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1.	Cardoso Pereira, Cássio, et al. (författare) Subtle structures with not-so-subtle functions : A data set of arthropod constructs and their host plants 2022 Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 103:4 Tidskriftsartikel (refereegranskat)abstract The construction of shelters on plants by arthropods might influence other organisms via changes in colonization, community richness, species composition, and functionality. Arthropods, including beetles, caterpillars, sawflies, spiders, and wasps often interact with host plants via the construction of shelters, building a variety of structures such as leaf ties, tents, rolls, and bags; leaf and stem galls, and hollowed out stems. Such constructs might have both an adaptive value in terms of protection (i.e., serve as shelters) but may also exert a strong influence on terrestrial community diversity in the engineered and neighboring hosts via colonization by secondary occupants. Although different traits of the host plant (e.g., physical, chemical, and architectural features) may affect the potential for ecosystem engineering by insects, such effects have been, to a certain degree, overlooked. Further analyses of how plant traits affect the occurrence of shelters may therefore enrich our understanding of the organizing principles of plant-based communities. This data set includes more than 1000 unique records of ecosystem engineering by arthropods, in the form of structures built on plants. All records have been published in the literature, and span both natural structures (91% of the records) and structures artificially created by researchers (9% of the records). The data were gathered between 1932 and 2021, across more than 50 countries and several ecosystems, ranging from polar to tropical zones. In addition to data on host plants and engineers, we aggregated data on the type of constructs and the identity of inquilines using these structures. This data set highlights the importance of these subtle structures for the organization of terrestrial arthropod communities, enabling hypotheses testing in ecological studies addressing ecosystem engineering and facilitation mediated by constructs. There are no copyright restrictions and please cite this paper when using the data in publications.
2.	Laubmeier, A. N., et al. (författare) From theory to experimental design : Quantifying a trait-based theory of predator-prey dynamics 2018 Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 13:4 Tidskriftsartikel (refereegranskat)abstract Successfully applying theoretical models to natural communities and predicting ecosystem behavior under changing conditions is the backbone of predictive ecology. However, the experiments required to test these models are dictated by practical constraints, and models are often opportunistically validated against data for which they were never intended. Alternatively, we can inform and improve experimental design by an in-depth pre-experimental analysis of the model, generating experiments better targeted at testing the validity of a theory. Here, we describe this process for a specific experiment. Starting from food web ecological theory, we formulate a model and design an experiment to optimally test the validity of the theory, supplementing traditional design considerations with model analysis. The experiment itself will be run and described in a separate paper. The theory we test is that trophic population dynamics are dictated by species traits, and we study this in a community of terrestrial arthropods. We depart from the Allometric Trophic Network (ATN) model and hypothesize that including habitat use, in addition to body mass, is necessary to better model trophic interactions. We therefore formulate new terms which account for micro-habitat use as well as intra-and interspecific interference in the ATN model. We design an experiment and an effective sampling regime to test this model and the underlying assumptions about the traits dominating trophic interactions. We arrive at a detailed sampling protocol to maximize information content in the empirical data obtained from the experiment and, relying on theoretical analysis of the proposed model, explore potential shortcomings of our design. Consequently, since this is a "pre-experimental" exercise aimed at improving the links between hypothesis formulation, model construction, experimental design and data collection, we hasten to publish our findings before analyzing data from the actual experiment, thus setting the stage for strong inference.
3.	Romero, Gustavo Q., et al. (författare) Climate variability and aridity modulate the role of leaf shelters for arthropods : A global experiment 2022 Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 28:11, s. 3694-3710 Tidskriftsartikel (refereegranskat)abstract Current climate change is disrupting biotic interactions and eroding biodiversity worldwide. However, species sensitive to aridity, high temperatures, and climate variability might find shelter in microclimatic refuges, such as leaf rolls built by arthropods. To explore how the importance of leaf shelters for terrestrial arthropods changes with latitude, elevation, and climate, we conducted a distributed experiment comparing arthropods in leaf rolls versus control leaves across 52 sites along an 11,790 km latitudinal gradient. We then probed the impact of short- versus long-term climatic impacts on roll use, by comparing the relative impact of conditions during the experiment versus average, baseline conditions at the site. Leaf shelters supported larger organisms and higher arthropod biomass and species diversity than non-rolled control leaves. However, the magnitude of the leaf rolls' effect differed between long- and short-term climate conditions, metrics (species richness, biomass, and body size), and trophic groups (predators vs. herbivores). The effect of leaf rolls on predator richness was influenced only by baseline climate, increasing in magnitude in regions experiencing increased long-term aridity, regardless of latitude, elevation, and weather during the experiment. This suggests that shelter use by predators may be innate, and thus, driven by natural selection. In contrast, the effect of leaf rolls on predator biomass and predator body size decreased with increasing temperature, and increased with increasing precipitation, respectively, during the experiment. The magnitude of shelter usage by herbivores increased with the abundance of predators and decreased with increasing temperature during the experiment. Taken together, these results highlight that leaf roll use may have both proximal and ultimate causes. Projected increases in climate variability and aridity are, therefore, likely to increase the importance of biotic refugia in mitigating the effects of climate change on species persistence.
4.	Wootton, Kate, et al. (författare) Beyond body size-new traits for new heights in trait-based modelling of predator-prey dynamics 2022 Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 17:7 July Tidskriftsartikel (refereegranskat)abstract Food webs map feeding interactions among species, providing a valuable tool for understanding and predicting community dynamics. Using species' body sizes is a promising avenue for parameterizing food-web models, but such approaches have not yet been able to fully recover observed community dynamics. Such discrepancies suggest that traits other than body size also play important roles. For example, differences in species' use of microhabitat or non-consumptive effects of intraguild predators may affect dynamics in ways not captured by body size. In Laubmeier et al. (2018), we developed a dynamic food-web model incorporating microhabitat and non-consumptive predator effects in addition to body size, and used simulations to suggest an optimal sampling design of a mesocosm experiment to test the model. Here, we perform the mesocosm experiment to generate empirical timeseries of insect herbivore and predator abundance dynamics. We minimize least squares error between the model and time-series to determine parameter values of four alternative models, which differ in terms of including vs excluding microhabitat use and non-consumptive predator-predator effects. We use both statistical and expert-knowledge criteria to compare the models and find including both microhabitat use and non-consumptive predatorpredator effects best explains observed aphid and predator population dynamics, followed by the model including microhabitat alone. This ranking suggests that microhabitat plays a larger role in driving population dynamics than non-consumptive predator-predator effects, although both are clearly important. Our results illustrate the importance of additional traits alongside body size in driving trophic interactions. They also point to the need to consider trophic interactions and population dynamics in a wider community context, where non-trophic impacts can dramatically modify the interplay between multiple predators and prey. Overall, we demonstrate the potential for utilizing traits beyond body size to improve traitbased models and the value of iterative cycling between theory, data and experiment to hone current insights into how traits affect food-web dynamics. © 2022 Wootton et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
5.	Wootton, Kate L., et al. (författare) Food webs coupled in space : Consumer foraging movement affects both stocks and fluxes 2023 Ingår i: Ecology. - : John Wiley & Sons. - 0012-9658 .- 1939-9170. ; 104:8 Tidskriftsartikel (refereegranskat)abstract The exchange of material and individuals between neighboring food webs is ubiquitous and affects ecosystem functioning. Here, we explore animal foraging movement between adjacent, heterogeneous habitats and its effect on a suite of interconnected ecosystem functions. Combining dynamic food web models with nutrient-recycling models, we study foraging across habitats that differ in fertility and plant diversity. We found that net foraging movement flowed from high to low fertility or high to low diversity and boosted stocks and flows across the whole loop of ecosystem functions, including biomass, detritus, and nutrients, in the recipient habitat. Contrary to common assumptions, however, the largest flows were often between the highest and intermediate fertility habitats rather than highest and lowest. The effect of consumer influx on ecosystem functions was similar to the effect of increasing fertility. Unlike fertility, however, consumer influx caused a shift toward highly predator-dominated biomass distributions, especially in habitats that were unable to support predators in the absence of consumer foraging. This shift resulted from both direct and indirect effects propagated through the interconnected ecosystem functions. Only by considering both stocks and fluxes across the whole loop of ecosystem functions do we uncover the mechanisms driving our results. In conclusion, the outcome of animal foraging movements will differ from that of dispersal and diffusion. Together we show how considering active types of animal movement and the interconnectedness of ecosystem functions can aid our understanding of the patchy landscapes of the Anthropocene.
6.	Wootton, Kate, et al. (författare) Towards a modular theory of trophic interactions 2023 Ingår i: Functional Ecology. - : John Wiley & Sons. - 0269-8463 .- 1365-2435. ; 37:1, s. 26-43 Tidskriftsartikel (refereegranskat)abstract Species traits and environmental conditions determine the occurrence and strength of trophic interactions. If we understand the relationship between these factors and trophic interactions, we can make more accurate predictions and build better trophic-interaction models. We can compare traits and conditions by considering their effect on different parts (steps) of a trophic interaction, such as the steps search and pursuit. By linking traits to relevant steps, we can use these relationships to build trophic-interaction models. Currently, this is done ad hoc, defining steps based on the species and traits of interest. This makes it difficult to compare across traits and species and gain an overarching understanding of how traits and the environment drive trophic interactions. We present a comprehensive approach for the explicit choice of interaction steps and species traits or environmental conditions, which is readily integrated into existing models. The core of this framework is that it is modular; we present eight steps that occur in all trophic interactions and use them to build a modular, general dynamic model. When applying the framework, one explicitly selects only the most relevant steps and uses those to build a specific model. To build our modular framework, we revisit and expand the functional and numerical response functions, dividing the trophic interaction into eight steps: (1) search, (2) prey detection, (3) attack decision, (4) pursuit, (5) subjugation, (6) ingestion, (7) digestion and (8) nutrient allocation. Together these steps form a general dynamical model where trophic interactions can be explicitly parameterized for multiple traits and environmental factors. We then concretize this approach by outlining how a specific community can be modelled by selecting key modules (steps) and parameterizing them for relevant factors. This we exemplify for a community of terrestrial arthropods using empirical data on body size and temperature responses. With species interactions at the core of community dynamics, our modular approach allows for quantification and comparisons of the importance of different steps, traits, and abiotic factors across ecosystems and trophic-interaction types, and provides a powerful tool for trait-based prediction of food-web structure and dynamics. A free Plain Language Summary can be found within the Supporting Information of this article.
7.	Abrego, Nerea, et al. (författare) Accounting for environmental variation in co-occurrence modelling reveals the importance of positive interactions in root-associated fungal communities 2020 Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 29:14, s. 2736-2746 Tidskriftsartikel (refereegranskat)abstract Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. We generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more probably reflect interactive associations. Our results indicate that not only negative but also positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.
8.	Abrego, Nerea, et al. (författare) Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient 2020 Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 10:16, s. 8989-9002 Tidskriftsartikel (refereegranskat)abstract How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root-associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities.
9.	Aguilera, Guillermo, et al. (författare) Crop diversity benefits carabid and pollinator communities in landscapes with semi‐natural habitats 2020 Ingår i: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. Tidskriftsartikel (refereegranskat)
10.	Aguilera Nuñez, Guillermo, et al. (författare) Organic fertilisation enhances generalist predators and suppresses aphid growth in the absence of specialist predators 2021 Ingår i: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. ; 58, s. 1455-1465 Tidskriftsartikel (refereegranskat)abstract Biological control by natural enemies is a valuable ecosystem service. The predator community in a crop field is a combination of predators dwelling in the field and those moving into it from the surrounding landscape. The former is mainly affected by field management, the latter more by the composition of the surrounding landscape. Yet, separate and combined effects of local and landscape management on pest suppression have seldom been investigated.We set-up mesocosms within an existing long-term agricultural field experiment to investigate the effects of local management of organic manure or inorganic mineral fertilisation, and simulated the spillover from the surrounding landscape of different predator types: no predators, generalist predators (wolf spiders) and specialist predators (ladybirds). We examined whether aphid density was driven by top-down or bottom-up processes under different fertilisation treatments, and how the magnitude of pest suppression was affected by predator community composition.We found positive synergistic effects between manure fertilisation and predator spillover on the suppression of aphid growth. Top-down suppression of aphids was more effective under manure fertilisation and in presence of specialist predators (ladybirds). Bottom-up effects on the plant biomass growth dominated in inorganically fertilised plots.Organic and inorganic fertilisation gave the same yield, but through different mechanisms. The abundance of locally emerging predators in the manure treatment increased top-down pest suppression yielding plant biomass levels comparable with inorganically fertilised plants, being the latter driven by bottom-up effects.Synthesis and applications. Organic fertilisation enhanced local emergence of predators increasing top-down pest suppression. In contrast, local predator communities were unable to suppress aphid populations in inorganic and no fertilisation treatments. Here, predator inflow from outside the crop field was essential for lowering aphid population growth. Managing landscapes to promote mobile predators emerges as particularly important for crop fields without manure amendments. We advise the active promotion of both local predators in the crop field and mobile predators in the landscape to secure the conservation of biological insect pest suppression.
11.	Andersson, Petter, 1975- (författare) The importance of search behavior and movements for spatial distributions of herbivorous insects 2011 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Insect populations commonly show large spatial variation in density, and much variation have been shown to be explained by the search behavior applied by the insect when locating habitat patches. This thesis explores the importance of odor-mediated attraction for immigration rates of herbivorous insects in relation to the size of the patches and the density of host plants within the patches. By using electroantennogram and measuring moth antennal responses to sex pheromones and thereby estimating the relative odor-mediated attraction from odor patches in field experiments (Paper I, III), I show that the length of the odor plumes emanating from the patches increase proportional with the square-root of the number of odor sources. In laboratory and field experiments (with the weevils Cionus scrophulariae and C. tuberculosus and the host plant figwort Scrophularia nodosa; Paper II) and meta-analyses on multiple insect herbivores (Paper III), I examined whether the relative increase in plume length could also predict the immigration rates of olfactory searching insects in relation to patches with increasing area and increasing density of host plants. The experiments (Paper II) and meta-analyses (Paper III) showed that the observed immigration rates of olfactory searching insects was well predicted by the relative increase in plume length, as estimated from the electroantennogram measurements (Paper I, III). The importance of immigration rates, relative to the effect of emigration and local growth was also investigated for the Cionus weevils in natural S. nodosa patches (Paper IV). This study showed that the density-patch size relationships of the weevils during early season were predicted by the net scaling of emigration and immigration rates, and differences in density-patch size relationships between the two species could be explained by inter-specific differences in their emigration rates from small patches. In conclusion, this thesis shows that search behavior can be used to predict immigration rates and spatial distributions of insects, with implications for pest control, conservation ecology and general ecological theory.
12.	Antão, Laura H., et al. (författare) Climate change reshuffles northern species within their niches 2022 Ingår i: Nature Climate Change. - : Springer Science and Business Media LLC. - 1758-678X .- 1758-6798. ; 12:6, s. 587-592 Tidskriftsartikel (refereegranskat)abstract Climate change is a pervasive threat to biodiversity. While range shifts are a known consequence of climate warming contributing to regional community change, less is known about how species’ positions shift within their climatic niches. Furthermore, whether the relative importance of different climatic variables prompting such shifts varies with changing climate remains unclear. Here we analysed four decades of data for 1,478 species of birds, mammals, butterflies, moths, plants and phytoplankton along a 1,200 km high latitudinal gradient. The relative importance of climatic drivers varied non-uniformly with progressing climate change. While species turnover among decades was limited, the relative position of species within their climatic niche shifted substantially. A greater proportion of species responded to climatic change at higher latitudes, where changes were stronger. These diverging climate imprints restructure a full biome, making it difficult to generalize biodiversity responses and raising concerns about ecosystem integrity in the face of accelerating climate change.
13.	Bahram, Mohammad, et al. (författare) Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee 2022 Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 17 Tidskriftsartikel (refereegranskat)abstract To assess a species’ impact on its environment–and the environment’s impact upon a species–we need to pinpoint its links to surrounding taxa. The honeybee (Apis mellifera) provides a promising model system for such an exercise. While pollination is an important ecosystem service, recent studies suggest that honeybees can also provide disservices. Developing a comprehensive understanding of the full suite of services and disservices that honeybees provide is a key priority for such a ubiquitous species. In this perspective paper, we propose that the DNA contents of honey can be used to establish the honeybee’s functional niche, as reflected by ecosystem services and disservices. Drawing upon previously published genomic data, we analysed the DNA found within 43 honey samples from Northern Europe. Based on metagenomic analysis, we find that the taxonomic composition of DNA is dominated by a low pathogenicity bee virus with 40.2% of the reads, followed by bacteria (16.7%), plants (9.4%) and only 1.1% from fungi. In terms of ecological roles of taxa associated with the bees or taxa in their environment, bee gut microbes dominate the honey DNA, with plants as the second most abundant group. A range of pathogens associated with plants, bees and other animals occur frequently, but with lower relative read abundance, across the samples. The associations found here reflect a versatile the honeybee’s role in the North-European ecosystem. Feeding on nectar and pollen, the honeybee interacts with plants–in particular with cultivated crops. In doing so, the honeybee appears to disperse common pathogens of plants, pollinators and other animals, but also microbes potentially protective of these pathogens. Thus, honey-borne DNA helps us define the honeybee’s functional niche, offering directions to expound the benefits and drawbacks of the associations to the honeybee itself and its interacting organisms.
14.	Blanchet, F. Guillaume, et al. (författare) Related herbivore species show similar temporal dynamics 2018 Ingår i: Journal of Animal Ecology. - : Wiley. - 0021-8790 .- 1365-2656. ; 87:3, s. 801-812 Tidskriftsartikel (refereegranskat)abstract 1. Within natural communities, different taxa display different dynamics in time. Why this is the case we do not fully know. This thwarts our ability to predict changes in community structure, which is important for both the conservation of rare species in natural communities and for the prediction of pest outbreaks in agriculture. 2. Species sharing phylogeny, natural enemies and/or life-history traits have been hypothesized to share similar temporal dynamics. We operationalized these concepts into testing whether feeding guild, voltinism, similarity in parasitoid community and/or phylogenetic relatedness explained similarities in temporal dynamics among herbivorous community members. 3. Focusing on two similar datasets from different geographical regions (Finland and Japan), we used asymmetric eigenvector maps as temporal variables to characterize species-and community-level dynamics of specialist insect herbivores on oak (Quercus). We then assessed whether feeding guild, voltinism, similarity in parasitoid community and/or phylogenetic relatedness explained similarities in temporal dynamics among taxa. 4. Species-specific temporal dynamics varied widely, ranging from directional decline or increase to more complex patterns. Phylogeny was a clear predictor of similarity in temporal dynamics at the Finnish site, whereas for the Japanese site, the data were uninformative regarding a phylogenetic imprint. Voltinism, feeding guild and parasitoid overlap explained little variation at either location. Despite the rapid temporal dynamics observed at the level of individual species, these changes did not translate into any consistent temporal changes at the community level in either Finland or Japan. 5. Overall, our findings offer no direct support for the notion that species sharing natural enemies and/or life-history traits would be characterized by similar temporal dynamics, but reveal a strong imprint of phylogenetic relatedness. As this phylogenetic signal cannot be attributed to guild, voltinism or parasitoids, it will likely derive from shared microhabitat, microclimate, anatomy, physiology or behaviour. This has important implications for predicting insect outbreaks and for informing insect conservation. We hope that future studies will assess the generality of our findings across plant-feeding insect communities and beyond, and establish the more precise mechanism(s) underlying the phylogenetic imprint.
15.	Bommarco, Riccardo, et al. (författare) International scientists formulate a roadmap for insect conservation and recovery 2020 Ingår i: Nature ecology & evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 4, s. 174-176 Tidskriftsartikel (refereegranskat)
16.	Cirtwill, Alyssa, et al. (författare) A quantitative framework for investigating the reliability of empirical network construction 2019 Ingår i: Methods in Ecology and Evolution. - : WILEY. - 2041-210X. ; 10:6, s. 902-911 Tidskriftsartikel (refereegranskat)abstract Descriptions of ecological networks typically assume that the same interspecific interactions occur each time a community is observed. This contrasts with the known stochasticity of ecological communities: community composition, species abundances and link structure all vary in space and time. Moreover, finite sampling generates variation in the set of interactions actually observed. For interactions that have not been observed, most datasets will not contain enough information for the ecologist to be confident that unobserved interactions truly did not occur. Here, we develop the conceptual and analytical tools needed to capture uncertainty in the estimation of pairwise interactions. To define the problem, we identify the different contributions to the uncertainty of an interaction. We then outline a framework to quantify the uncertainty around each interaction by combining data on observed co-occurrences with prior knowledge. We illustrate this framework using perhaps the most extensively sampled network to date. We found significant uncertainty in estimates for the probability of most pairwise interactions. This uncertainty can, however, be constrained with informative priors. This uncertainty scaled up to summary measures of network structure such as connectance and nestedness. Even with informative priors, we are likely to miss many interactions that may occur rarely or under different local conditions. Overall, we demonstrate the importance of acknowledging the uncertainty inherent in network studies, and the utility of treating interactions as probabilities in pinpointing areas where more study is needed. Most importantly, we stress that networks are best thought of as systems constructed from random variables, the stochastic nature of which must be acknowledged for an accurate representation. Doing so will fundamentally change network analyses and yield greater realism.
17.	Cirtwill, Alyssa, et al. (författare) Between-year changes in community composition shape species' roles in an Arctic plant-pollinator network 2018 Ingår i: Oikos. - : WILEY. - 0030-1299 .- 1600-0706. ; 127:8, s. 1163-1176 Tidskriftsartikel (refereegranskat)abstract Inter-annual turnover in community composition can affect the richness and functioning of ecological communities. If incoming and outgoing species do not interact with the same partners, ecological functions such as pollination may be disrupted. Here, we explore the extent to which turnover affects species' roles - as defined based on their participation in different motifs positions - in a series of temporally replicated plant-pollinator networks from high-Arctic Zackenberg, Greenland. We observed substantial turnover in the plant and pollinator assemblages, combined with significant variation in species' roles between networks. Variation in the roles of plants and pollinators tended to increase with the amount of community turnover, although a negative interaction between turnover in the plant and pollinator assemblages complicated this trend for the roles of pollinators. This suggests that increasing turnover in the future will result in changes to the roles of plants and likely those of pollinators. These changing roles may in turn affect the functioning or stability of this pollination network.
18.	Cirtwill, Alyssa R., et al. (författare) Flower-visitor and pollen-load data provide complementary insight into species and individual network roles 2024 Ingår i: Oikos. - : John Wiley & Sons. - 0030-1299 .- 1600-0706. ; :4 Tidskriftsartikel (refereegranskat)abstract Most animal pollination results from plant–insect interactions, but how we perceive these interactions may differ with the sampling method adopted. The two most common methods are observations of visits by pollinators to plants and observations of pollen loads carried by insects. Each method could favour the detection of different species and interactions, and pollen load observations typically reveal more interactions per individual insect than visit observations. Moreover, while observations concern plant and insect individuals, networks are frequently analysed at the level of species. Although networks constructed using visitation and pollen-load data have occasionally been compared in relatively specialised, bee-dominated systems, it is not known how sampling methodology will affect our perception of how species (and individuals within species) interact in a more generalist system. Here we use a Diptera-dominated high-Arctic plant–insect community to explore how sampling approach shapes several measures of species' interactions (focusing on specialisation), and what we can learn about how the interactions of individuals relate to those of species. We found that species degrees, interaction strengths, and species motif roles were significantly correlated across the two method-specific versions of the network. However, absolute differences in degrees and motif roles were greater than could be explained by the greater number of interactions per individual provided by the pollen-load data. Thus, despite the correlations between species roles in networks built using visitation and pollen-load data, we infer that these two perspectives yield fundamentally different summaries of the ways species fit into their communities. Further, individuals' roles generally predicted the species' overall role, but high variability among individuals means that species' roles cannot be used to predict those of particular individuals. These findings emphasize the importance of adopting a dual perspective on bipartite networks, as based on the different information inherent in insect visits and pollen loads.
19.	Danielsson, Rebecca, et al. (författare) Compound- and context-dependent effects of antibiotics on greenhouse gas emissions from livestock 2019 Ingår i: Royal Society Open Science. - : The Royal Society. - 2054-5703. ; 6 Tidskriftsartikel (refereegranskat)abstract The use of antibiotics in livestock production may trigger ecosystem disservices, including increased emissions of greenhouse gases. To evaluate this, we conducted two separate animal experiments, administering two widely used antibiotic compounds (benzylpenicillin and tetracycline) to dairy cows over a 4- or 5-day period locally and/or systemically. We then recorded enteric methane production, total gas production from dung decomposing under aerobic versus anaerobic conditions, prokaryotic community composition in rumen and dung, and accompanying changes in nutrient intake, rumen fermentation, and digestibility resulting from antibiotic administration. The focal antibiotics had no detectable effect on gas emissions from enteric fermentation or dung in aerobic conditions, while they decreased total gas production from anaerobic dung. Microbiome-level effects of benzylpenicillin proved markedly different from those previously recorded for tetracycline in dung, and did not differ by the mode of administration (local or systemic). Antibiotic effects on gas production differed substantially between dung maintained under aerobic versus anaerobic conditions and between compounds. These findings demonstrate compound- and context-dependent impacts of antibiotics on methane emissions and underlying processes, and highlight the need for a global synthesis of data on agricultural antibiotic use before understanding their climatic impacts.
20.	Danielsson, Rebecca, et al. (författare) Effect of tetracycline and penicillin on total gas production from dairy cow feces 2018 Ingår i: Rapport / Sveriges lantbruksuniversitet, Institutionen för husdjurens utfodring och vård. - 0347-9838. ; , s. 133-134 Konferensbidrag (refereegranskat)
21.	de La Peña Aguilera, Pablo, et al. (författare) Consistent imprints of elevation, soil temperature and moisture on plant and arthropod communities across two subarctic landscapes 2023 Ingår i: Insect Conservation and Diversity. - 1752-458X .- 1752-4598. ; 16, s. 684-700 Tidskriftsartikel (refereegranskat)abstract 1. Factors shaping arthropod and plant community structure at fine spatial scales are poorly understood. This includes microclimate, which likely plays a large role in shaping local community patterns, especially in heterogeneous landscapes characterised by high microclimatic variability in space and in time.2. We explored differences in local microclimatic conditions and regional species pools in two subarctic regions: Kilpisj & auml;rvi in north-west Finland and Varanger in north-east Norway. We then investigated the relationship between fine-scale climatic variation and local community characteristics (species richness and abundance) among plants and arthropods, differentiating the latter into two groups: flying and ground-dwelling arthropods collected by Malaise and pitfall traps, respectively. Arthropod taxa were identified through DNA metabarcoding. Finally, we examined if plant richness can be used to predict patterns in arthropod communities.3. Variation in soil temperature, moisture and snow depth proved similar between regions, despite differences in absolute elevation. For each group of organisms, we found that about half of the species were shared between Kilpisj & auml;rvi and Varanger, with a quarter unique to each region.4. Plants and arthropods responded largely to the same drivers. The richness and abun-dance of both groups decreased as elevation increased and were positively correlated with higher soil moisture and temperature values. Plant species richness was a poor predictor of local arthropod richness, in particular for ground-dwelling arthropods.5. Our results reveal how microclimatic variation within each region carves pro-nounced, yet consistent patterns in local community richness and abundance out of a joint species pool.
22.	de La Peña Aguilera, Pablo, et al. (författare) Little directional change in the timing of Arctic spring phenology over the past 25 years 2023 Ingår i: Current Biology. - 0960-9822 .- 1879-0445. ; 33, s. 3244- Tidskriftsartikel (refereegranskat)abstract With the global change in climate, the Arctic has been pinpointed as the region experiencing the fastest rates of change. As a result, Arctic biological responses-such as shifts in phenology-are expected to outpace those at lower latitudes. 15 years ago, a decade-long dataset from Zackenberg in High Arctic Greenland revealed rapid rates of phenological change.1 To explore how the timing of spring phenology has developed since, we revisit the Zackenberg time series on flowering plants, arthropods, and birds. Drawing on the full 25-year period of 1996-2020, we find little directional change in the timing of events despite ongoing climatic change. We attribute this finding to a shift in the temporal patterns of climate conditions, from previous directional change to current high inter-annual variability. Additionally, some taxa appear to have reached the limits of their phenological responses, resulting in a leveling off in their phenological responses in warm years. Our findings demonstrate the importance of long-term monitoring of taxa from across trophic levels within the community, allowing for detecting shifts in sensitivities and responses and thus for updated inference in the light of added information.
23.	Ekholm, Adam, et al. (författare) Community phenology of insects on oak : local differentiation along a climatic gradient 2021 Ingår i: Ecosphere. - : Wiley. - 2150-8925. ; 12:11 Tidskriftsartikel (refereegranskat)abstract Climate change is advancing the onset of phenological events, with the rate of advance varying among species and trophic levels. In addition, local populations of the same species may show genetic differences in their response to seasonal cues. If populations of interacting species differ in their response, then climate change may result in geographically varying shifts in the community-level distribution of interaction strength. We explored the magnitude of trophic- and species-level responses to temperature in a tritrophic system comprising pedunculate oak, insect herbivores, and their associated parasitoids. We sampled local realizations of this community at five sites along a transect spanning fifteen degrees of latitude. Samples from each trophic level at each site were exposed to the same set of five climatic regimes during overwintering in climate chambers. We then recorded the number of days and degree-days required for oak acorns to develop and insects to emerge. In terms of dates of events, phenology differed among populations. In terms of degree-days, we found that for two species pairs, the heat sum required to develop in spring differed by an additional ˜500 degree-days between trophic levels when overwintering at the highest temperature. For three species, within-population variation in the number of degree-days required for emergence was higher at warmer temperatures. Our findings suggest that changing temperatures can modify interactions within a community by altering the relative phenology of interacting species and that some interactions are more vulnerable than others to a shift in temperature. The geographic variation in the phenological response of a species suggests that there is a genetic component in determining the phenology of local populations. Such local variation blended with interspecific differences in responses makes it complex to understand how communities will respond to warmer temperatures.
24.	Ekholm, Adam, et al. (författare) Dispersal, host genotype and environment shape the spatial dynamics of a parasite in the wild 2017 Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 98:10, s. 2574-2584 Tidskriftsartikel (refereegranskat)abstract Dispersal, environment and genetic variation may all play a role in shaping host-parasite dynamics. Yet, in natural systems, their relative importance remains unresolved. Here, we do so for the epidemiology of a specialist parasite (Erysiphe alphitoides) on the pedunculate oak (Quercus robur). For this purpose, we combine evidence from a multi-year field survey and two dispersal experiments, all conducted at the landscape scale. Patterns detected in the field survey suggest that the parasite is structured as a metapopulation, with trees in denser oak stands characterized by higher parasite occupancy, higher colonization rates and lower extinction rates. The dispersal experiments revealed a major impact of the environment and of host genotype on the presence and abundance of the parasite, with a weaker but detectable imprint of dispersal limitation. Overall, our findings emphasize that dispersal, host genotype and the environment jointly shape the spatial dynamics of a parasite in the wild.
25.	Ekholm, Adam, et al. (författare) Herbivory in a changing climate-Effects of plant genotype and experimentally induced variation in plant phenology on two summer-active lepidopteran herbivores and one fungal pathogen 2022 Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 12:1 Tidskriftsartikel (refereegranskat)abstract With climate change, spring warming tends to advance plant leaf-out. While the timing of leaf-out has been shown to affect the quality of leaves for herbivores in spring, it is unclear whether such effects extend to herbivores active in summer. In this study, we first examined how spring and autumn phenology of seven Quercus robur genotypes responded to elevated temperatures in spring. We then tested whether the performance of two summer-active insect herbivores (Orthosia gothica and Polia nebulosa) and infection by a pathogen (Erysiphe alphitoides) were influenced by plant phenology, traits associated with genotype or the interaction between these two. Warm spring temperatures advanced both bud development and leaf senescence in Q. robur. Plants of different genotype differed in terms of both spring and autumn phenology. Plant phenology did not influence the performance of two insect herbivores and a pathogen, while traits associated with oak genotype had an effect on herbivore performance. Weight gain for O. gothica and ingestion for P. nebulosa differed by a factor of 4.38 and 2.23 among genotypes, respectively. Herbivore species active in summer were influenced by traits associated with plant genotype but not by phenology. This suggest that plant attackers active in summer may prove tolerant to shifts in host plant phenology-a pattern contrasting with previously documented effects on plant attackers active in spring and autumn.
26.	Ekholm, Adam, et al. (författare) Host plant phenology, insect outbreaks and herbivore communities - The importance of timing 2020 Ingår i: Journal of Animal Ecology. - : Wiley. - 0021-8790 .- 1365-2656. ; 89:3, s. 829-841 Tidskriftsartikel (refereegranskat)abstract Climate change may alter the dynamics of outbreak species by changing the phenological synchrony between herbivores and their host plants. As host plant phenology has a genotypic component that may interact with climate, infestation levels among genotypes might change accordingly. When the outbreaking herbivore is active early in the season, its infestation levels may also leave a detectable imprint on herbivores colonizing the plant later in the season. In this study, we first investigated how the spring phenology and genotype of Quercus robur influenced the density of the spring-active, outbreaking leaf miner Acrocercops brongniardellus. We then assessed how intraspecific density affected the performance of A. brongniardellus and how oak genotype and density of A. brongniardellus affected the insect herbivore community. We found that Q. robur individuals of late spring phenology were more strongly infested by A. brongniardellus. Conspecific pupae on heavily infested oaks tended to be lighter, and fewer heterospecific insect herbivores colonized the oak later in the season. Beyond its effects through phenology, plant genotype left an imprint on herbivore species richness and on two insect herbivores. Our results suggest a chain of knock-on effects from plant phenology, through the outbreaking species to the insect herbivore community. Given the finding of how phenological synchrony between the outbreak species and its host plant influences infestation levels, a shift in synchrony may then change outbreak dynamics and cause cascading effects on the insect community.
27.	Ekholm, Adam, et al. (författare) The forgotten season : the impact of autumn phenology on a specialist insect herbivore community on oak 2019 Ingår i: Ecological Entomology. - : Wiley. - 0307-6946 .- 1365-2311. ; 44:3, s. 425-435 Tidskriftsartikel (refereegranskat)abstract 1. Variation in spring phenology - like tree budburst - affects the structure of insect communities, but impacts of autumn phenology have been neglected. Many plant species have recently delayed their autumn phenology, and the timing of leaf senescence may be important for herbivorous insects.2. This study explored how an insect herbivore community associated with Quercus robur is influenced by variation in autumn phenology. For this, schools were asked to record, across the range of oak in Sweden, the autumn phenology of oaks and to conduct a survey of the insect community.3. To tease apart the relative impacts of climate from that of tree phenology, regional tree phenology was first modelled as a function of regional climate, and the tree-specific deviation from this relationship was then used as the metric of relative tree-specific phenology.4. At the regional scale, a warmer climate postponed oak leaf senescence. This was also reflected in the insect herbivore community: six out of 15 taxa occurred at a higher incidence and five out of 18 taxa were more abundant, in locations with a warmerclimate. Similarly, taxonomic richness and herbivory were higher in warmer locations.5. Trees with a relatively late autumn phenology had higher abundances of leaf miners (Phyllonorycter spp.). This caused lower community diversity and evenness on trees with later autumn phenology.6. The findings of the present study illustrate that both regional climate-driven patterns and local variation in oak autumn phenology contribute to shaping the insect herbivore community. Community patterns may thus shift with a changing climate.
28.	Faticov, Maria, et al. (författare) Climate and host genotype jointly shape tree phenology, disease levels and insect attacks 2020 Ingår i: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 129:3, s. 391-401 Tidskriftsartikel (refereegranskat)abstract One of the best known ecological consequences of climate change is the advancement of spring phenology. Yet, we lack insights into how changes in climate interact with intraspecific genetic variation in shaping spring and autumn phenology, and how such changes in phenology will translate into seasonal dynamics of tree-associated organisms. To elucidate the impact of warming and tree genotype on spring and autumn phenology, as well as the consequences for the population dynamics of a fungal pathogen Erysiphe alphitoides and plant-feeding insect Tuberculatus annulatus, we conducted an active field heating experiment using grafts of five oak genotypes Quercus robur. We found that experimental warming generally advanced oak bud burst in spring and delayed leaf senescence in autumn, while additional variation was explained by tree genotype and warming-by-genotype interactions. Warming or tree genotype did not affect disease levels at the beginning of the season, but shaped both disease levels and aphid density during the latter part of the season. Overall, our findings demonstrate that elevated temperature and genetic variation affect spring and autumn phenology, as well as the seasonal dynamics of higher trophic levels. Such effects may be either direct (i.e. temperature affecting tree phenology and attack independently) or indirect (as due to climate-induced changes in plant traits or the synchrony between trees and their attackers). To achieve a predictive understanding of the ecological responses and potential evolutionary changes of natural food webs in response to climate warming, we should merge the frameworks of global warming and community genetics.
29.	Faticov, Maria, et al. (författare) Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak Annan publikation (övrigt vetenskapligt/konstnärligt)
30.	Faticov, Maria, et al. (författare) Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak 2021 Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 231:5, s. 1770-1783 Tidskriftsartikel (refereegranskat)abstract Leaves interact with a wealth of microorganisms. Among these, fungi are highly diverse and are known to contribute to plant health, leaf senescence and early decomposition. However, patterns and drivers of the seasonal dynamics of foliar fungal communities are poorly understood. We used a multifactorial experiment to investigate the influence of warming and tree genotype on the foliar fungal community on the pedunculate oak Quercus robur across one growing season. Fungal species richness increased, evenness tended to decrease, and community composition strongly shifted during the growing season. Yeasts increased in relative abundance as the season progressed, while putative fungal pathogens decreased. Warming decreased species richness, reduced evenness and changed community composition, especially at the end of the growing season. Warming also negatively affected putative fungal pathogens. We only detected a minor imprint of tree genotype and warming x genotype interactions on species richness and community composition. Overall, our findings demonstrate that warming plays a larger role than plant genotype in shaping the seasonal dynamics of the foliar fungal community on oak. These warming-induced shifts in the foliar fungal community may have a pronounced impact on plant health, plant-fungal interactions and ecosystem functions.
31.	Faticov, Maria, et al. (författare) Different spatial structure of above- and belowground plant-associated fungal communities Annan publikation (övrigt vetenskapligt/konstnärligt)
32.	Faticov, Maria, 1991-, et al. (författare) Different spatial structure of plant-associated fungal communities above- and belowground 2023 Ingår i: Ecology and Evolution. - 2045-7758. ; 13:5 Tidskriftsartikel (refereegranskat)abstract The distribution and community assembly of above- and belowground microbial communities associated with individual plants remain poorly understood, despite its consequences for plant–microbe interactions and plant health. Depending on how microbial communities are structured, we can expect different effects of the microbial community on the health of individual plants and on ecosystem processes. Importantly, the relative role of different factors will likely differ with the scale examined. Here, we address the driving factors at a landscape level, where each individual unit (oak trees) is accessible to a joint species pool. This allowed to quantify the relative effect of environmental factors and dispersal on the distribution of two types of fungal communities: those associated with the leaves and those associated with the soil of Quercus robur trees in a landscape in southwestern Finland. Within each community type, we compared the role of microclimatic, phenological, and spatial variables, and across community types, we examined the degree of association between the respective communities. Most of the variation in the foliar fungal community was found within trees, whereas soil fungal community composition showed positive spatial autocorrelation up to 50 m. Microclimate, tree phenology, and tree spatial connectivity explained little variation in the foliar and soil fungal communities. Foliar and soil fungal communities differed strongly in community structure, with no significant concordance detected between them. We provide evidence that foliar and soil fungal communities assemble independent of each other and are structured by different ecological processes.
33.	Faticov, Maria, et al. (författare) Niche differentiation within a cryptic pathogen complex : climatic drivers and hyperparasitism across spatial scales Annan publikation (övrigt vetenskapligt/konstnärligt)
34.	Faticov, Maria, et al. (författare) Niche differentiation within a cryptic pathogen complex : climatic drivers and hyperparasitism at multiple spatial scales 2022 Ingår i: Ecography. - : Wiley. - 0906-7590 .- 1600-0587. ; 2022:2 Tidskriftsartikel (refereegranskat)abstract Pathogens are embedded in multi-trophic food webs, which often include co-occurring cryptic species within the same pathogen complex. Nonetheless, we still lack an understanding of what dimensions of the ecological niche might allow these cryptic species to coexist. We explored the role of climate, host characteristics (tree autumn phenology) and attack by the fungal hyperparasite Ampelomyces (a group of fungi attacking plant pathogens) in defining the niches of three powdery mildew species (Erysiphe alphitoides, E. hypophylla and E. quercicola) within a cryptic pathogen complex on the pedunculate oak Quercus robur at the continental (Europe), national (Sweden and France) and landscape scales (a 5 km2 island in southwestern Finland). Previous studies have shown that climate separated the niches of three powdery mildew species (E. alphitoides, E. hypophylla and E. quercicola) in Europe and two species (E. alphitoides and E. quercicola) in France. In our study, we did not detect a significant relationship between temperature or precipitation and the distribution of E. alphitoides and E. hypophylla present in Sweden, while at the landscape scale, temperature, but not relative humidity, negatively affected disease incidence of E. alphitoides in an exceptionally warm year. Tree variation in autumn phenology did not influence disease incidence of powdery mildew species, and hyperparasite presence did not differ among powdery mildew species at the continental, national and landscape scale. Climate did not affect the distribution of the hyperparasite at the continental scale and at the national scale in Sweden. However, climate affected the hyperparasite distribution in France, with a negative relationship between non-growing season temperature and presence of the hyperparasite. Overall, our findings, in combination with earlier evidence, suggest that climatic factors are more important than species interactions in defining the niches of cryptic species within a pathogen complex on oak.
35.	Hambäck, Peter A., et al. (författare) Spatial subsidies in spider diets vary with shoreline structure : Complementary evidence from molecular diet analysis and stable isotopes 2016 Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 6:23, s. 8431-8439 Tidskriftsartikel (refereegranskat)
36.	Iwaszkiewicz-Eggebrecht, Elzbieta, et al. (författare) FAVIS : Fast and versatile protocol for nondestructive metabarcoding of bulk insect samples 2023 Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 18:7, s. e0286272- Tidskriftsartikel (refereegranskat)abstract Insects are diverse and sustain essential ecosystem functions, yet remain understudied. Recent reports about declines in insect abundance and diversity have highlighted a pressing need for comprehensive large-scale monitoring. Metabarcoding (high-throughput bulk sequencing of marker gene amplicons) offers a cost-effective and relatively fast method for characterizing insect community samples. However, the methodology applied varies greatly among studies, thus complicating the design of large-scale and repeatable monitoring schemes. Here we describe a non-destructive metabarcoding protocol that is optimized for high-throughput processing of Malaise trap samples and other bulk insect samples. The protocol details the process from obtaining bulk samples up to submitting libraries for sequencing. It is divided into four sections: 1) Laboratory workspace preparation; 2) Sample processing-decanting ethanol, measuring the wet-weight biomass and the concentration of the preservative ethanol, performing non-destructive lysis and preserving the insect material for future work; 3) DNA extraction and purification; and 4) Library preparation and sequencing. The protocol relies on readily available reagents and materials. For steps that require expensive infrastructure, such as the DNA purification robots, we suggest alternative low-cost solutions. The use of this protocol yields a comprehensive assessment of the number of species present in a given sample, their relative read abundances and the overall insect biomass. To date, we have successfully applied the protocol to more than 7000 Malaise trap samples obtained from Sweden and Madagascar. We demonstrate the data yield from the protocol using a small subset of these samples.
37.	Iwaszkiewicz-Eggebrecht, Elzbieta, et al. (författare) Optimizing insect metabarcoding using replicated mock communities 2023 Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 14:4, s. 1130-1146 Tidskriftsartikel (refereegranskat)abstract Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms of presence-absence, abundance and biomass. Here we use mock community experiments and a simple probabilistic model to evaluate the effect of different DNA extraction protocols on metabarcoding performance. Specifically, we ask four questions: (Q1) How consistent are the recovered community profiles across replicate mock communities?; (Q2) How does the choice of lysis buffer affect the recovery of the original community?; (Q3) How are community estimates affected by differing lysis times and homogenization? and (Q4) Is it possible to obtain adequate species abundance estimates through the use of biological spike-ins? We show that estimates are quite variable across community replicates. In general, a mild lysis protocol is better at reconstructing species lists and approximate counts, while homogenization is better at retrieving biomass composition. Small insects are more likely to be detected in lysates, while some tough species require homogenization to be detected. Results are less consistent across biological replicates for lysates than for homogenates. Some species are associated with strong PCR amplification bias, which complicates the reconstruction of species counts. Yet, with adequate spike-in data, species abundance can be determined with roughly 40% standard error for homogenates, and with roughly 50% standard error for lysates, under ideal conditions. In the latter case, however, this often requires species-specific reference data, while spike-in data generalize better across species for homogenates. We conclude that a non-destructive, mild lysis approach shows the highest promise for the presence/absence description of the community, while also allowing future morphological or molecular work on the material. However, homogenization protocols perform better for characterizing community composition, in particular in terms of biomass.
38.	Iwaszkiewicz‐Eggebrecht, Elzbieta, et al. (författare) Optimizing insect metabarcoding using replicated mock communities 2023 Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 14:4, s. 1130-1146 Tidskriftsartikel (refereegranskat)
39.	Kaartinen, Riikka, et al. (författare) A rapid assessment of a poorly known insect group 2016 Ingår i: Insect Conservation and Diversity. - : Wiley. - 1752-458X .- 1752-4598. ; 9, s. 49-62 Tidskriftsartikel (refereegranskat)abstract 1. 'Conservation planning and ecological analyses require large-scale data on species' abundance and distribution. We describe a national effort to quickly establish the distributions of taxa with hard-to-identify adults but easily identifiable larval stages: cynipid gall wasps (Hymenoptera: Cynipidae, Cynipini) on oak (Quercus robur).2. The survey was implemented by volunteers across 239 sites over 687 km of latitude. It yielded 10 523 galls, which were identified by specialists. The material revealed two species new to Finland and the national distributions and local abundances of 16 species.3. The likelihood of finding a given species was significantly affected by the visual apparency of its galls. This suggests that some cryptic generations may have been missed in the sampling.4. At the national level, our study exposed systematic changes in the species richness of insect taxa associated with a patchily distributed host plant towards its range margin. Species' incidences decline as host trees grow increasingly scattered within the landscape.5. From a conservation perspective, the data increased eight-fold the known records of gall wasps from Finland, and informed the first assessment of national threat status of these taxa.6. Our study reveals how the efforts of the public may be efficiently harnessed for revealing the current status of poorly known taxa. In addition to delivering a first survey of the target taxa, and of factors affecting their distribution, such 'citizen science' may generate a permanent base of enthusiasts for the future monitoring of changes and trends.
40.	Kaartinen, Riikka, et al. (författare) Establishing a community-wide DNA barcode library as a new tool for arctic research 2016 Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 16, s. 809-822 Tidskriftsartikel (refereegranskat)abstract DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers. Drawing on this material, we estimate the coverage of previous morphology-based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology-based techniques. DNA barcodes (CO1) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based on barcode regions rbcLa and ITS2. Malaise catches revealed 122 BINs not detected by previous sampling and DNA barcoding. The insect community was dominated by a few highly abundant taxa. Even closely related taxa differed in phenology, emphasizing the need for species-level resolution when describing ongoing shifts in arctic communities and ecosystems. The DNA barcode library now established for Zackenberg offers new scope for such explorations, and for the detailed dissection of interspecific interactions throughout the community.
41.	Kaartinen, Riikka, et al. (författare) Species’ roles in food webs show fidelity across a highly variable oak forest 2015 Ingår i: Ecography. - : Wiley. - 0906-7590 .- 1600-0587. ; 38, s. 130-139 Tidskriftsartikel (refereegranskat)abstract Ecological communities are composed of many species and an intricate network of interactions between them. Because of their overall complexity, an intriguing approach to understanding network structure is by breaking it down into the structural roles of its constituent species. The structural role of a species can be directly measured based on how it appears in network motifs - the basic building blocks of complex networks. Here, we study the distribution of species' roles at three distinct spatio-temporal scales (i.e. species, network, and temporal) in host-parasitoid networks collected across 22 sites over two years within a fragmented landscape of oaks in southern Finland. We found that species' roles for hosts and parasitoids were heterogeneously distributed across the study system but that roles are strongly conserved over spatial scales. In addition, we found that species' roles were remarkably consistent between years even in the presence of disturbances (e.g. species turnover). Overall, our results suggest that species' roles are an intrinsic property of species that may be predictable over spatial and temporal scales.
42.	Kaartinen, Riikka, et al. (författare) Stable pollination service in a generalist high Arctic community despite the warming climate 2023 Ingår i: Ecological Monographs. - : Wiley. - 0012-9615 .- 1557-7015. ; 93 Tidskriftsartikel (refereegranskat)abstract Insects provide key pollination services in most terrestrial biomes, but this service depends on a multistep interaction between insect and plant. An insect needs to visit a flower, receive pollen from the anthers, move to another conspecific flower, and finally deposit the pollen on a receptive stigma. Each of these steps may be affected by climate change, and focusing on only one of them (e.g., flower visitation) may miss important signals of change in service provision. In this study, we combine data on visitation, pollen transport, and single-visit pollen deposition to estimate functional outcomes in the high Arctic plant-pollinator network of Zackenberg, Northeast Greenland, a model system for global warming-associated impacts in pollination services. Over two decades of rapid climate warming, we sampled the network repeatedly: in 1996, 1997, 2010, 2011, and 2016. Although the flowering plant and insect communities and their interactions varied substantially between years, as expected based on highly variable Arctic weather, there was no detectable directional change in either the structure of flower-visitor networks or estimated pollen deposition. For flower-visitor networks compiled over a single week, species phenologies caused major within-year variation in network structure despite consistency across years. Weekly networks for the middle of the flowering season emerged as especially important because most pollination service can be expected to be provided by these large, highly nested networks. Our findings suggest that pollination ecosystem service in the high Arctic is remarkably resilient. This resilience may reflect the plasticity of Arctic biota as an adaptation to extreme and unpredictable weather. However, most pollination service was contributed by relatively few fly taxa (Diptera: Spilogona sanctipauli and Drymeia segnis [Muscidae] and species of Rhamphomyia [Empididae]). If these key pollinators are negatively affected by climate change, network structure and the pollination service that depends on it would be seriously compromised.
43.	Kaartinen, Riikka, et al. (författare) Using citizen scientists to measure an ecosystem service nationwide 2013 Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 94, s. 2645-2652 Tidskriftsartikel (refereegranskat)abstract The decomposition of dung constitutes an ecosystem service of massive proportions. Previous studies addressing how it depends on individual invertebrate taxa have been focused on small spatial scales, neglecting the impact of large-scale factors like climate. Here, we use the concept of citizen science to quantify taxon-specific contributions to dung decomposition at the level of a nation. Young people across Finland manipulated the decomposer communities of cow pats, then measured changes in pat mass over the grazing season. In southern Finland most (90%) of the cattle dung hitting pastures decomposed in just two months, whereas 1100 km to the north the corresponding fraction was smaller (74%). Of the total invertebrate-caused decomposition (13% of dung pat mass, independent of latitude), large tunneling dor beetles in the genus Geotrupes account for 61%, hence removing dung twice as fast as do smaller dung-dwelling beetles and earthworms. Overall, this paper illustrates how ecologists may direct citizen scientists to implement massive ecological experiments. Compared to an approach based purely on professional scientists, we saved three-quarters of the costs. Ultimately, citizen science may offer a key tool for testing current ecological theories at relevant spatial scalesand for disseminating these theories in the process.
44.	Kahlert, Maria, et al. (författare) New molecular methods to assess biodiversity. Potentials and pitfalls of DNA metabarcoding: a workshop report 2019 Ingår i: Research Ideas and Outcomes. - : Pensoft Publishers. - 2367-7163. ; 5 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract This report presents the outcome of the joint work of PhD students and senior researchers working with DNA-based biodiversity assessment approaches with the goal to facilitate others the access to definitions and explanations about novel DNA-based methods. The work was performed during a PhD course (SLU PNS0169) at the Swedish University of Agricultural Sciences (SLU) in Uppsala, Sweden. The course was co-organized by the EU COST research network DNAqua-Net and the SLU Research Schools Focus on Soils and Water (FoSW) and Ecology - basics and applications. DNAqua-Net (COST Action CA15219, 2016-2020) is a network connecting researchers, water managers, politicians and other stakeholders with the aim to develop new genetic tools for bioassessment of aquatic ecosystems in Europe and beyond. The PhD course offered a comprehensive overview of the paradigm shift from traditional morphology-based species identification to novel identification approaches based on molecular markers. We covered the use of molecular tools in both basic research and applied use with a focus on aquatic ecosystem assessment, from species collection to the use of diversity in environmental legislation. The focus of the course was on DNA (meta)barcoding and aquatic organisms. The knowledge gained was shared with the general public by creating Wikipedia pages and through this collaborative Open Access publication, co-authored by all course participants.
45.	Kortsch, Susanne, et al. (författare) Landscape composition and pollinator traits interact to influence pollination success in an individual-based model 2023 Ingår i: Functional Ecology. - 0269-8463. ; 37:7, s. 2056-2071 Tidskriftsartikel (refereegranskat)abstract The arrangement of plant species within a landscape influences pollination via changes in pollinator movement trajectories and plant–pollinator encounter rates. Yet the combined effects of landscape composition and pollinator traits (especially specialisation) on pollination success remain hard to quantify empirically. We used an individual-based model to explore how landscape and pollinator specialisation (degree) interact to influence pollination. We modelled variation in the landscape by generating gradients of plant species intermixing—from no mixing to complete intermixing. Furthermore, we varied the level of pollinator specialisation by simulating plant–pollinator (six to eight species) networks of different connectance. We then compared the impacts of these drivers on three proxies for pollination: visitation rate, number of consecutive visits to the focal plant species and expected number of plants pollinated. We found that the spatial arrangements of plants and pollinator degree interact to determine pollination success, and that the influence of these drivers on pollination depends on how pollination is estimated. For most pollinators, visitation rate increases in more plant mixed landscapes. Compared to the two more functional measures of pollination, visitation rate overestimates pollination service. This is particularly severe in landscapes with high plant intermixing and for generalist pollinators. Interestingly, visitation rate is less influenced by pollinator traits (pollinator degree and body size) than are the two functional metrics, likely because ‘visitation rate’ ignores the order in which pollinators visit plants. However, the visitation sequence order is crucial for the expected number of plants pollinated, since only prior visits to conspecific individuals can contribute to pollination. We show here that this order strongly depends on the spatial arrangements of plants, on pollinator traits and on the interaction between them. Taken together, our findings suggest that visitation rate, the most commonly used proxy for pollination in network studies, should be complemented with more functional metrics which reflect the frequency with which individual pollinators revisit the same plant species. Our findings also suggest that measures of landscape structure such as plant intermixing and density—in combination with pollinators' level of specialism—can improve estimates of the probability of pollination. Read the free Plain Language Summary for this article on the Journal blog.
46.	Manca, Federica, et al. (författare) Unveiling the complexity and ecological function of aquatic macrophyte–animal networks in coastal ecosystems 2022 Ingår i: Biological Reviews. - : Wiley. - 1464-7931 .- 1469-185X. ; 97:4, s. 1306-1324 Tidskriftsartikel (refereegranskat)abstract Network theory offers innovative tools to explore the complex ecological mechanisms regulating species associations and interactions. Although interest in ecological networks has grown steadily during the last two decades, the application of network approaches has been unequally distributed across different study systems: while some kinds of interactions (e.g. plant–pollinator and host–parasite) have been extensively investigated, others remain relatively unexplored. Among the latter, aquatic macrophyte–animal associations in coastal environments have been largely neglected, despite their major role in littoral ecosystems. The ubiquity of macrophyte systems, their accessibility and multi-faceted ecological, economical and societal importance make macrophyte–animal systems an ideal subject for ecological network science. In fact, macrophyte–animal networks offer an aquatic counterpart to terrestrial plant–animal networks. In this review, we show how the application of network analysis to aquatic macrophyte–animal associations has the potential to broaden our understanding of how coastal ecosystems function. Network analysis can also provide a key to understanding how such ecosystems will respond to on-going and future threats from anthropogenic disturbance and environmental change. For this, we: (i) identify key issues that have limited the application of network theory and modelling to aquatic animal–macrophyte associations; (ii) illustrate through examples based on empirical data how network analysis can offer new insights on the complexity and functioning of coastal ecosystems; and (iii) provide suggestions for how to design future studies and establish this new research line into network ecology.
47.	Marquina, Daniel, et al. (författare) Establishing arthropod community composition using metabarcoding : Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches 2019 Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 19:6, s. 1516-1530 Tidskriftsartikel (refereegranskat)abstract DNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two different markers - COI and 16S - and three different sampling methods: (a) homogenized Malaise trap samples (homogenate), (b) preservative ethanol from the same samples, and (c) soil samples. Our results indicate that COI and 16S offer partly complementary information on Malaise trap samples, with each marker detecting a significant number of species not detected by the other. Different sampling methods offer highly divergent estimates of community composition. The community recovered from preservative ethanol of Malaise trap samples is significantly different from that recovered from homogenate. Small and weakly sclerotized insects tend to be overrepresented in ethanol while strong and large taxa are overrepresented in homogenate. For soil samples, highly degenerate COI primers pick up large amounts of nontarget DNA and only 16S provides adequate analyses of insect diversity. However, even with 16S, very little overlap in molecular operational taxonomic unit (MOTU) content was found between the trap and the soil samples. Our results demonstrate that none of the tested sampling approaches is satisfactory on its own. For instance, DNA extraction from preservative ethanol is not a valid replacement for destructive bulk extraction but a complement. In future metabarcoding studies, both should ideally be used together to achieve comprehensive representation of the target community.
48.	Marquina, Daniel, 1989-, et al. (författare) Evaluation of non-destructive DNA extraction protocols for insect metabarcoding : gentler and shorter is better 2022 Ingår i: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6, s. 187-201 Tidskriftsartikel (refereegranskat)abstract DNA metabarcoding can accelerate research on insect diversity, as it is cheap and fast compared to manual sorting and identification. Most metabarcoding protocols require homogenisation of the sample, preventing further work on the specimens. Mild digestion of the tissue by incubation in a lysis buffer has been proposed as an alternative, and, although some mild lysis protocols have already been presented, they have so far not been evaluated against each other. Here, we analyse how two mild lysis buffers (one more aggressive, one gentler in terms of tissue degradation), two different incubation times, and two DNA purification methods (a manual precipitation and an automated protocol) affect the accuracy of retrieving the true composition of mock communities using two mitochondrial markers (COI and 16S). We found that protocol-specific variation in concentration and purity of the DNA extracts produced had little effect on the recovery of species. However, the two lysis treatments differed in quantification of species abundances. Digestion in the gentler buffer and for a shorter time yielded better representation of original sample composition. Digestion in a more aggressive buffer or longer incubation time yielded lower alpha diversity values and increased differences between metabarcoding results and the true species-abundance distribution. We conclude that the details of non-destructive protocols can have a significant effect on metabarcoding performance. A short and mild lysis treatment appears the best choice for recovering the true composition of the sample. This not only improves accuracy, but also comes with a faster processing time than the other treatments.
49.	Marquina, Daniel, et al. (författare) Evaluation of non-destructive extraction protocols for metabarcoding of insects Annan publikation (övrigt vetenskapligt/konstnärligt)abstract Researchers in the field of insect diversity can greatly benefit from DNA metabarcoding due to its accuracy, low cost and short processing time compared to manual sorting and identification. But most existing metabarcoding protocols require homogenization of the sample, thus prohibiting any further work on the captured individuals. A mild digestion of the tissue by incubation of the specimens in a lysis buffer has been proposed as an alternative to sample homogenization. Several mild lysis protocols have been presented but they have not been properly evaluated against each other. Here, we analyze the effects of two different mild lysis buffers (one more aggressive than the other), two different incubation times, and two different DNA purification methods (a manual precipitation method and an automated robotic protocol) on metabarcoding performance. Performance was measured as the accuracy of retrieving the true composition of mock insect communities using two different mitochondrial markers (COI and 16S). We found that the variation in concentration and purity of the DNA extracts produced by the different lysis treatments and purification methods had little effect on the recovery of species. However, the two lysis treatments differed significantly in how well they allowed quantification of species abundances. Digestion in the gentler buffer and for a shorter time resulted in metabarcoding results that were more representative of the original sample, while a more aggressive buffer or a longer incubation reduced the values of alpha diversity and increased the differences between metabarcoding results and the true species- abundance distribution. In summary, our results show that the details of non-destructive DNA metabarcoding protocols can have a significant effect on performance. Specifically, our results suggest that a short and mild lysis treatment is the best choice for recovering the true composition of the processed sample. Short and mild lysis protocols not only improve accuracy, they also come with a lower cost and a faster processing time.
50.	Mikryukov, Vladimir, et al. (författare) Connecting the multiple dimensions of global soil fungal diversity 2023 Ingår i: Science advances. - 2375-2548. ; 9:48 Tidskriftsartikel (refereegranskat)abstract How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

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