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  • 1.
    Amiel, Joshua Johnstone
    et al.
    University of Sydney, Australia.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology. University of Sydney, Australia.
    Shine, Richard
    University of Sydney, Australia.
    Egg incubation effects generate positive correlations between size, speed and learning ability in young lizards2014In: Animal Cognition, ISSN 1435-9448, E-ISSN 1435-9456, Vol. 17, no 2, p. 337-347Article in journal (Refereed)
    Abstract [en]

    Previous studies have suggested that body size and locomotor performance are targets of Darwinian selection in reptiles. However, much of the variation in these traits may derive from phenotypically plastic responses to incubation temperature, rather than from underlying genetic variation. Intriguingly, incubation temperature may also influence cognitive traits such as learning ability. Therefore, we might expect correlations between a reptiles size, locomotor speed and learning ability either due to selection on all of these traits or due to environmental effects during egg incubation. In the present study, we incubated lizard eggs (Scincidae: Bassiana duperreyi) under hot and cold thermal regimes and then assessed differences in hatchling body size, running speed and learning ability. We measured learning ability using a Y-maze and a food reward. We found high correlations between size, speed and learning ability, using two different metrics to quantify learning (time to solution, and directness of route), and showed that environmental effects (incubation temperature) cause these correlations. If widespread, such correlations challenge any simple interpretation of fitness advantages due to body size or speed within a population; for example, survivors may be larger and faster than nonsurvivors because of differences in learning ability, not because of their size or speed.

  • 2.
    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.

  • 3.
    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.

  • 4.
    Gorsich, Erin E.
    et al.
    Colorado State Univ, CO 80523 USA.
    McKee, Clifton D.
    Colorado State Univ, CO 80523 USA.
    Grear, Daniel A.
    USDA APHIS Vet Serv, CO USA.
    Miller, Ryan S.
    USDA APHIS Vet Serv, CO USA.
    Portacci, Katie
    USDA APHIS Vet Serv, CO USA.
    Lindström, Tom
    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; Colorado State Univ, CO 80523 USA.
    Model-guided suggestions for targeted surveillance based on cattle shipments in the US2018In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 150, p. 52-59Article in journal (Refereed)
    Abstract [en]

    Risk-based sampling is an essential component of livestock health surveillance because it targets resources towards sub-populations with a higher risk of infection. Risk-based surveillance in U.S. livestock is limited because the locations of high-risk herds are often unknown and data to identify high-risk herds based on shipments are often unavailable. In this study, we use a novel, data-driven network model for the shipments of cattle in the U.S. (the U.S. Animal Movement Model, USAMM) to provide surveillance suggestions for cattle imported into the U.S. from Mexico. We describe the volume and locations where cattle are imported and analyze their predicted shipment patterns to identify counties that are most likely to receive shipments of imported cattle. Our results suggest that most imported cattle are sent to relatively few counties. Surveillance at 10 counties is predicted to sample 22-34% of imported cattle while surveillance at 50 counties is predicted to sample 43%-61% of imported cattle. These findings are based on the assumption that USAMM accurately describes the shipments of imported cattle because their shipments are not tracked separately from the remainder of the U.S. herd. However, we analyze two additional datasets - Interstate Certificates of Veterinary Inspection and brand inspection data - to ensure that the characteristics of potential post-import shipments do not change on an annual scale and are not dependent on the dataset informing our analyses. Overall, these results highlight the utility of USAMM to inform targeted surveillance strategies when complete shipment information is unavailable.

  • 5.
    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.

  • 6.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology . Linköping University, The Institute of Technology.
    Spatial Spread of Organisms: Modeling ecological and epidemiological processes2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis focuses on the spread of organisms in both ecological and epidemiological contexts. In most of the studies presented, displacement is modeled with a spatial kernel function, which is characterized by scale and shape. These are measured by the net squared displacement (or kernel variance) and kurtosis, respectively. If organisms disperse by the assumptions of a random walk or correlated random walk, a Gaussian shaped kernel is expected. Empirical studies often report deviations from this, and commonly leptokurtic distributions are found, often as a result of heterogeneity in the dispersal process.

    In the studies presented in two of the included papers, the importance of the kernel shape is tested, by using a family of kernels where the shape and scale can be separated effectively. Both studies utilize spectral density approaches for modeling the spatial environment. It is concluded that the shape is not important when studying the population distribution in a habitat/matrix context. The shape is however important when looking at the invasion of organisms in a patchy environment, when the arrangement of patches deviates from randomly distributed. The introduced method for generating patch distribution is also compared to empirical distributions of patches (farms and old trees). Here it is concluded that the assumptions used for modeling of the spatial environment are consistent with the observed patterns. These assumptions include fractal properties such that the same aggregational patterns are found at different scales.

    In a series of papers, movements of animals are considered as vectors for between-herd disease spread. The studies are based on data found in databases held by the Swedish Board of Agricultural (SJV), consisting of reported movements, as well as farm location and characteristics. The first study focuses on the distance related probability of contacts between herds. In the following papers, the analysis is expanded to include production type and herd size. Movement data of pigs (and cattle in Paper I) are analyzed with Bayesian models, implemented with Markov Chain Monte Carlo (MCMC). This is a flexible approach that allows for parameter estimations of complex models, and at the same time includes parameter uncertainty.

    In Paper IV, the effects of the included factors are investigated. It is shown that all three factors (herd size, production type structure and distance related probability of contacts) are expected to influence disease spread dynamics, however the production type structure is found to be the most important factor. This emphasizes the value of keeping such information in central databases. The models presented can be used as support for risk analysis and disease tracing. However, data reliability is always a problem, and implementation may be improved with better quality data.

    The thesis also shows that utilizing spatial kernels for description of the spatial spread of organisms is an appropriate approach. However, these kernels must be flexible and flawed assumptions about the shape may lead to erroneous conclusions. Hence, the joint distribution of kernel shape and scale should be estimated. The flexibility of Bayesian analysis, implemented with MCMC techniques, is a good approach for this, and further allows for implementation of more complex models where other factors may be included.

    List of papers
    1. Estimation of distance related probability of animal movements between holdings and implications for disease spread modeling
    Open this publication in new window or tab >>Estimation of distance related probability of animal movements between holdings and implications for disease spread modeling
    Show others...
    2009 (English)In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 91, no 2-4, p. 85-94Article in journal (Refereed) Published
    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.

    Place, publisher, year, edition, pages
    Elsevier, 2009
    Keywords
    Markov Chain Monte Carlo, Mixture models, Model selection, Animal movements, Disease transmission, Network analysis
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-20742 (URN)10.1016/j.prevetmed.2009.05.022 (DOI)
    Available from: 2009-09-18 Created: 2009-09-18 Last updated: 2017-12-13
    2. Estimating animal movement contacts between holdings of different production types
    Open this publication in new window or tab >>Estimating animal movement contacts between holdings of different production types
    2010 (English)In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 95, no 1-2, p. 23-31Article in journal (Refereed) Published
    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.

    Place, publisher, year, edition, pages
    Elsevier, 2010
    Keywords
    Markov Chain Monte Carlo; Animal databases; Animal movements; Production types
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-54834 (URN)10.1016/j.prevetmed.2010.03.002 (DOI)000278281600004 ()20356640 (PubMedID)
    Available from: 2010-04-15 Created: 2010-04-15 Last updated: 2017-12-12
    3. Bayesian analysis of animal movements related to factors at herdand between herd levels: Implications for disease spread modeling
    Open this publication in new window or tab >>Bayesian analysis of animal movements related to factors at herdand between herd levels: Implications for disease spread modeling
    2011 (English)In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 98, no 4, p. 230-242Article in journal (Other academic) Published
    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.

    Place, publisher, year, edition, pages
    Elsevier, 2011
    Keywords
    Markov Chain Monte Carlo; Hierarchical Bayesian; Mixture models; Indicator variable; Animal databases; Animal movements; Contact structure
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-54835 (URN)10.1016/j.prevetmed.2010.11.005 (DOI)000287904900002 ()
    Available from: 2010-04-15 Created: 2010-04-15 Last updated: 2017-12-12
    4. Expected effect of herd size, production type and between herd distances on the dynamic of between herd disease spread
    Open this publication in new window or tab >>Expected effect of herd size, production type and between herd distances on the dynamic of between herd disease spread
    2010 (English)Manuscript (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.

    Keywords
    Disease spread modeling, Heterogeneous contact structure
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-54837 (URN)20356640 (PubMedID)
    Available from: 2010-04-15 Created: 2010-04-15 Last updated: 2016-08-31
    5. Splitting the tail of the displacement kernel shows the unimportance of kurtosis
    Open this publication in new window or tab >>Splitting the tail of the displacement kernel shows the unimportance of kurtosis
    2008 (English)In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 89, no 7, p. 1784-1790Article in journal (Refereed) Published
    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.

    Keywords
    Displacement; kurtosis; long-distance dispersers; population distribution
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-43068 (URN)10.1890/07-1363.1 (DOI)71401 (Local ID)71401 (Archive number)71401 (OAI)
    Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2017-12-13
    6. The shape of the spatial kernel and its implications for biological invasions in patchy environments
    Open this publication in new window or tab >>The shape of the spatial kernel and its implications for biological invasions in patchy environments
    2011 (English)In: 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) Published
    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.

    Place, publisher, year, edition, pages
    Royal Society, 2011
    Keywords
    Kurtosis, Spread of disease, Point patterns, Spectral density, Dispersal, Invasion
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-54838 (URN)10.1098/rspb.2010.1902 (DOI)000289719100016 ()20356640 (PubMedID)
    Available from: 2010-04-15 Created: 2010-04-15 Last updated: 2017-12-12
    7. The effect on dispersal from complex correlations in small-scale movement
    Open this publication in new window or tab >>The effect on dispersal from complex correlations in small-scale movement
    2008 (English)In: Ecological Modelling, ISSN 0304-3800, E-ISSN 1872-7026, Vol. 213, no 2, p. 263-272Article in journal (Refereed) Published
    Abstract [en]

    Calculations of large-scale displacement distances were made to evaluate the combined effect of small-scale movement pattern of a Collembola, Protaphorura armata. The effect of presence of food and conspecific density on turning angle, step length and activity/motility was investigated. Calculations of net square displacement were made both by assuming correlated random walk (CRW) and by resampling data to account for correlation structures in movement patterns that violate the assumptions of CRW. In presence of food, individuals spent less time moving (decreased activity), but when they moved they showed larger turning angles than individuals moving in areas without food. Increased conspecific density did not affect time spent moving by individuals, but when step length decreased and turning angle increased. P. armata showed negative density-dependent dispersal and exhibited area-restricted search as a response to both food and increased conspecific density. The CRW was relatively robust to some violations of its underlying assumptions. However, the expected displacement increased substantially, as much as 50%, when accounting for observed auto-correlation in step length and correlation between step length and turning angle. Hence, an explanation for increased displacement and dispersal of a species can also be the result of a more complex correlation of its behaviour rather than solely altering specific movement parameters, for example increasing step length or decreasing turning angle. The results emphasise the importance of careful analysis of small-scale movement before using them as predictors of population distribution and invasion speed in heterogeneous landscapes. © 2007 Elsevier B.V. All rights reserved.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-44411 (URN)10.1016/j.ecolmodel.2007.12.011 (DOI)76579 (Local ID)76579 (Archive number)76579 (OAI)
    Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2017-12-13
  • 7.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, The Institute of Technology. University of Sydney, Australia .
    Brown, Gregory P.
    University of Sydney, Australia .
    Sisson, Scott A.
    University of New S Wales, Australia .
    Phillips, Benjamin L.
    James Cook University, Australia .
    Shine, Richard
    University of Sydney, Australia .
    Rapid shifts in dispersal behavior on an expanding range edge2013In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, no 33, p. 13452-13456Article in journal (Refereed)
    Abstract [en]

    Dispersal biology at an invasion front differs from that of populations within the range core, because novel evolutionary and ecological processes come into play in the nonequilibrium conditions at expanding range edges. In a world where species range limits are changing rapidly, we need to understand how individuals disperse at an invasion front. We analyzed an extensive dataset from radio-tracking invasive cane toads (Rhinella marina) over the first 8 y since they arrived at a site in tropical Australia. Movement patterns of toads in the invasion vanguard differed from those of individuals in the same area postcolonization. Our model discriminated encamped versus dispersive phases within each toads movements and demonstrated that pioneer toads spent longer periods in dispersive mode and displayed longer, more directed movements while they were in dispersive mode. These analyses predict that overall displacement per year is more than twice as far for toads at the invasion front compared with those tracked a few years later at the same site. Studies on established populations (or even those a few years postestablishment) thus may massively underestimate dispersal rates at the leading edge of an expanding population. This, in turn, will cause us to underpredict the rates at which invasive organisms move into new territory and at which native taxa can expand into newly available habitat under climate change.

  • 8.
    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.

  • 9.
    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.

  • 10.
    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.

  • 11.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Phillips, Benjamin L.
    School of Biosciences, University of Melbourne, Melbourne, VIC 3010 Australia.
    Brown, Gregory P.
    School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia.
    Shine, Richard
    School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia.
    Identifying the time scale of synchronousmovement: a study on tropical snakes2015In: Movement Ecology, E-ISSN 2051-3933, ISSN 2051-3933, Vol. 3, no 12, p. 1-9Article in journal (Refereed)
    Abstract [en]

    BACKGROUND:

    Individual movement is critical to organismal fitness and also influences broader population processes such as demographic stochasticity and gene flow. Climatic change and habitat fragmentation render the drivers of individual movement especially critical to understand. Rates of movement of free-ranging animals through the landscape are influenced both by intrinsic attributes of an organism (e.g., size, body condition, age), and by external forces (e.g., weather, predation risk). Statistical modelling can clarify the relative importance of those processes, because externally-imposed pressures should generate synchronous displacements among individuals within a population, whereas intrinsic factors should generate consistency through time within each individual. External and intrinsic factors may vary in importance at different time scales.

    RESULTS:

    In this study we focused on daily displacement of an ambush-foraging snake from tropical Australia (the Northern Death Adder Acanthophis praelongus), based on a radiotelemetric study. We used a mixture of spectral representation and Bayesian inference to study synchrony in snake displacement by phase shift analysis. We further studied autocorrelation in fluctuations of displacement distances as "one over f noise". Displacement distances were positively autocorrelated with all considered noise colour parameters estimated as >0. We show how the methodology can reveal time scales of particular interest for synchrony and found that for the analysed data, synchrony was only present at time scales above approximately three weeks.

    CONCLUSION:

    We conclude that the spectral representation combined with Bayesian inference is a promising approach for analysis of movement data. Applying the framework to telemetry data of A. praelongus, we were able to identify a cut-off time scale above which we found support for synchrony, thus revealing a time scale where global external drivers have a larger impact on the movement behaviour. Our results suggest that for the considered study period, movement at shorter time scales was primarily driven by factors at the individual level; daily fluctuations in weather conditions had little effect on snake movement.

  • 12.
    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.

  • 13.
    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.

  • 14.
    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.

  • 15.
    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.

  • 16.
    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.

  • 17.
    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.

  • 18.
    Lindström, Tom
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering. Colorado State University, CO 80523 USA; US National Institute Heatlh, MD USA; University of Exeter, England.
    Tildesley, Michael
    US National Institute Heatlh, MD USA; University of Nottingham, England.
    Webb, Colleen
    Colorado State University, CO 80523 USA; US National Institute Heatlh, MD USA.
    A Bayesian Ensemble Approach for Epidemiological Projections2015In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 11, no 4, p. e1004187-Article in journal (Refereed)
    Abstract [en]

    Mathematical models are powerful tools for epidemiology and can be used to compare control actions. However, different models and model parameterizations may provide different prediction of outcomes. In other fields of research, ensemble modeling has been used to combine multiple projections. We explore the possibility of applying such methods to epidemiology by adapting Bayesian techniques developed for climate forecasting. We exemplify the implementation with single model ensembles based on different parameterizations of the Warwick model run for the 2001 United Kingdom foot and mouth disease outbreak and compare the efficacy of different control actions. This allows us to investigate the effect that discrepancy among projections based on different modeling assumptions has on the ensemble prediction. A sensitivity analysis showed that the choice of prior can have a pronounced effect on the posterior estimates of quantities of interest, in particular for ensembles with large discrepancy among projections. However, by using a hierarchical extension of the method we show that prior sensitivity can be circumvented. We further extend the method to include a priori beliefs about different modeling assumptions and demonstrate that the effect of this can have different consequences depending on the discrepancy among projections. We propose that the method is a promising analytical tool for ensemble modeling of disease outbreaks.

  • 19.
    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.

  • 20.
    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.

  • 21.
    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.

  • 22.
    Price-Rees, Samantha J.
    et al.
    University of Sydney, Australia.
    Lindström, Tom
    University of Sydney, Australia.
    Brown, Gregory P.
    Shine, Richard
    The effects of weather conditions on dispersal behaviour of free-ranging lizards (Tiliqua, Scincidae) in tropical Australia2014In: Functional Ecology, Vol. 28, no 2, p. 440-449Article in journal (Refereed)
    Abstract [en]

    Summary Animals may switch between alternative modes of movement (e.g. philopatry vs. dispersal) in response to complex interactions between internal state, landscape characteristics, dispersal capacity and navigational capacity. In this study, we use an extensive data set from GPS telemetry of free-ranging lizards (bluetongue skinks, Tiliqua spp.) in the Australian wet-dry tropics, to examine how abiotic conditions (temperature, air pressure, precipitation, humidity and wind speed) influence lizard dispersal. The GPS transmitters provided >60,000 records of lizard location from 49 individuals (41 T. scincoides intermedia, 8 T. multifasciata) monitored for a mean of 65 days each. We used a maximum likelihood analytical tool to objectively distinguish intra-patch movements from dispersive movements. Threshold levels of dispersal to differentiate between these two movement phases averaged 36–42 m displacement per hour, depending on species and site. Whether bluetongue lizards within the study population dispersed (rather than remained encamped) was highly associated with weather variables, notably air temperature and atmospheric pressure. Fine-scale (hourly) weather conditions were better predictors of lizard dispersal than daily mean values. Lizards primarily dispersed between widely scattered patches of core-habitat under fine, hot, clear weather conditions. Air pressure tended to predict lizard dispersal more accurately than did more commonly analysed variables such as temperature and precipitation.

  • 23.
    Pértille, Fábio
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Univ Sao Paulo, Brazil.
    Da Silva, Vinicius H.
    Wageningen Univ and Res, Netherlands; Netherlands Inst Ecol NIOO KNAW, Netherlands; Swedish Univ Agr Sci, Sweden.
    Johansson, Anna M.
    Swedish Univ Agr Sci, Sweden.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Coutinho, Luiz L.
    Univ Sao Paulo, Brazil.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Guerrero Bosagna, Carlos
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification2019In: Epigenetics, ISSN 1559-2294, E-ISSN 1559-2308Article in journal (Refereed)
    Abstract [en]

    DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic flexibility in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic specificity in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation.

  • 24.
    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.

  • 25.
    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.

  • 26.
    Webb, Colleen T.
    et al.
    Colorado State University, CO 80523 USA.
    Ferrari, Matthew
    Penn State University, PA 16802 USA.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering. Colorado State University, CO 80523 USA.
    Carpenter, Tim
    Massey University, New Zealand.
    Duerr, Salome
    University of Bern, Switzerland.
    Garner, Graeme
    Department Agriculture, Australia.
    Jewell, Chris
    Massey University, Palmerston North, New Zealand.
    Stevenson, Mark
    University of Melbourne, Australia.
    Ward, Michael P.
    University of Sydney, Australia.
    Werkman, Marleen
    CVI, Netherlands.
    Backer, Jantien
    CVI, Netherlands.
    Tildesley, Michael
    University of Warwick, England.
    Ensemble modelling and structured decision-making to support Emergency Disease Management2017In: Preventive Veterinary Medicine, ISSN 0167-5877, E-ISSN 1873-1716, Vol. 138, p. 124-133Article in journal (Refereed)
    Abstract [en]

    Epidemiological models in animal health are commonly used as decision-support tools to understand the impact of various control actions on infection spread in susceptible populations. Different models contain different assumptions and parameterizations, and policy decisions might be improved by considering outputs from multiple models. However, a transparent decision-support framework to integrate outputs from multiple models is nascent in epidemiology. Ensemble modelling and structured decision-making integrate the outputs of multiple models, compare policy actions and support policy decision-making. We briefly review the epidemiological application of ensemble modelling and structured decision-making and illustrate the potential of these methods using foot and mouth disease (FMD) models. In case study one, we apply structured decision-making to compare five possible control actions across three FMD models and show which control actions and outbreak costs are robustly supported and which are impacted by model uncertainty. In case study two, we develop a methodology for weighting the outputs of different models and show how different weighting schemes may impact the choice of control action. Using these case studies, we broadly illustrate the potential of ensemble modelling and structured decision-making in epidemiology to provide better information for decision-making and outline necessary development of these methods for their further application. Crown Copyright (C) 2017 Published by Elsevier B.V. All rights reserved.

  • 27.
    Westerberg, Lars
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Ecology .
    Lindström, Tom
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology .
    Nilsson, E.
    Wennergren, Uno
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology .
    The effect on dispersal from complex correlations in small-scale movement2008In: Ecological Modelling, ISSN 0304-3800, E-ISSN 1872-7026, Vol. 213, no 2, p. 263-272Article in journal (Refereed)
    Abstract [en]

    Calculations of large-scale displacement distances were made to evaluate the combined effect of small-scale movement pattern of a Collembola, Protaphorura armata. The effect of presence of food and conspecific density on turning angle, step length and activity/motility was investigated. Calculations of net square displacement were made both by assuming correlated random walk (CRW) and by resampling data to account for correlation structures in movement patterns that violate the assumptions of CRW. In presence of food, individuals spent less time moving (decreased activity), but when they moved they showed larger turning angles than individuals moving in areas without food. Increased conspecific density did not affect time spent moving by individuals, but when step length decreased and turning angle increased. P. armata showed negative density-dependent dispersal and exhibited area-restricted search as a response to both food and increased conspecific density. The CRW was relatively robust to some violations of its underlying assumptions. However, the expected displacement increased substantially, as much as 50%, when accounting for observed auto-correlation in step length and correlation between step length and turning angle. Hence, an explanation for increased displacement and dispersal of a species can also be the result of a more complex correlation of its behaviour rather than solely altering specific movement parameters, for example increasing step length or decreasing turning angle. The results emphasise the importance of careful analysis of small-scale movement before using them as predictors of population distribution and invasion speed in heterogeneous landscapes. © 2007 Elsevier B.V. All rights reserved.

  • 28.
    Österman, Hanna
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Lindgren, Isa
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Altimiras, Jordi
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Chronic hypoxia during development does not trigger pathologic remodeling of the chicken embryonic heart but reduces cardiomyocyte number2015In: American Journal of Physiology. Regulatory Integrative and Comparative Physiology, ISSN 0363-6119, E-ISSN 1522-1490, Vol. 309, no 10, p. R1204-R1214Article in journal (Refereed)
    Abstract [en]

    Fetal growth restriction programs an increased risk of cardiovascular disease in adulthood, but the actual mechanisms of this developmental programming are not fully understood. Previous studies in mammalian models suggest that hearts of growth-restricted fetuses have reduced cardiomyocyte number due to reduced proliferation and premature cardiomyocyte maturation. Chicken embryos incubated under chronic hypoxia are also growth-restricted, have smaller hearts, and show signs of cardiac insufficiency posthatching. The aim of the present study was to investigate how chronic hypoxia (14% O-2) during development affects cardiomyocyte mass and how myocardial structure is altered. Hypoxic incubation reproduced the well-characterized embryonic growth restriction and an increased ventricle-to-body mass ratio (at E11, E15, E17, and E19) with reduced absolute heart mass only at E19. Cell density, apoptosis, and cardiomyocyte size were insensitive to hypoxia at E15 and E19, and no signs of ventricular wall remodeling or myocardial fibrosis were detected. Bayesian modeling provided strong support for hypoxia affecting absolute mass and proliferation rates at E15, indicating that the growth impairment, at least partly, occurs earlier in development. Neither E15 nor E19 hearts contained binucleated cardiomyocytes, indicating that fetal hypoxia does not trigger early maturation of cardiomyocytes in the chicken, which contrasts with previous results from hypoxic rat pups. In conclusion, prenatal hypoxia in the chick embryo results in a reduction in the number of cardiomyocytes without inducing ventricular remodeling, cell hypertrophy, or premature cardiomyocyte maturation.

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