fungal richness peaked in winter and species belonging to Cortinarius, Serendipita and Sebacina were more frequent in winter than during summer. Structure of ECM fungal communities was primarily affected by spatial factors. However, after accounting for spatial effects, significant seasonal variation was evident revealing correspondence with seasonal changes in environmental conditions. We demonstrate that arctic ECM richness and community structure differ between summer (growing-season) and winter, possibly due to reduced activity of the core community, and addition of fungi adapted for winter conditions forming a winter-active fungal community. Significant month × year interactions were observed both for fungal richness and community composition, indicating unpredictable between-year variation. Our study indicates that addressing seasonal changes requires replication over several years. This article is protected by copyright. All rights reserved.