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  • 1.
    Akram, Usman
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Metson, Genevieve
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering. Linköping University, Centre for Climate Science and Policy Research, CSPR.
    Quttineh, Nils-Hassan
    Linköping University, Department of Mathematics, Optimization . Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Closing Pakistan’s yield gaps through nutrient recycling2018In: Frontiers in Sustainable Food Systems, E-ISSN 2571-581X, p. 1-14, article id 00024Article in journal (Refereed)
    Abstract [en]

    Achieving food security will require closing yield gaps in many regions, including Pakistan. Although fertilizer subsidies have facilitated increased nitrogen (N) application rates, many staple crop yields have yet to reach their maximum potential. Considering that current animal manure and human excreta (bio-supply) recycling rates are low, there is substantial potential to increase the reuse of nutrients in bio-supply. We quantified 2010 crop N, phosphorus (P), and potassium (K) needs along with bio-supply nutrient availability for Pakistani districts, and compared these values to synthetic fertilizer use and costs. We found that synthetic fertilizer use combined with low bio-supply recycling resulted in a substantial gap between nutrient supply and P and K crop needs, which would cost 3 billion USD to fill with synthetic fertilizers. If all bio-supply was recycled, it could eliminate K synthetic fertilizer needs and decrease N synthetic fertilizer needs to 43% of what was purchased in 2010. Under a full recycling scenario, farmers would still require an additional 0.28 million tons of synthetic P fertilizers, costing 2.77 billion USD. However, it may not be prohibitively expensive to correct P deficiencies. Pakistan already spends this amount of money on fertilizers. If funds used for synthetic N were reallocated to synthetic P purchases in a full bio-supply recycling scenario, crop needs could be met. Most recycling could happen within districts, with only 6% of bio-supply requiring between-district transport when optimized to meet national N crop needs. Increased recycling in Pakistan could be a viable way to decrease yield gaps.

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    Closing Pakistan’s Yield Gaps Through Nutrient Recycling
  • 2.
    Akram, Usman
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Quttineh, Nils-Hassan
    Linköping University, Department of Mathematics, Optimization . Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Tonderski, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Metson, Genevieve
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Enhancing nutrient recycling from excreta to meet crop nutrient needs in Sweden - a spatial analysis2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 10264Article in journal (Refereed)
    Abstract [en]

    Increased recycling of nutrient-rich organic waste to meet crop nutrient needs is an essential component of a more sustainable food system. However, agricultural specialization continues to pose a significant challenge to balancing crop nutrient needs and the nutrient supply from animal manure and human excreta locally. For Sweden, this study found that recycling all excreta (in 2007) could meet up to 75% of crop nitrogen and 81% of phosphorus needs, but that this would exceed crop potassium needs by 51%. Recycling excreta within municipalities could meet 63% of crop P nutrient needs, but large regional differences and imbalances need to be corrected to avoid over or under fertilizing. Over 50% of the total nitrogen and phosphorus in excreta is contained in just 40% of municipalities, and those have a surplus of excreta nutrients compared to crop needs. Reallocation of surpluses (nationally optimized for phosphorus) towards deficit municipalities, would cost 192 million USD (for 24 079 km of truck travel). This is 3.7 times more than the total NPK fertilizer value being transported. These results indicate that Sweden could reduce its dependence on synthetic fertilizers through investments in excreta recycling, but this would likely require valuing also other recycling benefits.

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  • 3.
    Akram, Usman
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology.
    Quttineh, Nils-Hassan
    Linköping University, Department of Mathematics, Optimization .
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology.
    Tonderski, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Metson, Geneviéve S.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology.
    Optimizing Nutrient Recycling From Excreta in Sweden and Pakistan: Higher Spatial Resolution Makes Transportation More Attractive2019In: Frontiers in Sustainable Food Systems, ISSN 2571-581X, Vol. 3Article in journal (Refereed)
    Abstract [en]

    Recycling essential plant nutrients like nitrogen (N), phosphorus (P), and potassium (K) from organic waste such as human and animal excreta will be an essential part of sustainable food systems and a circular economy. However, transportation is often cited as a major barrier to increased recycling as organic waste is heavy and bulky, and distances between areas of abundant waste may be far from areas with a need for fertilizers. We investigated the effect of increased input data spatial resolution to an optimization model on the weight, distance, and spatial patterns of transport. The model was run in Sweden and in Pakistan to examine cost-effectiveness of transporting excess excreta to areas of crop need after local recycling. Increasing the resolution of input data from political boundaries (municipalities and districts) to 0.083 decimal grids increased the amount of N requiring transport by 12% in Pakistan and increased P requiring transport by 14% in Sweden. The average distance decreased by 67% (to 44 km) in Pakistan but increased by 1 km in Sweden. Further increasing the resolution to 5 km grids in Sweden decreased the average transportation distance by 9 km (down to 123 km). In both countries, increasing resolution also decreased the number of long-distance heavy transports, and as such costs did not increase as much as total distance and weight transported. Ultimately, transportation in Pakistan seemed financially beneficial: the cost of transport only represented 13% of the NPK fertilizer value transported, and total recycling could even cover 78% of additional fertilizer purchases required. In Sweden, the cost of transporting excreta did not seem cost effective without valuing other potential benefits of increased recycling: costs were three times higher than the fertilizer value transported in excreta at the 5 km resolution. In summary, increasing input data resolution created a more realistic picture of recycling needs. This also highlighted more favorable cost to fertilizer value ratios which could make it easier to move forward with industry and government partners to facilitate productive recycling. Our analysis shows that in both countries increased recycling can result in better spatial nutrient balances.

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  • 4.
    Andersson, Jonathan
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Kozlov, Vladimir
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Radosavljevic, Sonja
    Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden.
    Tkachev, Vladimir
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Density-Dependent Feedback in Age-Structured Populations2019In: Journal of Mathematical Sciences, ISSN 1072-3374, E-ISSN 1573-8795, Vol. 242, no 1, p. 2-24Article in journal (Refereed)
    Abstract [en]

    The population size has far-reaching effects on the fitness of the population, that, in its turn influences the population extinction or persistence. Understanding the density- and age-dependent factors will facilitate more accurate predictions about the population dynamics and its asymptotic behaviour. In this paper, we develop a rigourous mathematical analysis to study positive and negative effects of increased population density in the classical nonlinear age-structured population model introduced by Gurtin \& MacCamy in the late 1970s. One of our main results expresses the global stability of the system in terms of the newborn function only. We also derive the existence of a threshold population size implying the population extinction, which is well-known in population dynamics as an Allee effect.

  • 5.
    Brommesson, Peter
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Spatiotemporal Variation in Distance Dependent Animal Movement Contacts: One Size Doesnt Fit All2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 10, p. e0164008-Article in journal (Refereed)
    Abstract [en]

    The structure of contacts that mediate transmission has a pronounced effect on the outbreak dynamics of infectious disease and simulation models are powerful tools to inform policy decisions. Most simulation models of livestock disease spread rely to some degree on predictions of animal movement between holdings. Typically, movements are more common between nearby farms than between those located far away from each other. Here, we assessed spatiotemporal variation in such distance dependence of animal movement contacts from an epidemiological perspective. We evaluated and compared nine statistical models, applied to Swedish movement data from 2008. The models differed in at what level ( if at all), they accounted for regional and/or seasonal heterogeneities in the distance dependence of the contacts. Using a kernel approach to describe how probability of contacts between farms changes with distance, we developed a hierarchical Bayesian framework and estimated parameters by using Markov Chain Monte Carlo techniques. We evaluated models by three different approaches of model selection. First, we used Deviance Information Criterion to evaluate their performance relative to each other. Secondly, we estimated the log predictive posterior distribution, this was also used to evaluate their relative performance. Thirdly, we performed posterior predictive checks by simulating movements with each of the parameterized models and evaluated their ability to recapture relevant summary statistics. Independent of selection criteria, we found that accounting for regional heterogeneity improved model accuracy. We also found that accounting for seasonal heterogeneity was beneficial, in terms of model accuracy, according to two of three methods used for model selection. Our results have important implications for livestock disease spread models where movement is an important risk factor for between farm transmission. We argue that modelers should refrain from using methods to simulate animal movements that assume the same pattern across all regions and seasons without explicitly testing for spatiotemporal variation.

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  • 6.
    Buhnerkempe, Michael G.
    et al.
    Colorado State University, CO 80523 USA .
    Tildesley, Michael J.
    University of Warwick, England .
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Grear, Daniel A.
    Colorado State University, CO 80523 USA .
    Portacci, Katie
    US Anim and Plant Health Inspect Serv, CO USA US Anim and Plant Health Inspect Serv, CO USA .
    Miller, Ryan S.
    US Anim and Plant Health Inspect Serv, CO USA US Anim and Plant Health Inspect Serv, CO USA .
    Lombard, Jason E.
    US Anim and Plant Health Inspect Serv, CO USA US Anim and Plant Health Inspect Serv, CO USA .
    Werkman, Marleen
    University of Warwick, England .
    Keeling, Matt J.
    University of Warwick, England .
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Webb, Colleen T.
    Colorado State University, CO 80523 USA .
    The Impact of Movements and Animal Density on Continental Scale Cattle Disease Outbreaks in the United States2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 3, p. 0091724-Article in journal (Refereed)
    Abstract [en]

    Globalization has increased the potential for the introduction and spread of novel pathogens over large spatial scales necessitating continental-scale disease models to guide emergency preparedness. Livestock disease spread models, such as those for the 2001 foot-and-mouth disease (FMD) epidemic in the United Kingdom, represent some of the best case studies of large-scale disease spread. However, generalization of these models to explore disease outcomes in other systems, such as the United Statess cattle industry, has been hampered by differences in system size and complexity and the absence of suitable livestock movement data. Here, a unique database of US cattle shipments allows estimation of synthetic movement networks that inform a near-continental scale disease model of a potential FMD-like (i.e., rapidly spreading) epidemic in US cattle. The largest epidemics may affect over one-third of the US and 120,000 cattle premises, but cattle movement restrictions from infected counties, as opposed to national movement moratoriums, are found to effectively contain outbreaks. Slow detection or weak compliance may necessitate more severe state-level bans for similar control. Such results highlight the role of large-scale disease models in emergency preparedness, particularly for systems lacking comprehensive movement and outbreak data, and the need to rapidly implement multi-scale contingency plans during a potential US outbreak.

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  • 7.
    Edstam, Monika M.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Blomqvist, Kristina
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Eklöf, Anna
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Edqvist, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Coexpression patterns indicate that GPI-anchored non-specific lipid transfer proteins are involved in accumulation of cuticular wax, suberin and sporopollenin2013In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 83, no 6, p. 625-649Article in journal (Refereed)
    Abstract [en]

    The non-specific lipid transfer proteins (nsLTP) are unique to land plants. The nsLTPs are characterized by a compact structure with a central hydrophobic cavity and can be classified to different types based on sequence similarity, intron position or spacing between the cysteine residues. The type G nsLTPs (LTPGs) have a GPI-anchor in the C-terminal region which attaches the protein to the exterior side of the plasma membrane. The function of these proteins, which are encoded by large gene families, has not been systematically investigated so far. In this study we have explored microarray data to investigate the expression pattern of the LTPGs in Arabidopsis and rice. We identified that the LTPG genes in each plant can be arranged in three expression modules with significant coexpression within the modules. According to expression patterns and module sizes, the Arabidopsis module AtI is functionally equivalent to the rice module OsI, AtII corresponds to OsII and AtIII is functionally comparable to OsIII. Starting from modules AtI, AtII and AtIII we generated extended networks with Arabidopsis genes coexpressed with the modules. Gene ontology analyses of the obtained networks suggest roles for LTPGs in the synthesis or deposition of cuticular waxes, suberin and sporopollenin. The AtI-module is primarily involved with cuticular wax, the AtII-module with suberin and the AtIII-module with sporopollenin. Further transcript analysis revealed that several transcript forms exist for several of the LTPG genes in both Arabidopsis and rice. The data suggests that the GPI-anchor attachment and localization of LTPGs may be controlled to some extent by alternative splicing.

  • 8.
    Frisk, Mikael
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Jonsson, Annie
    Skovde Univ, Sweden.
    Sellman, Stefan
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Flisberg, Patrik
    Forestry Res Inst Sweden, Sweden.
    Roennqvist, Mikael
    Univ Laval, Canada.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Route optimization as an instrument to improve animal welfare and economics in pre-slaughter logistics2018In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 3, article id e0193223Article in journal (Refereed)
    Abstract [en]

    Each year, more than three million animals are transported from farms to abattoirs in Sweden. Animal transport is related to economic and environmental costs and a negative impact on animal welfare. Time and the number of pick-up stops between farms and abattoirs are two key parameters for animal welfare. Both are highly dependent on efficient and qualitative transportation planning, which may be difficult if done manually. We have examined the benefits of using route optimization in cattle transportation planning. To simulate the effects of various planning time windows and transportation time regulations and number of pick-up stops along each route, we have used data that represent one year of cattle transport. Our optimization model is a development of a model used in forestry transport that solves a general pick-up and delivery vehicle routing problem. The objective is to minimize transportation costs. We have shown that the length of the planning time window has a significant impact on the animal transport time, the total driving time and the total distance driven; these parameters that will not only affect animal welfare but also affect the economy and environment in the pre-slaughter logistic chain. In addition, we have shown that changes in animal transportation regulations, such as minimizing the number of allowed pick-up stops on each route or minimizing animal transportation time, will have positive effects on animal welfare measured in transportation hours and number of pick-up stops. However, this leads to an increase in working time and driven distances, leading to higher transportation costs for the transport and negative environmental impact.

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  • 9.
    Ghersheen, Samia
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Kozlov, Vladimir
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Tkachev, Vladimir
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Dynamical behaviour of SIR model with coinfection: The case of finite carrying capacity2019In: Mathematical methods in the applied sciences, ISSN 0170-4214, E-ISSN 1099-1476, Vol. 42, no 17, p. 5805-5826Article in journal (Refereed)
    Abstract [en]

    Multiple viruses are widely studied because of their negative effect on the health of host as well as on whole population. The dynamics of coinfection are important in this case. We formulated an susceptible infected recovered (SIR) model that describes the coinfection of the two viral strains in a single host population with an addition of limited growth of susceptible in terms of carrying capacity. The model describes five classes of a population: susceptible, infected by first virus, infected by second virus, infected by both viruses, and completely immune class. We proved that for any set of parameter values, there exists a globally stable equilibrium point. This guarantees that the disease always persists in the population with a deeper connection between the intensity of infection and carrying capacity of population. Increase in resources in terms of carrying capacity promotes the risk of infection, which may lead to destabilization of the population.

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  • 10.
    Ghersheen, Samia
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Kozlov, Vladimir
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Tkachev, Vladimir
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Mathematical analysis of complex SIR model with coinfection and density dependence2019In: Computational and Mathematical Methods, ISSN 2577-7408, Vol. 1, no 4Article in journal (Refereed)
    Abstract [en]

    An SIR model with the coinfection of the two infectious agents in a single host population is considered. The model includes the environmental carry capacity in each class of population. A special case of this model is analyzed, and several threshold conditions are obtained, which describes the establishment of diseases in the population. We prove that, for small carrying capacity K, there exists a globally stable disease-free equilibrium point. Furthermore, we establish the continuity of the transition dynamics of the stable equilibrium point, that is, we prove that, (1) for small values of K, there exists a unique globally stable equilibrium point, and (b) it moves continuously as K is growing (while its face type may change). This indicates that the carrying capacity is the crucial parameter and an increase in resources in terms of carrying capacity promotes the risk of infection.

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    Mathematical analysis of complex SIR model with coinfection and density dependence
  • 11.
    Gudmundson, Sara
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Eklöf, Anna
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Environmental variability uncovers disruptive effects of species interactions on population dynamics2015In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, no 1812, p. 67-75Article in journal (Refereed)
    Abstract [en]

    How species respond to changes in environmental variability has been shown for single species, but the question remains whether these results are transferable to species when incorporated in ecological communities. Here, we address this issue by analysing the same species exposed to a range of environmental variabilities when (i) isolated or (ii) embedded in a food web. We find that all species in food webs exposed to temporally uncorrelated environments (white noise) show the same type of dynamics as isolated species, whereas species in food webs exposed to positively autocorrelated environments (red noise) can respond completely differently compared with isolated species. This is owing to species following their equilibrium densities in a positively autocorrelated environment that in turn enables species species interactions to come into play. Our results give new insights into species response to environmental variation. They especially highlight the importance of considering both species interactions and environmental autocorrelation when studying population dynamics in a fluctuating environment.

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  • 12.
    Gudmundson, Sara
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Lögdberg, Frida
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Stability patterns of spatial food webs in coloured environmentsManuscript (preprint) (Other academic)
    Abstract [en]

    In times when climate change is expected to cause an increased environmental variability it is important to understand how species respond to disturbances. We explore how the stability of species respond to changes in environmental noise by introducing noise colour to different spatial and multi-trophic model systems: (1) a diamond shaped food web with stable oscillations, (2) a stabilized diamond shaped food web, and (3) a food web with stable dynamics. We conclude that adding space and additional trophic levels makes species response to environmental noise colour consistent. All three food webs and species decreased in stability with increased redness, positive temporal autocorrelation, of the environmental noise. Hence, interactions between noise colour and species responsiveness previously found in single- and multi-species models were not found when comparing more natural food webs differing in stability properties. When adding a spatial dimension, all food webs and species increased in stability. Both the diamond shaped and the stabilized diamond shaped food web were significantly more stable than the food web with more typical stable dynamics when existing in a variable and spatial setting. The major route to explain stability and the existence of a diverse world may then be the variable and spatial complexity of nature.

  • 13. Habtewold, T
    et al.
    Landin, Jan
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Ecology .
    Wennergren, Uno
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology .
    Bergman, Karl-Olof
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Ecology .
    Lifetable for the tef grasshopper, Aiolopus longicornis, under laboratory conditions and demographic effects of the pathogen Nosema locustae1995In: Biological control (Print), ISSN 1049-9644, E-ISSN 1090-2112, Vol. 5, p. 497-502Article in journal (Refereed)
  • 14.
    Hakansson, N.
    et al.
    Skovde University, Sweden.
    Flisberg, P.
    Forestry Research Institute Sweden, Sweden.
    Algers, B.
    Swedish University of Agriculture Science, Sweden.
    Jonsson, A.
    Skovde University, Sweden.
    Ronnqvist, M.
    Forestry Research Institute Sweden, Sweden; University of Laval, Canada.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Improvement of animal welfare by strategic analysis and logistic optimisation of animal slaughter transportation2016In: Animal Welfare, ISSN 0962-7286, Vol. 25, no 2, p. 255-263Article in journal (Refereed)
    Abstract [en]

    The transportation of animals to slaughterhouses is a major welfare concern. The number of slaughterhouses has decreased over time in Europe due to centralisation. This is expected to increase transport time for animals and as a consequence negatively affect animal welfare. We propose an optimisation model based on a facility location model to perform strategic analysis to improve transportation logistics. The model is tested on the Swedish slaughter transport system. We show that, by strategic planning and redirection of transports while keeping the slaughterhouse capacities as of the originaldata, the potential exists to reduce transport distance by 25% for pigs and 40% for cattle. Furthermore, we demonstrated that approximately 50% of Swedish slaughterhouses can be shut down with a minimal effect on total transport distances. This implies that in terms of the overall welfare picture, the decision of which animals to send where plays a for more significant role than the number of slaughterhouses. In addition, by changing relative weights on distances in the optimisation function the amount of individualtransports with longjourney times can be decreased. We also show results from altered slaughterhouse capacity and geographical location of slaughterhouses. This is the first time an entire country has been analysed in great detail with respect to the location, capacity and number of slaughterhouses. The focus is mainly on the analysis of unique and detailed information of actual animal transports in Sweden and a demonstration of the potential impact redirection of the transports and/ or altering of slaughterhouses can have on animal welfare.

  • 15.
    Håkansson, Nina
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Flisberg, P.
    The Forestry Research Institute of Sweden, Uppsala, Sweden.
    Algers, B.
    Swedish University of Agricultural Sciences, Skara, Sweden.
    Rönnqvist, M.
    Norwegian School of Economics and Business Administration, Bergen, Norway.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    A strategic analysis of slaughterhouses and animal transportation in SwedenManuscript (preprint) (Other academic)
    Abstract [en]

    The number of slaughterhouses in Sweden has decreased over time. Fewer slaughterhouses are expected to affect the transport time for animals and as a consequence animal welfare. We have analyzed the transportto- slaughter system, for pigs and cattle, using transport-data from 2008, geographical information for slaughterhouses and farms, and actual route distances between facilities. We made a strategic analysis of the existing slaughterhouses and tested the impact of numbers decreasing further.

    With strategic planning the potential reduction of transport distance is 25% for pigs and 40% for cattle. About 50% of the slaughterhouses in Sweden could be closed down with small effect on the total transport work. This implies that for the national total animal welfare which animals are sent where, is much more important than the number of slaughterhouses. However for the welfare (transport time and distance) of the animals in long transports number of slaughterhouses (regular or mobile) is important. Animal welfare weights of distances in the objective function decreases the amount of transports with long route times. We have investigated where in Sweden it would be beneficial to use mobile slaughterhouses. Animals are usually not sent to closest slaughterhouse; we show how slaughterhouse capacity must change if that transport strategy was applied.

  • 16.
    Håkansson, Nina
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Henningsson, Markus
    Linköping University, Department of Management and Engineering, Industrial Marketing and Industrial Economics. Linköping University, The Institute of Technology.
    Rönnqvist, M.
    NHH, Bergen, Norway.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Route planning reduces the costs of animal transportation: Animal welfare versus economics2007In: XIII International Congress in Animal Hygiene, June 17–21, 2007, Tartu, Estonia: Animal Health, Animal Welfare and Biosecurity, Volume 1 / [ed] A. Aaland, 2007, p. 1044-1048Conference paper (Refereed)
    Abstract [en]

    Animals are more stressed on long transport routes with stops at many farms. The positions of farms and abattoirs are the basic properties that set the limits for route planning. Mobile abattoirs can reduce the cost of transportation and increase the welfare for the animals. The trade-offs between welfare and profit can be reduced by effective route planning. We have, by computer simulations, investigated how trade-offs differs between areas in Sweden and in general landscapes. The general results are applicable to any area and hence for animal transportation in general.

  • 17.
    Håkansson, Nina
    et al.
    Skovde University.
    Jonsson, A.
    Skovde University.
    Lennartsson, Jenny
    Skovde University.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Generating structure specific networks2010In: Advances in Complex Systems, ISSN 0219-5259, Vol. 13, no 2, p. 239-250Article in journal (Refereed)
    Abstract [en]

    Theoretical exploration of network structure significance requires a range of different networks for comparison. Here, we present a new method to construct networks in a spatial setting that uses spectral methods in combination with a probability distribution function. Nearly all previous algorithms for network construction have assumed randomized distribution of links or a distribution dependent on the degree of the nodes. We relax those assumptions. Our algorithm is capable of creating spectral networks along a gradient from random to highly clustered or diverse networks. Number of nodes and link density are specified from start and the structure is tuned by three parameters (gamma, sigma, kappa). The structure is measured by fragmentation, degree assortativity, clustering and group betweenness of the networks. The parameter gamma regulates the aggregation in the spatial node pattern and sigma and kappa regulates the probability of link forming.

  • 18.
    Jonsson, Annie
    et al.
    Univ Skovde, Sweden.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Approximations of population growth in a noisy environment: on the dichotomy of non-age and age structure2019In: Theoretical Ecology, ISSN 1874-1738, E-ISSN 1874-1746, Vol. 12, no 1, p. 99-110Article in journal (Refereed)
    Abstract [en]

    By simulations of population growth exposed to environmental noise, we compared realised long-run growth rate of age structured populations of four different life histories, with four approximations. One approximation used a non-structured population model, including specific population growth rates for each time step, determined by actual vital rates, while the other three used age-structured data to estimate a mean growth rate, then applicable for all time steps. In general, approximations were reasonable accurate. Yet some were completely erroneous and inaccurate enough to move stationary populations to become species on the red list as an endangered species according to International Union for Conservation of Nature (IUNC). The inaccuracies depended, in the following decreasing order, on: life history, what part of the demography the noise was acting on, and noise colour. The non-structured growth approximation had smaller errors with red noise while the three age-structured approximations had their largest errors with red noise. Since it is generally understood that the most common noise in nature is red noise, we conclude that the non-structured approximation will be the best predictor of population growth in most cases. We also conclude that evenness in distribution over age classes is a possible predictor for the sensitivity of long-run growth rate to type of approximation and therefore a promising object for further studies. Finally, our results indicate that in general, more focus ought to be on reducing the error in the data collection on population densities, especially for studies over longer time periods, than of collecting age-specific data.

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  • 19.
    Kozlov, Vladimir
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Radosavljevic, Sonja
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Tkachev, Vladimir
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Persistence analysis of the age-structured population model on several patches2016In: Proceedings of the 16th International Conference on Mathematical Methods in Science and Engineering, July 4-8, Rota, Cadiz, Spain, Vol. III / [ed] J. Vigo-Aguiar, Universidad de Cádiz , 2016, Vol. 3, p. 717-727Chapter in book (Refereed)
    Abstract [en]

    We consider a system of nonlinear partial differential equations that describes an age-structured population living in changing environment on $N$ patches. We prove existence and uniqueness of solution and analyze large time behavior of the system in time-independent case and for periodically changing environment. Under the assumption that every patch can be reached from every other patch, directly or through several intermediary patches, and that net reproductive operator has spectral radius larger than one, we prove that population is persistent on all patches. If the spectral radius is less or equal one, extinction on all patches is imminent.

  • 20.
    Kozlov, Vladimir
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Radosavljevic, Sonja
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Turesson, Bengt-Ove
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Estimating effective boundaries of population growth in a variable environment2016In: Boundary Value Problems, ISSN 1687-2762, E-ISSN 1687-2770, p. 1-28, article id 2016:172Article in journal (Refereed)
    Abstract [en]

    We study the impact of age-structure and temporal environmental variability on the persistence of populations. We use a linear age-structured model with time-dependent vital rates. It is the same as the one presented by Chipot in (Arch. Ration. Mech. Anal. 82(1):13-25, 1983), but the assumptions on the vital rates are slightly different. Our main interest is in describing the large-time behavior of a population provided that we know its initial distribution and transient vital rates. Using upper and lower solutions for the characteristic equation, we define time-dependent upper and lower boundaries for a solution in a constant environment. Moreover, we estimate solutions for the general time-dependent case and also for a special case when the environment is changing periodically.

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  • 21.
    Kozlov, Vladimir
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Radosavljevic, Sonja
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Large time behavior of the logistic age-structured population model in a changing environment2017In: Asymptotic Analysis, ISSN 0921-7134, E-ISSN 1875-8576, Vol. 102, no 1-2, p. 34p. 21-54Article in journal (Refereed)
    Abstract [en]

    Population growth is governed by many external and internal factors. In order to study their effects on population dynamics, we develop an age-structured time-dependent population model with logistic-type nonlinearity. We prove existence of a unique nonnegative bounded solution. Our main concern is to study asymptotic behavior of a solution in the general case, and especially for a periodic environment. We use the method of lower and upper solutions known in the theory of integral equations to formulate lower and upper boundaries of population density. In the periodic case, we discover a connection between the period of oscillation and its effect on population growth. [ABSTRACT FROM AUTHOR]

  • 22.
    Kozlov, Vladimir
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Tkachev, Vladimir
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Vakulenko, Sergey
    St. Petersburg National Research University of Information Technologies, Saint Petersburg, Russia.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Global stability and persistence of complex foodwebs2019In: Annali di Matematica Pura ed Applicata, ISSN 0373-3114, E-ISSN 1618-1891, Vol. 198, no 5, p. 1693-1709Article in journal (Refereed)
    Abstract [en]

    We develop a novel approach to study the global behaviour of large foodwebs for ecosystems where several species share multiple resources. The model extends and generalizes some previous works and takes into account self-limitation. Under certain explicit conditions, we establish the global convergence and persistence of solutions.

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  • 23.
    Kozlov, Vladimir
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Vakulenko, Sergey
    Russian Academic Science, Russia; St Petersburg National Research University of Informat Technology Mech, Russia.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Biodiversity, extinctions, and evolution of ecosystems with shared resources2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 95, no 3, article id 032413Article in journal (Refereed)
    Abstract [en]

    We investigate the formation of stable ecological networks where many species share the same resource. We show that such a stable ecosystem naturally occurs as a result of extinctions. We obtain an analytical relation for the number of coexisting species, and we find a relation describing how many species that may become extinct as a result of a sharp environmental change. We introduce a special parameter that is a combination of species traits and resource characteristics used in the model formulation. This parameter describes the pressure on the system to converge, by extinctions. When that stress parameter is large, we obtain that the species traits are concentrated at certain values. This stress parameter is thereby a parameter that determines the level of final biodiversity of the system. Moreover, we show that the dynamics of this limit system can be described by simple differential equations.

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  • 24.
    Kozlov, Vladimir
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Vakulenko, Sergey
    Russian Academic Science, Russia; St Petersburg National Research University of Informat Technology Mech, Russia.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Hamiltonian dynamics for complex food webs2016In: PHYSICAL REVIEW E, ISSN 1539-3755, Vol. 93, no 3, p. 032413-Article in journal (Refereed)
    Abstract [en]

    We investigate stability and dynamics of large ecological networks by introducing classical methods of dynamical system theory from physics, including Hamiltonian and averaging methods. Our analysis exploits the topological structure of the network, namely the existence of strongly connected nodes (hubs) in the networks. We reveal new relations between topology, interaction structure, and network dynamics. We describe mechanisms of catastrophic phenomena leading to sharp changes of dynamics and hence completely altering the ecosystem. We also show how these phenomena depend on the structure of interaction between species. We can conclude that a Hamiltonian structure of biological interactions leads to stability and large biodiversity.

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  • 25.
    Kozlov, Vladimir
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Vakulenko, Sergey
    Russian Academic Science, Russia; ITMO University, Russia.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Stability of Ecosystems Under Invasions2016In: Bulletin of Mathematical Biology, ISSN 0092-8240, E-ISSN 1522-9602, Vol. 78, no 11, p. 2186-2211Article in journal (Refereed)
    Abstract [en]

    This paper considers a model of foodwebs taking into account species extinction and invasion. We show that system stability depends not only on usual parameters (mortality rates, self-limitation coefficients, and resource abundances), but also on an additional parameter ("biodiversity potential"). The main result is as follows. For foodwebs with random parameters, we obtain an estimate of probability that the foodweb exposed to invasion survives. This estimate involves different system parameters, size and its topological properties.

  • 26.
    Kozlov, Vladimir
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Vakulenko, Sergey
    Inst. for Mech. Eng. Problems, Russian Acad. Sci., St. Petersburg, ITMO University, St. Petersburg, Russia; Saint Petersburg State University of Industrial Technology and Design, St. Petersburg, Russia.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Tkachev, Vladimir
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Biodiversity and robustness of large ecosystems2018In: Ecological Complexity: An International Journal on Biocomplexity in the Environment and Theoretical Ecology, ISSN 1476-945X, E-ISSN 1476-9840, Vol. 36, p. 101-109Article in journal (Refereed)
    Abstract [en]

    We study the biodiversity problem for resource competition systems with extinctions and self-limitationeffects. Our main result establishes estimates of biodiversity in terms of the fundamental parameters ofthe model. We also prove the global stability of solutions for systems with extinctions and large turnoverrate. We show that when the extinction threshold is distinct from zero, the large time dynamics of systemis fundamentally non-predictable. In the last part of the paper we obtain explicit analytical estimates ofecosystem robustness with respect to variations of resource supply which support the R* rule for a systemwith random parameters.

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  • 27.
    Lennartsson, Jenny
    et al.
    Systems Biology Research Centre, Skövde University, Skövde, Sweden.
    Håkansson, Nina
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Jonsson, A.
    Systems Biology Research Centre, Skövde University, Skövde, Sweden.
    SpecNet: a spatial network algorithm that generates a wide range of specific structures2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 8Article in journal (Refereed)
    Abstract [en]

    Network measures are used to predict the behavior of different systems. To be able to investigate how various structures behave and interact we need a wide range of theoretical networks to explore. Both spatial and non-spatial methods exist for generating networks but they are limited in the ability of producing wide range of network structures. We extend an earlier version of a spatial spectral network algorithm to generate a large variety of networks across almost all the theoretical spectra of the following network measures: average clustering coefficient, degree assortativity, fragmentation index, and mean degree. We compare this extended spatial spectral network-generating algorithm with a non-spatial algorithm regarding their ability to create networks with different structures and network measures. The spatial spectral network-generating algorithm can generate networks over a much broader scale than the non-spatial and other known network algorithms. To exemplify the ability to regenerate real networks, we regenerate networks with structures similar to two real Swedish swine transport networks. Results show that the spatial algorithm is an appropriate model with correlation coefficients at 0.99. This novel algorithm can even create negative assortativity and managed to achieve assortativity values that spans over almost the entire theoretical range.

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  • 28.
    Lennartsson, Jenny
    et al.
    Systems Biology Research Centre, Skövde University, Skövde, Sweden.
    Jonsson, Annie
    Systems Biology Research Centre, Skövde University, Skövde, Sweden.
    Håkansson, Nina
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Is a Sampled Network a Good Enough Descriptor? Missing Links and Appropriate Choice of RepresentationManuscript (preprint) (Other academic)
    Abstract [en]

    Missing links due to sampling difficulties can be a limitation in network analysis. Measurements and analysis of networks with insufficient data may make the actual properties indistinct and thus include too much uncertainty to lead to accurate inferences. In addition, in dynamical networks with low link degrees and high stochasticity one sample of the network structure during a finite time window may not be sufficient for general conclusions. Our interest here is to examine the possible consequences of analysis of networks with insufficient data. We studied how mean link degree in sampled networks affects predictions of the spread of disease. Networks with weighted links were used to run scenarios that assumed distance-dependent probabilities of disease transmission when applying general simulation methodology. These scenarios were compared with scenarios including randomly drawn probabilities of disease transmission. For both types of scenarios, we also tested two link-forming methods, one based on distance-dependence and the other on a random approach. Our findings imply that sampled networks must be improved by using statistical measures before attempting to estimate or predict the spread of disease. We conclude that, under the assumption of weighted links, predictions about the extent of an epidemic can be drawn only at mean degrees that are much higher than found in empirical studies. In reality, neither sampling procedures nor disease transmissions are completely dependent on distance. Our results show how this aspect enforces an even higher level of mean degree to be present in order to achieve reasonable predictions.

  • 29.
    Lennartsson, Jenny
    et al.
    Systems Biology Research Centre, Skövde University, Skövde, Sweden.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Jonsson, Annie
    Systems Biology Research Centre, Skövde University, Skövde, Sweden.
    Network measures efficiency as predictors for disease transmission in spatial farm networksManuscript (preprint) (Other academic)
    Abstract [en]

    Networks can be categorised using different measures of connectivity and topology of the network. We have examined if such network measures can be used as predictors of disease transmission in networks. In this study, virtual networks with a wide range of different structures are generated using the SpecNet algorithm. Measures are calculated for both the network as a whole and for individual nodes. The virtual networks generated a large variation in number of infected farms. In general, a large variation was still present for networks with equal value of a measure which implies that single network measures may not be sufficient as predictor for spread of disease. Yet, mean degree and the average clustering coefficient were the global network measures that could best explain the variation in the number of infected farms of a network. At the local level the degree and the clustering coefficient of the initially infected farm explain most of the variation in the number of infected farms. Hence, our results also points out that one should also consider the characteristics of the initially infected farm when predicting  the spread of a disease.

  • 30.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Grear, Daniel A.
    Colorado State University, USA .
    Buhnerkempe, Michael
    Colorado State University, USA .
    Webb, Colleen T.
    Colorado State University, USA .
    Miller, Ryan S.
    US Anim and Plant Health Inspect Serv, CO USA .
    Portacci, Katie
    US Anim and Plant Health Inspect Serv, CO USA .
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    A Bayesian Approach for Modeling Cattle Movements in the United States: Scaling up a Partially Observed Network2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 1Article in journal (Refereed)
    Abstract [en]

    Networks are rarely completely observed and prediction of unobserved edges is an important problem, especially in disease spread modeling where networks are used to represent the pattern of contacts. We focus on a partially observed cattle movement network in the U.S. and present a method for scaling up to a full network based on Bayesian inference, with the aim of informing epidemic disease spread models in the United States. The observed network is a 10% state stratified sample of Interstate Certificates of Veterinary Inspection that are required for interstate movement; describing approximately 20,000 movements from 47 of the contiguous states, with origins and destinations aggregated at the county level. We address how to scale up the 10% sample and predict unobserved intrastate movements based on observed movement distances. Edge prediction based on a distance kernel is not straightforward because the probability of movement does not always decline monotonically with distance due to underlying industry infrastructure. Hence, we propose a spatially explicit model where the probability of movement depends on distance, number of premises per county and historical imports of animals. Our model performs well in recapturing overall metrics of the observed network at the node level (U.S. counties), including degree centrality and betweenness; and performs better compared to randomized networks. Kernel generated movement networks also recapture observed global network metrics, including network size, transitivity, reciprocity, and assortativity better than randomized networks. In addition, predicted movements are similar to observed when aggregated at the state level (a broader geographic level relevant for policy) and are concentrated around states where key infrastructures, such as feedlots, are common. We conclude that the method generally performs well in predicting both coarse geographical patterns and network structure and is a promising method to generate full networks that incorporate the uncertainty of sampled and unobserved contacts.

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  • 31.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Håkansson, Nina
    Skövde University.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    The shape of the spatial kernel and its implications for biological invasions in patchy environments2011In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 278, no 1711, p. 1564-1571Article in journal (Refereed)
    Abstract [en]

    Ecological and epidemiological invasions occur in a spatial context. In the study presented we tested how these processes relate to the distance dependence of spread or dispersal between spatial entities such as habitat patches or infective units. The distance dependence was described by a spatial kernel which can be characterized by its shape, quantified by kurtosis, and width, quantified by the kernel variance. We also introduced a method to analyze or generate non randomly distributed infective units or patches as point pattern landscapes. The method is based on Fourier transform and consists of two measures in the spectral representation; Continuity that relates to autocorrelation and Contrast that refers to difference in density of patches, or infective units, in different areas of the landscape. The method was also used to analyze some relevant empirical data where our results are expected to have implications for ecological or epidemiological studies. We analyzed distributions of large old trees (Quercus and Ulmus) as well as the distributions of farms (both cattle and pig) in Sweden. We tested the invasion speed in generated landscapes with different amount of Continuity and Contrast. The results showed that kurtosis, i.e. the kernel shape, was not important for predicting the invasion speed in randomly distributed patches or infective units. However, depending on the assumptions of dispersal, it may be highly important when the distribution of patches or infective units deviates from randomness, in particular when the Contrast is high. We conclude that speed of invasions and spread of diseases depends on its spatial context through the spatial kernel intertwined to the spatial structure. This implies high demands on the empirical data; it requires knowledge of both shape and width of the spatial kernel as well as spatial structure of patches or infective units.

  • 32.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Håkansson, Nina
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology .
    Westerberg, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Ecology . Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Splitting the tail of the displacement kernel shows the unimportance of kurtosis2008In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 89, no 7, p. 1784-1790Article in journal (Refereed)
    Abstract [en]

    Animals disperse in space through different movement behaviors, resulting in different displacement distances. This is often described with a displacement kernel where the long-distance dispersers are within the tail of the kernel. A displacement with a large proportion of long-distance dispersers may have impact on different aspects of spatial ecology such as invasion speed, population persistence, and distribution. It is, however, unclear whether the kurtosis of the kernel plays a major role since a fatter tail also influences the variance of the kernel. We modeled displacement in landscapes with different amounts and configurations of habitats and handled kurtosis and variance separately to study how these affected population distribution and transition time. We conclude that kurtosis is not important for any of these aspects of spatial ecology. The variance of the kernel, on the other hand, was of great importance to both population distribution and transition time. We argue that separating variance and kurtosis can cast new light on the way in which long-distance dispersers are important in ecological processes. Consequences for empirical studies are discussed.

  • 33.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Sisson, Scott A.
    University of New S Wales, Australia .
    Hakansson, Nina
    Skovde University, Sweden .
    Bergman, Karl-Olof
    Linköping University, Department of Physics, Chemistry and Biology, Ecology. Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    A spectral and Bayesian approach for analysis of fluctuations and synchrony in ecological datasets2012In: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 3, no 6, p. 1019-1027Article in journal (Refereed)
    Abstract [en]

    Autocorrelation within ecological time series and synchrony between them may provide insight into the main drivers of observed dynamics. We here present methods that analyse autocorrelation and synchrony in ecological datasets using a spectral approach combined with Bayesian inference. To exemplify, we implement the method on dendrochronological data of the pedunculate oak (Quercus robur). The data consist of 110 years of growth of 10 live trees and seven trees that died during a synchronized oak death in Sweden in c. 2002-2007. We find that the highest posterior density is found for a noise colour of tree growth of gamma approximate to 0.95 (i.e. pink noise) with little difference between trees, suggesting climatic variation as a driving factor. This is further supported by the presence of synchrony, which we estimate based on phase-shift analysis. We conclude that the synchrony is time-scale dependent with higher synchrony at larger time-scales. We further show that there is no difference between the growth patterns of the alive and dead tree groups. This suggests that the trees were driven by the same factors prior to the synchronized death. We argue that this method is a promising approach for linking theoretical models with empirical data.

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  • 34.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Sisson, Scott A.
    School of Mathematics and Statistics, University of New South Wales, Sydney 2052, Australia.
    Nöremark, Maria
    Department of Disease Control and Epidemiology, SVA, National Veterinary Institute, 751 89 Uppsala, Sweden.
    Jonsson, Annie
    Research Centre of Systems Biology, Ecological Modelling, University of Skövde, 541 28 Skövde, Sweden.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Estimation of distance related probability of animal movements between holdings and implications for disease spread modeling2009In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 91, no 2-4, p. 85-94Article in journal (Refereed)
    Abstract [en]

    Between holding contacts are more common over short distances and this may have implications for the dynamics of disease spread through these contacts. A reliable estimation of how contacts depend on distance is therefore important when modeling livestock diseases. In this study, we have developed a method for analyzing distant dependent contacts and applied it to animal movement data from Sweden. The data were analyzed with two competing models. The first model assumes that contacts arise from a purely distance dependent process. The second is a mixture model and assumes that, in addition, some contacts arise independent of distance. Parameters were estimated with a Bayesian Markov Chain Monte Carlo (MCMC) approach and the model probabilities were compared. We also investigated possible between model differences in predicted contact structures, using a collection of network measures. We found that the mixture model was a much better model for the data analyzed. Also, the network measures showed that the models differed considerably in predictions of contact structures, which is expected to be important for disease spread dynamics. We conclude that a model with contacts being both dependent on, and independent of, distance was preferred for modeling the example animal movement contact data.

  • 35.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Sisson, Scott A.
    School of Mathematics and Statistics, University of New South Wales, Sydney 2052, Australia.
    Stenberg Lewerin, Susanna
    Department of Disease Control and Epidemiology, SVA, National Veterinary Institute, 751 89 Uppsala, Sweden.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Bayesian analysis of animal movements related to factors at herdand between herd levels: Implications for disease spread modeling2011In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 98, no 4, p. 230-242Article in journal (Other academic)
    Abstract [en]

    A method to assess the influence of between herd distances, production types and herd sizes on patterns of between herd contacts is presented. It was applied on pig movement data from a central database of Swedish Board of Agriculture. To determine the influence of these factors on the contact between holdings we used a Bayesian model and Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. The analysis showed that the contact pattern via animal movements is highly heterogeneous and influenced by all three factors, production type, herd size, and distance between farms. Most production types showed a positive relationship between maximum capacity and the probability of both incoming and outgoing movements. In agreement with previous studies, holdings also differed in both the number of contacts as well as with what holding types contact occurred with. Also, the scale and shape of distance dependence in contact probability was shown to differ depending on the production types of holdings.

    To demonstrate how the methodology may be used for risk assessment, disease transmissions via animal movements were simulated with the model used for analysis of contacts, and parameterized by the analyzed posterior distribution. A Generalized Linear Model showed that herds with production types Sow pool center, Multiplying herd and Nucleus herd have higher risk of generating a large number of new infections. Multiplying herds are also expected to generate many long distance transmissions, while transmissions generated by Sow pool centers are confined to more local areas. We argue that the methodology presented may be a useful tool for improvement of risk assessment based on data found in central databases.

  • 36.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Sisson, Scott A
    School of Mathematics and Statistics, University of New South Wales, Sydney 2052, Australia.
    Stenberg Lewerin, Susanna
    Department of Disease Control and Epidemiology, SVA, National Veterinary Institute, 751 89 Uppsala, Sweden.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Estimating animal movement contacts between holdings of different production types2010In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 95, no 1-2, p. 23-31Article in journal (Refereed)
    Abstract [en]

    Animal movement poses a great risk for disease transmission between holdings. Heterogeneous contact patterns are known to influence the dynamics of disease transmission and should be included in modeling. Using pig movement data from Sweden as an example, we present a method for quantification of between holding contact probabilities based on different production types. The data contained seven production types: Sow pool center, Sow pool satellite, Farrow-to-finish, Nucleus herd, Piglet producer, Multiplying herd and Fattening herd. The method also estimates how much different production types will determine the contact pattern of holdings that have more than one type. The method is based on Bayesian analysis and uses data from central databases of animal movement. Holdings with different production types are estimated to vary in the frequency of contacts as well as in what type of holding they have contact with, and the direction of the contacts. Movements from Multiplying herds to Sow pool centers, Nucleus herds to other Nucleus herds, Sow pool centers to Sow pool satellites, Sow pool satellites to Sow pool centers and Nucleus herds to Multiplying herds were estimated to be most common relative to the abundance of the production types. We show with a simulation study that these contact patterns may also be expected to result in substantial differences in disease transmission via animal movements, depending on the index holding. Simulating transmission for a 1 year period showed that the median number of infected holdings was 1 (i.e. only the index holding infected) if the infection started at a Fattening herd and 2161 if the infection started on a Nucleus herd. We conclude that it is valuable to include production types in models of disease transmission and the method presented in this paper may be used for such models when appropriate data is available. We also argue that keeping records of production types is of great value since it may be helpful in risk assessments.

  • 37.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Stenberg Lewerin, Susanna
    Department of Disease Control and Epidemiology, SVA, National Veterinary Institute, 751 89 Uppsala, Sweden.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Expected effect of herd size, production type and between herd distances on the dynamic of between herd disease spread2010Manuscript (preprint) (Other academic)
    Abstract [en]

    Studies of between herd contacts may provide important insight to disease transmission dynamics. By comparing the result from models with different level of details in the description of animal movement we studied how factors influence the final epidemic size as well as the stochastic behavior of an outbreak. We investigated the effect of contact heterogeneity of pig herds in Sweden due to herd size, between herd distance and production type. Our comparative study suggests that the production type structure is the most influential factor. Hence, our results imply that production type is the most important factor to obtain valid data for and include when modeling and analyzing this system. The study also revealed that all included factors reduce the final epidemic size and also have, yet more diverse, effects on initial rate of disease spread. This implies that a large set of factors ought to be included to assess relevant predictions when modeling disease spread between herds. Furthermore our results show that a more detailed model predicts more stochasticity in the outbreak dynamics and conclude that this is an important factor to consider in risk assessment.

  • 38.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Sternberg Lewerin, Susanna
    National Vet Institute.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Influence on disease spread dynamics of herd characteristics in a structured livestock industry2012In: Journal of the Royal Society Interface, ISSN 1742-5689, E-ISSN 1742-5662, Vol. 9, no 71, p. 1287-1294Article in journal (Refereed)
    Abstract [en]

    Studies of between-herd contacts may provide important insight to disease transmission dynamics. By comparing the result from models with different levels of detail in the description of animal movement, we studied how factors influence the final epidemic size as well as the dynamic behaviour of an outbreak. We investigated the effect of contact heterogeneity of pig herds in Sweden due to herd size, between-herd distance and production type. Our comparative study suggests that the production-type structure is the most influential factor. Hence, our results imply that production type is the most important factor to obtain valid data for and include when modelling and analysing this system. The study also revealed that all included factors reduce the final epidemic size and also have yet more diverse effects on initial rate of disease spread. This implies that a large set of factors ought to be included to assess relevant predictions when modelling disease spread between herds. Furthermore, our results show that a more detailed model changes predictions regarding the variability in the outbreak dynamics and conclude that this is an important factor to consider in risk assessment.

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  • 39.
    Lögdberg, Frida
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Håkansson, Nina
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    The Importance of Distance-Dependent Synchrony of Coloured NoiseManuscript (preprint) (Other academic)
    Abstract [en]

    Local populations in patches close to each other would probably be influenced by similar environmental conditions. When increasing the distance between the patches the local population will experience less synchronized environments. Since, the degree of synchrony is important for the overall extinction risk it is probably likewise important to include distance dependence in environmental variation when studying environmental forcing on spatially subdivided populations. Thus, we will investigate the importance of including such distance dependent synchrony when studying coloured environmental variation applied to populations in explicit landscapes. We will introduce a method based on controlling the phases when generating 1/fnoise. The results showed large differences between fast or slow density regulation responses in populations. Extinction risk was several magnitudes larger when including distance dependent synchrony compared to randomly distributing environmental time series for overcompensatory dynamics. There was one exception; it is not necessary to include distance dependent synchrony for landscape with random patch distribution. For undercompensatory dynamics the effect from distant dependent synchrony was only apparent in the most aggregated patch  configurations.

  • 40.
    Lögdberg, Frida
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Effects of Noise Color and Synchrony on Extinction Risk in Patchy EnvironmentsManuscript (preprint) (Other academic)
    Abstract [en]

    We studied interplay between landscape configuration and two characteristics known to affect population extinction risks: environmental fluctuations and population dynamics. Specifically, we tested effects of noise colour (i.e. the temporal autocorrelation) and the synchrony (i.e. spatial correlation) of environmental fluctuations by simulations using models of populations with overor undercompensatory dynamics. The results demonstrated that landscape configuration has a profound effect on extinction risks. Interaction between landscape configuration and environmental fluctuations was seen as stronger effects of noise colour (decreased extinction risk with increased redness) in random landscapes and more evident effects of synchrony in aggregated landscapes. The impact of landscape structure was more striking for over- than undercompensatory dynamics; showing strongly reduced extinction risk in aggregated landscapes compared to random configurations. Results on extinction risks using data on geographical positions of old oaks (Quercus robur) concurred with those of generated landscapes. Our findings indicate that a population on the limits of its existence is extremely sensitive to both spatial configuration and temporal variation of resources. The results underline that there are no shortcuts in ecology. Correct characterization of landscape configuration, environmental fluctuations, and population dynamics is necessary when estimatin  and analysing the causes of extinction risks.

  • 41.
    Lögdberg, Frida
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Biological Filtering of Noise Colour and SynchronyManuscript (preprint) (Other academic)
    Abstract [en]

    Environmental variation is a major force driving fluctuations in population densities. Here, we investigated the impact of such variation on population dynamics by studying noise color and synchrony of environmental variation compared to noise color and synchrony of variation of local population densities. We used Ricker models with over- or undercompensatory density-dependent regulation, and local populations were connected by dispersal. For both noise color and synchrony, we measured the shift between environmental variation and fluctuations in population densities. We also analyzed how the shifts were affected by dispersal rate and type of density regulation. Populations with undercompensatory dynamics showed the classical picture of increasing positive shifts in synchrony with increasing dispersal rates. The color of the environmental variation also affected the positive shift in synchrony, which was increased by reddened noise in populations with undercompensatory dynamics. Populations with overcompensatory dynamics showed no shifts in synchrony regardless of dispersal rates. Shifts in noise color exhibited the same pattern: populations with overcompensatory dynamics displayed only minor shifts in noise color, whereas those with undercompensatory dynamics had distinct positive shifts that increased with dispersal rates and also depended on the degree of synchrony. These findings demonstrate that noise color and synchrony are determined by and equal to synchrony and close to the color of environmental variation in populations with overcompensatory dynamics, but differ from the corresponding aspects of environmental variation in populations with undercompensatory dynamics. The shifts in populations with undercompensatory dynamics are determined by several factors: degree of population responsiveness, dispersal rates, and both the color and synchrony of environmental variation.

  • 42.
    Lögdberg, Frida
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Spectral Color, Synchrony and Extinction Risk2012In: THEORETICAL ECOLOGY, ISSN 1874-1738, Vol. 5, no 4, p. 545-554Article in journal (Refereed)
    Abstract [en]

    The autocorrelation of environmental variation, also called noise color, influences the population dynamics and the probability of extinction risk. Increasing the distance, the variations over time for two sites will become more unsynchronized. Thus, both degree of synchrony and noise color are parts of the same environmental variation affecting population dynamics in a spatial setting. We present a novel method of generating environmental noise controlling for its noise color and synchrony. We apply these time series to carrying capacity (K) or (indirectly) to growth rate (r), and altered the population regulation response between over- and under-compensatory. A novel finding is that the qualitative effects of noise color on extinction risk do not differ with degree of synchrony. Our results for highly responsive dynamics (large growth rates and overcompensatory dynamics) agree with previous non-spatial studies by showing that the redder the noise, the lower the extinction risk. The results for less responsive dynamics are more complex, indicating that intermediate noise color causes a larger extinction risk compared to whiter or redder color. To explain this hump-shaped response, we use classical descriptions of how means and variances of population density depend on noise color. These results allow a new straightforward interpretation of how extinction risk depends on population dynamics, noise color, and synchrony.

  • 43.
    Möhlmann, Tim
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering. Wageningen Univ and Res, Netherlands.
    Bekendam, A. M.
    Wageningen Univ and Res, Netherlands.
    van Kemenade, I.
    Wageningen Univ and Res, Netherlands.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Favia, G.
    Univ Camerino, Italy.
    Takken, W.
    Wageningen Univ and Res, Netherlands.
    Koenraadt, C. J. M.
    Wageningen Univ and Res, Netherlands.
    Latitudinal diversity of biting midge species within the Obsoletus group across three habitats in Europe2019In: Medical and Veterinary Entomology, ISSN 0269-283X, E-ISSN 1365-2915, Vol. 33, no 3, p. 420-426Article in journal (Refereed)
    Abstract [en]

    Culicoides species from the Obsoletus group are important vectors of bluetongue and Schmallenberg virus. This group consists of several species that cannot easily be identified using morphological characteristics. Therefore, limited information is available about their distribution and habitat preferences. In this study, we aimed to elucidate the species composition of the Obsoletus group in three habitat types at climatically different latitudes across Europe. Traps were placed in three habitat types in three countries at different latitudes. After DNA extraction, biting midges were identified using PCR and gel electrophoresis. Extraction of DNA using Chelex proved to be a cost and time efficient method for species identification. A latitudinal effect on the relative abundance of species from the Obsoletus group was found. Species composition was unique for most country-habitat combinations. The majority of biting midges were either C. obsoletus s.s. or C. scoticus, and both species were found at all latitudes and habitats. Their wide distribution and their high abundance at livestock farms make these species likely candidates for rapid farm-to-farm transmission of pathogens throughout Europe. Our results emphasize the need to differentiate Obsoletus group species to better understand their ecology and contribution to pathogen transmission.

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  • 44.
    Möhlmann, Tim
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering. Wageningen University of and Research Centre, Netherlands.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Tälle, Malin
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Favia, Guido
    University of Camerino, Italy.
    Damiani, Claudia
    University of Camerino, Italy.
    Bracchetti, Luca
    University of Camerino, Italy.
    Koenraadt, Constantianus J. M.
    Wageningen University of and Research Centre, Netherlands.
    Community analysis of the abundance and diversity of mosquito species (Diptera: Culicidae) in three European countries at different latitudes2017In: Parasites & Vectors, ISSN 1756-3305, E-ISSN 1756-3305, Vol. 10, article id 510Article in journal (Refereed)
    Abstract [en]

    Background: Studies on mosquito species diversity in Europe often focus on a specific habitat, region or country. Moreover, different trap types are used for these sampling studies, making it difficult to compare and validate results across Europe. To facilitate comparisons of trapping sites and community analysis, the present study used two trap types for monitoring mosquito species diversity in three habitat types for three different countries in Europe. Methods: Mosquitoes were trapped using Biogents Sentinel (BGS), and Mosquito Magnet Liberty Plus (MMLP) traps at a total of 27 locations in Sweden, the Netherlands and Italy, comprising farm, peri-urban and wetland habitats. From July 2014 to June 2015 all locations were sampled monthly, except for the winter months. Indices of species richness, evenness and diversity were calculated, and community analyses were carried out with non-metric multidimensional scaling (NMDS) techniques. Results: A total of 11,745 female mosquitoes were trapped during 887 collections. More than 90% of the mosquitoes belonged to the genera Culex and Aedes, with Culex pipiens being the most abundant species. The highest mosquito diversity was found in Sweden. Within Sweden, species diversity was highest in wetland habitats, whereas in the Netherlands and Italy this was highest at farms. The NMDS analyses showed clear differences in mosquito communities among countries, but not among habitat types. The MMLP trapped a higher diversity of mosquito species than the BGS traps. Also, MMLP traps trapped higher numbers of mosquitoes, except for the genera Culex and Culiseta in Italy. Conclusions: A core mosquito community could be identified for the three countries, with Culex pipiens as the most abundant species. Differences in mosquito species communities were more defined by the three countries included in the study than by the three habitat types. Differences in mosquito community composition across countries may have implications for disease emergence and further spread throughout Europe. Future research should, therefore, focus on how field data of vector communities can be incorporated into models, to better assess the risk of mosquito-borne disease outbreaks.

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  • 45.
    Möhlmann, Tim
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering. Wageningen Univ and Res, Netherlands.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Tälle, Malin
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Favia, Guido
    Univ Camerino, Italy.
    Damiani, Claudia
    Univ Camerino, Italy.
    Bracchetti, Luca
    Univ Camerino, Italy.
    Takken, Willem
    Wageningen Univ and Res, Netherlands.
    Koenraadt, Constantianus J. M.
    Wageningen Univ and Res, Netherlands.
    Community analysis of the abundance and diversity of biting midge species (Diptera: Ceratopogonidae) in three European countries at different latitudes2018In: Parasites & Vectors, ISSN 1756-3305, E-ISSN 1756-3305, Vol. 11, article id 217Article in journal (Refereed)
    Abstract [en]

    Background: The outbreaks of bluetongue and Schmallenberg disease in Europe have increased efforts to understand the ecology of Culicoides biting midges and their role in pathogen transmission. However, most studies have focused on a specific habitat, region, or country. To facilitate wider comparisons, and to obtain a better understanding of the spread of disease through Europe, the present study focused on monitoring biting midge species diversity in three different habitat types and three countries across Europe. Methods: Biting midges were trapped using Onderstepoort Veterinary Institute light traps at a total of 27 locations in Sweden, the Netherlands and Italy, comprising farm, peri-urban and wetland habitats. From July 2014 to June 2015 all locations were sampled monthly, except for during the winter months. Trapped midges were counted and identified morphologically. Indices on species richness, evenness and diversity were calculated. Community compositions were analysed using non-metric multidimensional scaling (NMDS) techniques. Results: A total of 50,085 female midges were trapped during 442 collection nights. More than 88% of these belonged to the Obsoletus group. The highest midge diversity was found in Sweden, while species richness was highest in the Netherlands, and most specimens were trapped in Italy. For habitats within countries, diversity of the trapped midges was lowest for farms in all countries. Differences in biting midge species communities were more distinct across the three countries than the three habitat types. Conclusions: A core midge community could be identified, in which the Obsoletus group was the most abundant. Variations in vector communities across countries imply different patterns of disease spread throughout Europe. How specific species and their associated communities affect disease risk is still unclear. Our results emphasize the importance of midge diversity data at community level, how this differs across large geographic range within Europe, and its implications on assessing risks of midge-borne disease outbreaks.

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  • 46.
    Noremark, Maria
    et al.
    Swedish University Agriculture Science.
    Hakansson, Nina
    University of Skövde.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology.
    Sternberg Lewerin, Susanna
    SVA.
    Spatial and temporal investigations of reported movements, births and deaths of cattle and pigs in Sweden2009In: Acta Veterinaria Scandinavica, ISSN 1751-0147, E-ISSN 1751-0147, Vol. 51, no 37Article in journal (Refereed)
    Abstract [en]

    Background: Livestock movements can affect the spread and control of contagious diseases and new data recording systems enable analysis of these movements. The results can be used for contingency planning, modelling of disease spread and design of disease control programs. Methods: Data on the Swedish cattle and pig populations during the period July 2005 until June 2006 were obtained from databases held by the Swedish Board of Agriculture. Movements of cattle and pigs were investigated from geographical and temporal perspectives, births and deaths of cattle were investigated from a temporal perspective and the geographical distribution of holdings was also investigated. Results: Most movements of cattle and pigs were to holdings within 100 km, but movements up to 1200 km occurred. Consequently, the majority of movements occurred within the same county or to adjacent counties. Approximately 54% of the cattle holdings and 45% of the pig holdings did not purchase any live animals. Seasonal variations in births and deaths of cattle were identified, with peaks in spring. Cattle movements peaked in spring and autumn. The maximum number of holdings within a 3 km radius of one holding was 45 for cattle and 23 for pigs, with large variations among counties. Missing data and reporting bias ( digit preference) were detected in the data. Conclusion: The databases are valuable tools in contact tracing. However since movements can be reported up to a week after the event and some data are missing they cannot replace other methods in the acute phase of an outbreak. We identified long distance transports of cattle and pigs, and these findings support an implementation of a total standstill in the country in the case of an outbreak of foot-and-mouth disease. The databases contain valuable information and improvements in data quality would make them even more useful.

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  • 47. Pedersen Brandt, Anneli
    et al.
    Karlsson, Laila
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Ecology .
    Wennergren, Uno
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology .
    Lettuce grown in silver laden soil at two different activity levels of soil microorganisms2005In: Journal of Applied Botany and Food Quality, ISSN 1613-9216, Vol. 79, no 1, p. 33-37Article in journal (Refereed)
    Abstract [en]

    Lettuce biomass, silver accumulation in lettuce, and effect of activity of soil microorganisms on these items, were studied in a series of experiments. Lettuce was cultivated in two kinds of soil with different organic matter concentrations. Initially the soil was either sterile or non-sterile, and had been supplied with different silver nitrate concentrations. Lettuce growth was significantly negatively affected by silver, especially in initially sterile soil with a lower organic matter content. There was also a significantly enhanced silver accumulation at larger silver supply in initially sterile soil with the lower organic matter content, otherwise there was no enhanced silver accumulation. There was a significant difference in respiration rate after harvest between the initially sterile soil and the non-sterile soil. In soil with the lower organic matter content, microorganism activity was inhibited by silver. In conclusion, silver accumulation increased and growth decreased in the lettuce grown in soil containing silver when the microorganism community in the soil had been affected by sterilization. The negative effects of silver on both lettuce and microorganisms were more distinct when the soil had a lower organic matter content.

  • 48.
    Sellman, Stefan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Tsao, Kimberly
    Colorado State Univ, CO 80523 USA.
    Tildesley, Michael J.
    Univ Warwick, England; Univ Warwick, England.
    Brommesson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Webb, Colleen T.
    Colorado State Univ, CO 80523 USA.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Keeling, Matt J.
    Univ Warwick, England; Univ Warwick, England.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Need for speed: An optimized gridding approach for spatially explicit disease simulations2018In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 14, no 4, article id e1006086Article in journal (Refereed)
    Abstract [en]

    Numerical models for simulating outbreaks of infectious diseases are powerful tools for informing surveillance and control strategy decisions. However, large-scale spatially explicit models can be limited by the amount of computational resources they require, which poses a problem when multiple scenarios need to be explored to provide policy recommendations. We introduce an easily implemented method that can reduce computation time in a standard Susceptible-Exposed-Infectious-Removed (SEIR) model without introducing any further approximations or truncations. It is based on a hierarchical infection process that operates on entire groups of spatially related nodes (cells in a grid) in order to efficiently filter out large volumes of susceptible nodes that would otherwise have required expensive calculations. After the filtering of the cells, only a subset of the nodes that were originally at risk are then evaluated for actual infection. The increase in efficiency is sensitive to the exact configuration of the grid, and we describe a simple method to find an estimate of the optimal configuration of a given landscape as well as a method to partition the landscape into a grid configuration. To investigate its efficiency, we compare the introduced methods to other algorithms and evaluate computation time, focusing on simulated outbreaks of foot-and-mouth disease (FMD) on the farm population of the USA, the UK and Sweden, as well as on three randomly generated populations with varying degree of clustering. The introduced method provided up to 500 times faster calculations than pairwise computation, and consistently performed as well or better than other available methods. This enables large scale, spatially explicit simulations such as for the entire continental USA without sacrificing realism or predictive power.

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  • 49.
    Tälle, Malin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Wiréhn, Lotten
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Centre for Climate Science and Policy Research, CSPR.
    Ellström, Daniel
    Linköping University, Department of Management and Engineering, Industrial Economics. Linköping University, Faculty of Science & Engineering.
    Hjerpe, Mattias
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Centre for Climate Science and Policy Research, CSPR.
    Huge-Brodin, Maria
    Linköping University, Department of Management and Engineering, Logistics & Quality Management. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Schmid Neset, Tina
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Centre for Climate Science and Policy Research, CSPR.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Metson, Genevieve
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Synergies and Trade-Offs for Sustainable Food Production in Sweden: An Integrated Approach2019In: Sustainability, ISSN 2071-1050, E-ISSN 2071-1050, Vol. 11, no 3, article id 601Article in journal (Refereed)
    Abstract [en]

    The production of food can have large impacts on sustainable development in relation to various socio-ecological dimensions, like climate change, the environment, animal welfare, livestock epidemiology, and the economy. To achieve a sustainable food production system in Sweden, an integrated approach that considers all five of these dimensions, and all parts of the food production chain, is necessary. This paper systematically reviewed the literature related to food production in Sweden, especially in association with resource distribution and recycling logistics, and identified potential sustainability interventions and assessed their effects according to the five dimensions. Participation of stakeholders across the food production chain contributed with the focus of the literature search and subsequent synthesis. In general, there were synergies between the sustainability interventions and their effect on climate change and the environment, while there often were trade-offs between effects on the economy and the other dimensions. Few interventions considered effects on animal welfare or livestock epidemiology and few studies dealt with resource distribution and recycling logistics. This indicates that there is a need for future research that considers this in particular, as well as research that considers the whole food production chain and all dimensions at once, and investigates effects across multiple scales.

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  • 50.
    Vogels, Chantal B. F.
    et al.
    University of Wageningen and Research Centre, Netherlands.
    Möhlmann, Tim
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering. University of Wageningen and Research Centre, Netherlands.
    Melsen, Diede
    University of Wageningen and Research Centre, Netherlands.
    Favia, Guido
    University of Camerino, Italy.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Koenraadt, Constantianus J. M.
    University of Wageningen and Research Centre, Netherlands.
    Latitudinal Diversity of Culex pipiens Biotypes and Hybrids in Farm, Peri-Urban, and Wetland Habitats in Europe2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 11, article id e0166959Article in journal (Refereed)
    Abstract [en]

    Despite the presence of Culex (Cx.) pipiens mosquitoes and circulation of West Nile virus (WNV), WNV outbreaks have so far not occurred in northern Europe. The species Cx. pipiens consists of two morphologically identical biotypes, pipiens and molestus, which can form hybrids. Until now, population dynamic studies of Cx. pipiens have not differentiated between biotypes and hybrids at the European scale, nor have they used comparative surveillance approaches. We therefore aimed to elucidate the relative abundance of Cx. pipiens biotypes and hybrids in three habitat types at different latitudes across Europe, using two different surveillance traps. BG-Sentinel and Mosquito-Magnet Liberty Plus traps were placed in three habitat types (farms, peri-urban, wetlands), in three European countries (Sweden, The Netherlands, Italy). Collected Cx. pipiens mosquitoes were identified to biotype with real-time PCR. Both trap types collected equal ratios of the biotypes and their hybrids. From northern to southern latitudes there was a significant decrease of pipiens and an increase of molestus. Habitat types influenced the relative ratios of biotypes and hybrids, but results were not consistent across latitudes. Our results emphasize the need to differentiate Cx. pipiens to the biotype level, especially for proper future WNV risk assessments for Europe.

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