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  • 1. Adami, C.
    et al.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    Erratum: Evolutionary instability of zero-determinant strategies demonstrates that winning is not everything (Nature Communications (2013) 4:2193 DOI: 10.1038/ncomms3193)2014Inngår i: Nature Communications, E-ISSN 2041-1723, Vol. 5, artikkel-id 3764Artikkel i tidsskrift (Fagfellevurdert)
  • 2. Adami, C.
    et al.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    Evolutionary instability of zero-determinant strategies demonstrates that winning is not everything2013Inngår i: Nature Communications, E-ISSN 2041-1723, Vol. 4, artikkel-id 2193Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Zero-determinant strategies are a new class of probabilistic and conditional strategies that are able to unilaterally set the expected payoff of an opponent in iterated plays of the Prisoner's Dilemma irrespective of the opponent's strategy (coercive strategies), or else to set the ratio between the player's and their opponent's expected payoff (extortionate strategies). Here we show that zero-determinant strategies are at most weakly dominant, are not evolutionarily stable, and will instead evolve into less coercive strategies. We show that zero-determinant strategies with an informational advantage over other players that allows them to recognize each other can be evolutionarily stable (and able to exploit other players). However, such an advantage is bound to be short-lived as opposing strategies evolve to counteract the recognition. © 2013 Macmillan Publishers Limited. All rights reserved.

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  • 3. Adami, C.
    et al.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    Thermodynamics of evolutionary games2018Inngår i: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, nr 6, artikkel-id 062136Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    How cooperation can evolve between players is an unsolved problem of biology. Here we use Hamiltonian dynamics of models of the Ising type to describe populations of cooperating and defecting players to show that the equilibrium fraction of cooperators is given by the expectation value of a thermal observable akin to a magnetization. We apply the formalism to the public goods game with three players and show that a phase transition between cooperation and defection occurs that is equivalent to a transition in one-dimensional Ising crystals with long-range interactions. We then investigate the effect of punishment on cooperation and find that punishment plays the role of a magnetic field that leads to an "alignment" between players, thus encouraging cooperation. We suggest that a thermal Hamiltonian picture of the evolution of cooperation can generate other insights about the dynamics of evolving groups by mining the rich literature of critical dynamics in low-dimensional spin systems. © 2018 American Physical Society.

  • 4. Adami, C.
    et al.
    Qian, J.
    Rupp, M.
    Hintze, Arend
    Keck Graduate Institute of Applied Life Sciences, Claremont, United States; Michigan State University, East Lansing, United States.
    Information content of colored motifs in complex networks2011Inngår i: Artificial Life, ISSN 1064-5462, E-ISSN 1530-9185, Vol. 17, nr 4, s. 375-390Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study complex networks in which the nodes are tagged with different colors depending on their function (colored graphs), using information theory applied to the distribution of motifs in such networks. We find that colored motifs can be viewed as the building blocks of the networks (much more than the uncolored structural motifs can be) and that the relative frequency with which these motifs appear in the network can be used to define its information content. This information is defined in such a way that a network with random coloration (but keeping the relative number of nodes with different colors the same) has zero color information content. Thus, colored motif information captures the exceptionality of coloring in the motifs that is maintained via selection. We study the motif information content of the C. elegans brain as well as the evolution of colored motif information in networks that reflect the interaction between instructions in genomes of digital life organisms. While we find that colored motif information appears to capture essential functionality in the C. elegans brain (where the color assignment of nodes is straightforward), it is not obvious whether the colored motif information content always increases during evolution, as would be expected from a measure that captures network complexity. For a single choice of color assignment of instructions in the digital life form Avida, we find rather that colored motif information content increases or decreases during evolution, depending on how the genomes are organized, and therefore could be an interesting tool to dissect genomic rearrangements. © 2011 Massachusetts Institute of Technology.

  • 5. Adami, C.
    et al.
    Schossau, J.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    Evolution and stability of altruist strategies in microbial games2012Inngår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 85, nr 1, artikkel-id 011914Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    When microbes compete for limited resources, they often engage in chemical warfare using bacterial toxins. This competition can be understood in terms of evolutionary game theory (EGT). We study the predictions of EGT for the bacterial "suicide bomber" game in terms of the phase portraits of population dynamics, for parameter combinations that cover all interesting games for two-players, and seven of the 38 possible phase portraits of the three-player game. We compare these predictions to simulations of these competitions in finite well-mixed populations, but also allowing for probabilistic rather than pure strategies, as well as Darwinian adaptation over tens of thousands of generations. We find that Darwinian evolution of probabilistic strategies stabilizes games of the rock-paper-scissors type that emerge for parameters describing realistic bacterial populations, and point to ways in which the population fixed point can be selected by changing those parameters. © 2012 American Physical Society.

  • 6. Adami, C.
    et al.
    Schossau, J.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    Evolutionary game theory using agent-based methods2016Inngår i: Physics of Life Reviews, ISSN 1571-0645, E-ISSN 1873-1457, Vol. 19, s. 1-26Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Evolutionary game theory is a successful mathematical framework geared towards understanding the selective pressures that affect the evolution of the strategies of agents engaged in interactions with potential conflicts. While a mathematical treatment of the costs and benefits of decisions can predict the optimal strategy in simple settings, more realistic settings such as finite populations, non-vanishing mutations rates, stochastic decisions, communication between agents, and spatial interactions, require agent-based methods where each agent is modeled as an individual, carries its own genes that determine its decisions, and where the evolutionary outcome can only be ascertained by evolving the population of agents forward in time. While highlighting standard mathematical results, we compare those to agent-based methods that can go beyond the limitations of equations and simulate the complexity of heterogeneous populations and an ever-changing set of interactors. We conclude that agent-based methods can predict evolutionary outcomes where purely mathematical treatments cannot tread (for example in the weak selection–strong mutation limit), but that mathematics is crucial to validate the computational simulations. © 2016 Elsevier B.V.

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  • 7. Adami, C.
    et al.
    Schossau, J.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    The reasonable effectiveness of agent-based simulations in evolutionary game theory: Reply to comments on “Evolutionary game theory using agent-based methods”2016Inngår i: Physics of Life Reviews, ISSN 1571-0645, E-ISSN 1873-1457, Vol. 19, s. 38-42Artikkel i tidsskrift (Fagfellevurdert)
  • 8. Albantakis, L.
    et al.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    Koch, C.
    Adami, C.
    Tononi, G.
    Evolution of Integrated Causal Structures in Animats Exposed to Environments of Increasing Complexity2014Inngår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 10, nr 12Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Natural selection favors the evolution of brains that can capture fitness-relevant features of the environment's causal structure. We investigated the evolution of small, adaptive logic-gate networks (“animats”) in task environments where falling blocks of different sizes have to be caught or avoided in a ‘Tetris-like’ game. Solving these tasks requires the integration of sensor inputs and memory. Evolved networks were evaluated using measures of information integration, including the number of evolved concepts and the total amount of integrated conceptual information. The results show that, over the course of the animats' adaptation, i) the number of concepts grows; ii) integrated conceptual information increases; iii) this increase depends on the complexity of the environment, especially on the requirement for sequential memory. These results suggest that the need to capture the causal structure of a rich environment, given limited sensors and internal mechanisms, is an important driving force for organisms to develop highly integrated networks (“brains”) with many concepts, leading to an increase in their internal complexity. © 2014 Albantakis et al.

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  • 9. Alvarez-Castro, J.M.
    et al.
    Carlborg, Ö.
    Rönnegård, Lars
    Högskolan Dalarna, Akademin Industri och samhälle, Statistik.
    Estimation and interpretation of genetic effects with epistasis using the NOIA model2012Inngår i: Quantitative trait loci (QTL): Methods and Protocols / [ed] Scott A. Rifkin, Humana Press, 2012, s. 191-204Kapittel i bok, del av antologi (Annet vitenskapelig)
    Abstract [en]

    We introduce this communication with a brief outline of the historical landmarks in genetic modeling, especially concerning epistasis. Then, we present methods for the use of genetic modeling in QTL analyses. In particular, we summarize the essential expressions of the natural and orthogonal interactions (NOIA) model of genetic effects. Our motivation for reviewing that theory here is twofold. First, this review presents a digest of the expressions for the application of the NOIA model, which are often mixed with intermediate and additional formulae in the original articles. Second, we make the required theory handy for the reader to relate the genetic concepts to the particular mathematical expressions underlying them. We illustrate those relations by providing graphical interpretations and a diagram summarizing the key features for applying genetic modeling with epistasis in comprehensive QTL analyses. Finally, we briefly review some examples of the application of NOIA to real data and the way it improves the interpretability of the results.

  • 10. Armbruster, W. S.
    Pélabon, C
    Pérez-Barrales, R.
    Maad, Johanne
    Department of Biology, NTNU, NO-7491, Trondheim, Norway.
    The adaptive accuracy of flowers: Measurement and microevolutionary patterns2009Inngår i: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 103, nr 9, s. 1529-1545Artikkel i tidsskrift (Fagfellevurdert)
  • 11. Besnier, Francois
    et al.
    Wahlberg, Per
    Rönnegård, Lars
    Högskolan Dalarna, Akademin Industri och samhälle, Statistik.
    Ek, Weronika
    Andersson, Leif
    Siegel, Paul
    Carlborg, Örjan
    Fine mapping and replication of QTL in outbred chicken advanced intercross lines2011Inngår i: Genetics Selection Evolution, ISSN 0999-193X, E-ISSN 1297-9686, Vol. 43, artikkel-id 3Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature.

    Methods: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight.

    Results: Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL.

    Conclusions: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.

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  • 12. Boberg, E.
    Jonsson, M.
    Maad, Johanne
    Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
    Ågren, J.
    Nilsson, L. A.
    Pollinator shifts and the evolution of spur length in the moth-pollinated orchid Platanthera bifolia2014Inngår i: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 113, nr 2, s. 267-275Artikkel i tidsskrift (Fagfellevurdert)
  • 13. Bohm, C.
    et al.
    Ackles, A. L.
    Ofria, C.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    On sexual selection in the presence of multiple costly displays2020Inngår i: Proceedings of the 2019 Conference on Artificial Life: How Can Artificial Life Help Solve Societal Challenges, ALIFE 2019, MIT Press , 2020, s. 247-254Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Sexual selection is a powerful yet poorly understood evolutionary force. Research into sexual selection, whether biological, computational, or mathematical, has tended to take a top-down approach studying complex natural systems. Many simplifying assumptions must be made in order to make these systems tractable, but it is unclear if these simplifications result in a system which still represents natural ecological and evolutionary dynamics. Here, we take a bottom-up approach in which we construct simple computational systems from subsets of biologically plausible components and focus on examining the underlying dynamics resulting from the interactions of those components. We use this method to investigate sexual selection in general and the sexy sons theory in particular. The minimally necessary components are therefore genomes, genome-determined displays and preferences, and a process capable of overseeing parent selection and mating. We demonstrate the efficacy of our approach (i.e we observe the evolution of female preference) and provide support for sexy sons theory, including illustrating the oscillatory behavior that developed in the presence of multiple costly display traits. Copyright © ALIFE 2019.All rights reserved.

  • 14.
    Dekkers, Koen F
    et al.
    Uppsala University, Uppsala.
    Sayols-Baixeras, Sergi
    Uppsala University, Uppsala; Instituto de Salud Carlos III, Madrid, Spain.
    Baldanzi, Gabriel
    Uppsala University, Uppsala.
    Nowak, Christoph
    Karolinska Institute, Huddinge.
    Hammar, Ulf
    Uppsala University, Uppsala.
    Nguyen, Diem
    Uppsala University, Uppsala.
    Varotsis, Georgios
    Uppsala University, Uppsala.
    Brunkwall, Louise
    Lund University, Malmö.
    Ärnlöv, Johan
    Högskolan Dalarna, Institutionen för hälsa och välfärd, Medicinsk vetenskap.
    Fall, Tove
    Uppsala University, Uppsala, Sweden.
    An online atlas of human plasma metabolite signatures of gut microbiome composition2022Inngår i: Nature Communications, E-ISSN 2041-1723, Vol. 13, nr 1, artikkel-id 5370Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Human gut microbiota produce a variety of molecules, some of which enter the bloodstream and impact health. Conversely, dietary or pharmacological compounds may affect the microbiota before entering the circulation. Characterization of these interactions is an important step towards understanding the effects of the gut microbiota on health. In this cross-sectional study, we used deep metagenomic sequencing and ultra-high-performance liquid chromatography linked to mass spectrometry for a detailed characterization of the gut microbiota and plasma metabolome, respectively, of 8583 participants invited at age 50 to 64 from the population-based Swedish CArdioPulmonary bioImage Study. Here, we find that the gut microbiota explain up to 58% of the variance of individual plasma metabolites and we present 997 associations between alpha diversity and plasma metabolites and 546,819 associations between specific gut metagenomic species and plasma metabolites in an online atlas ( https://gutsyatlas.serve.scilifelab.se/ ). We exemplify the potential of this resource by presenting novel associations between dietary factors and oral medication with the gut microbiome, and microbial species strongly associated with the uremic toxin p-cresol sulfate. This resource can be used as the basis for targeted studies of perturbation of specific metabolites and for identification of candidate plasma biomarkers of gut microbiota composition.

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  • 15. Dekkers, Koen F
    et al.
    Sayols-Baixeras, Sergi
    Baldanzi, Gabriel
    Nowak, Christoph
    Hammar, Ulf
    Nguyen, Diem
    Varotsis, Georgios
    Brunkwall, Louise
    Ärnlöv, Johan
    Högskolan Dalarna, Institutionen för hälsa och välfärd, Medicinsk vetenskap. Karolinska Institutet, Huddinge.
    Fall, Tove
    Author Correction: An online atlas of human plasma metabolite signatures of gut microbiome composition2023Inngår i: Nature Communications, E-ISSN 2041-1723, Vol. 14, nr 1, artikkel-id 2971Artikkel i tidsskrift (Fagfellevurdert)
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  • 16. Edlund, J. A.
    et al.
    Chaumont, N.
    Hintze, Arend
    Keck Graduate Institute of Applied Life Sciences, Claremont, United States; Michigan State University, East Lansing, United States.
    Koch, C.
    Tononi, G.
    Adami, C.
    Integrated information increases with fitness in the evolution of animats2011Inngår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 7, nr 10, artikkel-id e1002236Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    One of the hallmarks of biological organisms is their ability to integrate disparate information sources to optimize their behavior in complex environments. How this capability can be quantified and related to the functional complexity of an organism remains a challenging problem, in particular since organismal functional complexity is not well-defined. We present here several candidate measures that quantify information and integration, and study their dependence on fitness as an artificial agent ("animat") evolves over thousands of generations to solve a navigation task in a simple, simulated environment. We compare the ability of these measures to predict high fitness with more conventional information-theoretic processing measures. As the animat adapts by increasing its "fit" to the world, information integration and processing increase commensurately along the evolutionary line of descent. We suggest that the correlation of fitness with information integration and with processing measures implies that high fitness requires both information processing as well as integration, but that information integration may be a better measure when the task requires memory. A correlation of measures of information integration (but also information processing) and fitness strongly suggests that these measures reflect the functional complexity of the animat, and that such measures can be used to quantify functional complexity even in the absence of fitness data. © 2011 Edlund et al.

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  • 17. Eriksson, Ronnie
    et al.
    Jobs, Magnus
    Högskolan Dalarna, Akademin Utbildning, hälsa och samhälle, Medicinsk vetenskap.
    Ekstrand, Charlotta
    Ullberg, Måns
    Hermann, Björn
    Landegren, Ulf
    Nilsson, Mats
    Blomberg, Jonas
    Multiplex and quantifiable detection of nucleic acid from pathogenic fungi using padlock probes, generic real-time PCR and specific suspension array readout2009Inngår i: Journal of Microbiological Methods, ISSN 0167-7012, E-ISSN 1872-8359, Vol. 78, nr 2, s. 195-202Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A new concept for multiplex detection and quantification of microbes is here demonstrated on a range of infectious fungal species. Padlock probe methodology in conjunction with qPCR and Luminex™ technology was used for simultaneous detection of ten fungal species in one single experiment. By combining the multiplexing properties of padlock probes and Luminex™ detection with the well established quantitative characteristics of qPCR, quantitative microbe detection was done in 10-plex mode. A padlock probe is an oligonucleotide that via a ligation reaction forms circular DNA when hybridizing to specific target DNA. The region of the padlock probe that does not participate in target DNA hybridization contains generic primer sequences for amplification and a tag sequence for Luminex™ detection. This was the fundament for well performing multiplexing. Circularized padlock probes were initially amplified by rolling circle amplification (RCA), followed by a SybrGreen™ real time PCR which allowed an additive quantitative assessment of target DNA in the sample. Detection and quantification of amplified padlock probes were then done on color coded Luminex™ microspheres carrying anti-tag sequences. A novel technique, using labeled oligonucleotides to prevent reannealing of amplimers by covering the flanks of the address sequence, improved the signal to noise ratio in the detection step considerably. The method correctly detected fungi in a variety of clinical samples and offered quantitative information on fungal nucleic acid.

  • 18. Espeland, Marianne
    et al.
    Irestedt, Martin
    Johanson, Kjell Arne
    Akerlund, Monika
    Bergh, Jan-Erik
    Högskolan Dalarna, Akademin Utbildning, hälsa och samhälle, Biologi.
    Kallersjo, Mari
    Dichlorvos exposure impedes extraction and amplification of DNA from insects in museum collections2010Inngår i: Frontiers in Zoology, E-ISSN 1742-9994, Vol. 7, artikkel-id 2Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: The insecticides dichlorvos, paradichlorobenzene and naphthalene have been commonly used to eradicate pest insects from natural history collections. However, it is not known how these chemicals affect the DNA of the specimens in the collections. We thus tested the effect of dichlorvos, paradichlorobenzene and naphthalene on DNA of insects (Musca domestica) by extracting and amplifying DNA from specimens exposed to insecticides in two different concentrations over increasing time intervals. Results: The results clearly show that dichlorvos impedes both extraction and amplification of mitochondrial and nuclear DNA after relatively short time, whereas paradichlorobenzene and naphthalene do not. Conclusion: Collections treated with paradichlorobenzene and naphthalene, are better preserved concerning DNA, than those treated with dichlorvos. Non toxic pest control methods should, however, be preferred due to physical damage of specimens and putative health risks by chemicals.

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  • 19.
    Feuk, Alexander
    Högskolan Dalarna, Institutionen för kultur och samhälle.
    Konsten att höra växter: En studie om växtsonifiering – ur konstnärliga och naturvetenskapliga perspektiv2023Independent thesis Advanced level (degree of Master (One Year)), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Växtsonifiering är processen av att översätta elektrisk aktivitet i växter till ljud och ingår huvudsakligen i två discipliner, ljudkonst och botanik. Syftet med denna studie är att bidra med kunskap om hur växtsonifiering kan användas i både konstnärliga och naturvetenskapliga syften. I studien undersöks konstnärliga möjligheter genom tre musikaliska verk som är skapade via växtsonifiering samt genom analys av konventioner inom modern växtmusik. Naturvetenskapliga användningsområden för växtsonifiering undersöks i studien genom standardiserade experiment på tre olika växter, en monstera [Monstera deliciosa] och två separata rosengeranier [Pelargonium graveolens]. Genom att utsätta växterna för olika typer av beröring samtidigt som de är uppkopplade till en synthesizer via två elektroder undersöks det ifall reaktioner från växterna uppenbarar sig i de data som genereras. Studien visar på att växtsonifiering kan vara ett användbart verktyg till att bland annat skapa ambienta ljudlandskap och musik, men att det även finns fler konstnärliga möjligheter. Det övergripande resultatet av experimenten visar på att växtsonifiering kan vara ett användbart komplement till analys av visuella data, men att det enskilt inte är den bästa metoden för studerandet av växters fysiologi. Studien visar även på hur växtsonifiering kan brukas i syfte att förstå saker om naturen som inte är synligt för blotta ögat

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  • 20. Goldsby, H. J.
    et al.
    Young, R. L.
    Schossau, J.
    Hofmann, H. A.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    Serendipitous scaffolding to improve a genetic algorithm's speed and quality2018Inngår i: GECCO 2018 - Proceedings of the 2018 Genetic and Evolutionary Computation Conference, Association for Computing Machinery, Inc , 2018, s. 959-966Konferansepaper (Fagfellevurdert)
    Abstract [en]

    A central challenge to evolutionary computation is enabling techniques to evolve increasingly complex target end products. Frequently, direct approaches that reward only the target end product itself are not successful because the path between the starting conditions and the target end product traverses through a complex fitness landscape, where the directly accessible intermediary states may be require deleterious or even simply neutral mutations. As such, a host of techniques have sprung up to support evolutionary computation techniques taking these paths. One technique is scaffolding where intermediary targets are used to provide a path from the starting state to the end state. While scaffolding can be successful within well-understood domains it also poses the challenge of identifying useful intermediaries. Within this paper we first identify some shortcomings of scaffolding approaches ' namely, that poorly selected intermediaries may in fact hurt the evolutionary computation's chance of producing the desired target end product. We then describe a light-weight approach to selecting intermediate scaffolding states that improve the efficacy of the evolutionary computation. © 2018 Association for Computing Machinery.

  • 21. Gullstrand, Lennart
    et al.
    Nilsson, Johnny
    Gymnastik- och idrottshögskolan, GIH, Laboratoriet för biomekanik och motorisk kontroll (BMC).
    A new method for recording the temporal pattern of stride during treadmill running2009Inngår i: Sports Engineering, ISSN 1369-7072, E-ISSN 1460-2687, nr 11, s. 195-200Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The aim of this study was to investigate the reliability of a new infrared light based method (IR40) for recording temporal stride patterns during treadmill running. The IR40 device, emitting a tight web of 40 infrared light beams 10 mm above the treadmill running surface, was compared to a previously validated electro-pneumatic contact shoe (CS) method while nine well-trained athletes ran at 2.8, 3.3, 3.9, 4.4, 5.0, and 5.6 m s−1. Disconnection and reconnection of the IR beams marked the stance phase. The sampling rate was 500 Hz for both methods. The stance phase duration was on average 11.5 (±8.4) ms longer with the IR40 than with the CS depending on earlier touch down (8.3 ± 6.2 ms) and delayed toe off (3.2 ± 5.3 ms) registrations. Significantly different stance phases were recorded between all velocities and for both methods. Thus, despite the fact that the IR40 systematically measured a somewhat longer stance phase duration than CS, the IR40 is nonetheless useful for temporal stride analysis during treadmill running.      

  • 22.
    Hellqvist, Claes
    et al.
    Högskolan Dalarna, Akademin Industri och samhälle, Träteknologi.
    Lindström, Anders
    Högskolan Dalarna, Akademin Industri och samhälle, Träteknologi.
    Praktisk plantering av miniplantor - resultat efter två år i fält: Uppdrag Holmen AB2004Rapport (Annet vitenskapelig)
  • 23.
    Hernandez Velasco, Marco
    et al.
    Högskolan Dalarna, Akademin Industri och samhälle, Energiteknik.
    Mattsson, Anders
    Högskolan Dalarna, Akademin Industri och samhälle, Skog- och träteknik.
    Light quality and intensity of light-emitting diodes during pre-cultivation of Picea abies (L.) Karst. and Pinus sylvestris L. seedlings - impact on growth performance, seedling quality and energy consumption2019Inngår i: Scandinavian Journal of Forest Research, ISSN 0282-7581, E-ISSN 1651-1891, Vol. 34, nr 3, s. 159-177Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Three different LED lamps with continuous spectra were compared against commonly used fluorescent lights. The lamps were characterized by light output, energy consumption and spectral quality for plant growth. The biological effects of light quality were compared by pre-cultivating seedlings of Picea abies (L.) Karst. and Pinus sylvestris L. under each spectrum for 35 days in a growth chamber with controlled temperature, humidity and photoperiod. The seedlings were then transplanted and cultivated for one vegetation period at the nursery, then planted outdoors on a forest field trial and followed for three years. The seedlings showed similar growth performance for all spectra tested. LED lamps have several advantages to fluorescent light such as energy consumption, longer life span and adjustable light intensity. Regarding light intensity the effects on growth performance were studied for both species using the most promising LED spectra. The photosynthetically active radiation (PAR) was maintained at 50, 100, 200 and 400 mu mol m(-2) s(-1). Unlike energy consumption, seedling development did not display a linear relationship to light intensity. Instead, the results show an optimum light level between 100 and 200 mu mol m(-2) s(-1) for the shade tolerant Picea abies seedlings and a level of around 200 mu mol m(-2) s(-1) for the more shade intolerant Pinus sylvestris seedlings.

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  • 24.
    Hintze, Arend
    et al.
    Keck Graduate Institute of Applied Life Sciences, Claremont, United States.
    Adami, C.
    Darwinian evolution of cooperation via punishment in the "public goods" game2010Inngår i: Artificial Life XII: Proceedings of the 12th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2010, 2010, s. 445-450Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The evolution of cooperation has been a perennial problem for evolutionary biology because cooperation is undermined by selfish cheaters (or "free riders") that profit from cooper-ators but do not invest any resources themselves. In a purely "selfish" view of evolution, those cheaters should be favored. Evolutionary game theory has been able to show that under certain conditions, cooperation nonetheless evolves stably. One of these scenarios utilizes the power of punishment to suppress free riders, but only if players interact in a structured population where cooperators are likely to be surrounded by other cooperators. Here we show that cooperation via punishment can evolve even in well-mixed populations that play the "public goods" game, if the synergy effect of cooperation is high enough. As the synergy is increased, populations transition from defection to cooperation in a manner reminiscent of a phase transition. If punishment is turned off the critical synergy is significantly higher, illustrating that indeed punishment aids in establishing cooperation. We also show that the critical point depends on the mutation rate so that higher mutation rates actually promote cooperation, by ensuring that punishment never disappears.

  • 25.
    Hintze, Arend
    et al.
    Keck Graduate Institute of Applied Life Sciences, Claremont, United States.
    Adami, C.
    Evolution of complex modular biological networks2008Inngår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 4, nr 2Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their modularity of function, with modules defined as sets of genes that are strongly interconnected but whose function is separable from those of other modules. Here, we investigate the in silico evolution of modularity and robustness in complex artificial metabolic networks that encode an increasing amount of information about their environment while acquiring ubiquitous features of biological, social, and engineering networks, such as scale-free edge distribution, small-world property, and fault-tolerance. These networks evolve in environments that differ in their predictability, and allow us to study modularity from topological, information-theoretic, and gene-epistatic points of view using new tools that do not depend on any preconceived notion of modularity. We find that for our evolved complex networks as well as for the yeast protein-protein interaction network, synthetic lethal gene pairs consist mostly of redundant genes that lie close to each other and therefore within modules, while knockdown suppressor gene pairs are farther apart and often straddle modules, suggesting that knockdown rescue is mediated by alternative pathways or modules. The combination of network modularity tools together with genetic interaction data constitutes a powerful approach to study and dissect the role of modularity in the evolution and function of biological networks. © 2008 Hintze and Adami.

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  • 26.
    Hintze, Arend
    et al.
    Keck Graduate Institute of Applied Life Sciences, Claremont, United States.
    Adami, C.
    Modularity and anti-modularity in networks with arbitrary degree distribution2010Inngår i: Biology Direct, E-ISSN 1745-6150, Vol. 5, artikkel-id 32Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Much work in systems biology, but also in the analysis of social network and communication and transport infrastructure, involves an in-depth analysis of local and global properties of those networks, and how these properties relate to the function of the network within the integrated system. Most often, systematic controls for such networks are difficult to obtain, because the features of the network under study are thought to be germane to that function. In most such cases, a surrogate network that carries any or all of the features under consideration, while created artificially and in the absence of any selective pressure relating to the function of the network being studied, would be of considerable interest.Results: Here, we present an algorithmic model for growing networks with a broad range of biologically and technologically relevant degree distributions using only a small set of parameters. Specifying network connectivity via an assortativity matrix allows us to grow networks with arbitrary degree distributions and arbitrary modularity. We show that the degree distribution is controlled mainly by the ratio of node to edge addition probabilities, and the probability for node duplication. We compare topological and functional modularity measures, study their dependence on the number and strength of modules, and introduce the concept of anti-modularity: a property of networks in which nodes from one functional group preferentially do not attach to other nodes of that group. We also investigate global properties of networks as a function of the network's growth parameters, such as smallest path length, correlation coefficient, small-world-ness, and the nature of the percolation phase transition. We search the space of networks for those that are most like some well-known biological examples, and analyze the biological significance of the parameters that gave rise to them.Conclusions: Growing networks with specified characters (degree distribution and modularity) provides the opportunity to create surrogates for biological and technological networks, and to test hypotheses about the processes that gave rise to them. We find that many celebrated network properties may be a consequence of the way in which these networks grew, rather than a necessary consequence of how they work or function.Reviewers: This article was reviewed by Erik van Nimwegen, Teresa Przytycka (nominated by Claus Wilke), and Leonid Mirny. For the full reviews, please go to the Reviewer's Comments section. © 2010 Hintze and Adami; licensee BioMed Central Ltd.

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  • 27.
    Hintze, Arend
    et al.
    Michigan State University, East Lansing, United States.
    Adami, C.
    Punishment in public goods games leads to meta-stable phase transitions and hysteresis2015Inngår i: Physical Biology, ISSN 1478-3967, E-ISSN 1478-3975, Vol. 12, nr 4, artikkel-id 046005Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The evolution of cooperation has been a perennial problem in evolutionary biology because cooperation can be undermined by selfish cheaters who gain an advantage in the short run, while compromising the long-term viability of the population. Evolutionary game theory has shown that under certain conditions, cooperation nonetheless evolves stably, for example if players have the opportunity to punish cheaters that benefit from a public good yet refuse to pay into the common pool. However, punishment has remained enigmatic because it is costly and difficult to maintain. On the other hand, cooperation emerges naturally in the public goods game if the synergy of the public good (the factor multiplying the public good investment) is sufficiently high. In terms of this synergy parameter, the transition from defection to cooperation can be viewed as a phase transition with the synergy as the critical parameter. We show here that punishment reduces the critical value at which cooperation occurs, but also creates the possibility of meta-stable phase transitions, where populations can 'tunnel' into the cooperating phase below the critical value. At the same time, cooperating populations are unstable even above the critical value, because a group of defectors that are large enough can 'nucleate' such a transition. We study the mean-field theoretical predictions via agent-based simulations of finite populations using an evolutionary approach where the decisions to cooperate or to punish are encoded genetically in terms of evolvable probabilities. We recover the theoretical predictions and demonstrate that the population shows hysteresis, as expected in systems that exhibit super-heating and super-cooling. We conclude that punishment can stabilize populations of cooperators below the critical point, but it is a two-edged sword: it can also stabilize defectors above the critical point. © 2015 IOP Publishing Ltd.

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  • 28.
    Hintze, Arend
    et al.
    Michigan State University, East Lansing, United States.
    Hertwig, R.
    The evolution of generosity in the ultimatum game2016Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 6, artikkel-id 34102Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    When humans fail to make optimal decisions in strategic games and economic gambles, researchers typically try to explain why that behaviour is biased. To this end, they search for mechanisms that cause human behaviour to deviate from what seems to be the rational optimum. But perhaps human behaviour is not biased; perhaps research assumptions about the optimality of strategies are incomplete. In the one-shot anonymous symmetric ultimatum game (UG), humans fail to play optimally as defined by the Nash equilibrium. However, the distinction between kin and non-kin - with kin detection being a key evolutionary adaption - is often neglected when deriving the "optimal" strategy. We computationally evolved strategies in the UG that were equipped with an evolvable probability to discern kin from non-kin. When an opponent was not kin, agents evolved strategies that were similar to those used by humans. We therefore conclude that the strategy humans play is not irrational. The deviation between behaviour and the Nash equilibrium may rather be attributable to key evolutionary adaptations, such as kin detection. Our findings further suggest that social preference models are likely to capture mechanisms that permit people to play optimally in an evolutionary context. Once this context is taken into account, human behaviour no longer appears irrational © The Author(s) 2016.

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  • 29.
    Hintze, Arend
    et al.
    Michigan State University, East Lansing, United States.
    Mirmomeni, M.
    Evolution of autonomous hierarchy formation and maintenance2014Inngår i: Artificial Life 14 - Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2014, MIT Press Journals , 2014, s. 366-367Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Hierarchy among social animals is ubiquitous, and affects the social structures of gregarious species not only by interaction among species within the population, but also through other social forces such as mating, nesting location, amount and the quality of food they receive, or reproductive success. Since T. Schjelderup-Ebbe developed the structural definition of dominance and hierarchy in 1922 (see, e.g., Drews (1993)), different aspects of this social behavior have been addressed. However, exactly how hierarchies can emerge and be maintained among social species is still a conundrum. To investigate this issue, here we analyze a population of autonomous agents ('animates') through the course of evolution. The results of our experiments demonstrate the importance of memory and brain plasticity for the emergence of hierarchy and dominance behavior. © Artificial Life 14 - Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2014. All rights reserved.

  • 30.
    Hintze, Arend
    et al.
    Michigan State University, East Lansing, United States.
    Olson, R. S.
    Adami, C.
    Hertwig, R.
    Risk sensitivity as an evolutionary adaptation2015Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 5, artikkel-id 8242Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Risk aversion is a common behavior universal to humans and animals alike. Economists have traditionally defined risk preferences by the curvature of the utility function. Psychologists and behavioral economists also make use of concepts such as loss aversion and probability weighting to model risk aversion. Neurophysiological evidence suggests that loss aversion has its origins in relatively ancient neural circuitries (e.g., ventral striatum). Could there thus be an evolutionary origin to risk aversion? We study this question by evolving strategies that adapt to play the equivalent mean payoff gamble. We hypothesize that risk aversion in this gamble is beneficial as an adaptation to living in small groups, and find that a preference for risk averse strategies only evolves in small populations of less than 1,000 individuals, or in populations segmented into groups of 150 individuals or fewer - numbers thought to be comparable to what humans encountered in the past. We observe that risk aversion only evolves when the gamble is a rare event that has a large impact on the individual's fitness. As such, we suggest that rare, high-risk, high-payoff events such as mating and mate competition could have driven the evolution of risk averse behavior in humans living in small groups.

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  • 31.
    Hintze, Arend
    et al.
    Michigan State University, East Lansing, United States.
    Olson, R. S.
    Lehman, J.
    Orthogonally evolved AI to improve difficulty adjustment in video games2016Inngår i: Applications of Evolutionary Computation. EvoApplications 2016. Lecture Notes in Computer Science, vol 9597 / [ed] Squillero G., Burelli P., Springer Verlag , 2016, Vol. 9597, s. 525-540Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Computer games are most engaging when their difficulty is well matched to the player’s ability, thereby providing an experience in which the player is neither overwhelmed nor bored. In games where the player interacts with computer-controlled opponents, the difficulty of the game can be adjusted not only by changing the distribution of opponents or game resources, but also through modifying the skill of the opponents. Applying evolutionary algorithms to evolve the artificial intelligence that controls opponent agents is one established method for adjusting opponent difficulty. Less-evolved agents (i.e., agents subject to fewer generations of evolution) make for easier opponents, while highlyevolved agents are more challenging to overcome. In this publication we test a new approach for difficulty adjustment in games: orthogonally evolved AI, where the player receives support from collaborating agents that are co-evolved with opponent agents (where collaborators and opponents have orthogonal incentives). The advantage is that game difficulty can be adjusted more granularly by manipulating two independent axes: by having more or less adept collaborators, and by having more or less adept opponents. Furthermore, human interaction can modulate (and be informed by) the performance and behavior of collaborating agents. In this way, orthogonally evolved AI both facilitates smoother difficulty adjustment and enables new game experiences. © Springer International Publishing Switzerland 2016.

  • 32.
    Hintze, Arend
    et al.
    Michigan State University, East Lansing, United States.
    Phillips, N.
    Hertwig, R.
    The Janus face of Darwinian competition2015Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 5, artikkel-id 13662Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Without competition, organisms would not evolve any meaningful physical or cognitive abilities. Competition can thus be understood as the driving force behind Darwinian evolution. But does this imply that more competitive environments necessarily evolve organisms with more sophisticated cognitive abilities than do less competitive environments? Or is there a tipping point at which competition does more harm than good? We examine the evolution of decision strategies among virtual agents performing a repetitive sampling task in three distinct environments. The environments differ in the degree to which the actions of a competitor can affect the fitness of the sampling agent, and in the variance of the sample. Under weak competition, agents evolve decision strategies that sample often and make accurate decisions, which not only improve their own fitness, but are good for the entire population. Under extreme competition, however, the dark side of the Janus face of Darwinian competition emerges: Agents are forced to sacrifice accuracy for speed and are prevented from sampling as often as higher variance in the environment would require. Modest competition is therefore a good driver for the evolution of cognitive abilities and of the population as a whole, whereas too much competition is devastating.

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  • 33. Husby, Arild
    et al.
    Kawakami, Takeshi
    Rönnegård, Lars
    Högskolan Dalarna, Akademin Industri och samhälle, Statistik. SLU.
    Smeds, Linnéa
    Ellegren, Hans
    Qvarnström, Anna
    Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait2015Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, nr 1806Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.

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  • 34. Iliopoulos, D.
    et al.
    Hintze, Arend
    Keck Graduate Institute of Applied Life Sciences, Claremont, United States.
    Adami, C.
    Critical dynamics in the evolution of stochastic strategies for the iterated Prisoner's Dilemma2010Inngår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 6, nr 10, artikkel-id 1000948Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The observed cooperation on the level of genes, cells, tissues, and individuals has been the object of intense study by evolutionary biologists, mainly because cooperation often flourishes in biological systems in apparent contradiction to the selfish goal of survival inherent in Darwinian evolution. In order to resolve this paradox, evolutionary game theory has focused on the Prisoner's Dilemma (PD), which incorporates the essence of this conflict. Here, we encode strategies for the iterated Prisoner's Dilemma (IPD) in terms of conditional probabilities that represent the response of decision pathways given previous plays. We find that if these stochastic strategies are encoded as genes that undergo Darwinian evolution, the environmental conditions that the strategies are adapting to determine the fixed point of the evolutionary trajectory, which could be either cooperation or defection. A transition between cooperative and defective attractors occurs as a function of different parameters such as mutation rate, replacement rate, and memory, all of which affect a player's ability to predict an opponent's behavior. These results imply that in populations of players that can use previous decisions to plan future ones, cooperation depends critically on whether the players can rely on facing the same strategies that they have adapted to. Defection, on the other hand, is the optimal adaptive response in environments that change so quickly that the information gathered from previous plays cannot usefully be integrated for a response. © 2010 Iliopoulos et al.

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  • 35. Incorvaia, Darren C.
    et al.
    Hintze, Arend
    Högskolan Dalarna, Institutionen för information och teknik, Mikrodataanalys. Michigan State Univ.
    Dyer, Fred C.
    Spatial allocation without spatial recruitment in bumblebees2021Inngår i: Behavioral Ecology, ISSN 1045-2249, E-ISSN 1465-7279, Vol. 32, nr 2, s. 265-276Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Any foraging animal is expected to allocate its efforts among resource patches that vary in quality across time and space. For social insects, this problem is shifted to the colony level: the task of allocating foraging workers to the best patches currently available. To deal with this task, honeybees rely upon differential recruitment via the dance language, while some ants use differential recruitment on odor trails. Bumblebees, close relatives of honeybees, should also benefit from optimizing spatial allocation but lack any targeted recruitment system. How bumblebees solve this problem is thus of immense interest to evolutionary biologists studying collective behavior. It has been thought that bumblebees could solve the spatial allocation problem by relying on the summed individual decisions of foragers, who occasionally sample and shift to alternative resources. We use field experiments to test the hypothesis that bumblebees augment individual exploration with social information. Specifically, we provide behavioral evidence that, when higher-concentration sucrose arrives at the nest, employed foragers abandon their patches to begin searching for the better option; they are more likely to accept novel resources if they match the quality of the sucrose solution experienced in the nest. We explored this strategy further by building an agent-based model of bumblebee foraging. This model supports the hypothesis that using social information to inform search decisions is advantageous over individual search alone. Our results show that bumblebees use a collective foraging strategy built on social modulation of individual decisions, providing further insight into the evolution of collective behavior.

  • 36. Jack, C. N.
    et al.
    Friesen, M. L.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    Sheneman, L.
    Third-party mutualists have contrasting effects on host invasion under the enemy-release and biotic-resistance hypotheses2017Inngår i: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 31, nr 6, s. 829-845Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plants engage in complex multipartite interactions with mutualists and antagonists, but these interactions are rarely included in studies that explore plant invasiveness. When considered in isolation, we know that beneficial microbes can enhance an exotic plant’s invasive ability and that herbivorous insects often decrease an exotic plant’s likeliness of success. However, the effect of these partners on plant fitness has not been well characterized when all three species coevolve. We use computational evolutionary modeling of a trait-based system to test how microbes and herbivores simultaneously coevolving with an invading plant affect the invaders’ probability of becoming established. Specifically, we designed a model that explores how a beneficial microbe would influence the outcome of an interaction between a plant and herbivore. To model novel interactions, we included a phenotypic trait shared by each species. Making this trait continuous and selectable allows us to explore how trait similarities between coevolving plants, herbivores and microbes affect fitness. Using this model, we answer the following questions: (1) Can a beneficial plant-microbe interaction influence the evolutionary outcome of antagonistic interactions between plants and herbivores? (2) How does the initial trait similarity between interacting organisms affect the likelihood of plant survival in novel locations? (3) Does the effect of tripartite interactions on the invasion success of a plant depend on whether organisms interact through trait similarity [Enemy Release Hypothesis (ERH)] or dissimilarity (Biotic Resistance Hypothesis)? We found that it was much more difficult for plants to invade under the ERH but that beneficial microbes increase the probability of plant survival in a novel range under both hypotheses. To our knowledge, this model is the first to use tripartite interactions to explore novel species introductions. It represents a step towards gaining a better understanding of the factors influencing establishment of exotic species to prevent future invasions. © 2017, The Author(s).

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  • 37. Jahns, J.
    et al.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    How the integration of group and individual level selection affects the evolution of cooperation2020Inngår i: ALIFE 2018 - 2018 Conference on Artificial Life: Beyond AI, MIT Press , 2020, s. 530-535Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Many evolutionary models that explore the emergence of cooperation rely on either individual level selection or group level selection. However, natural systems are often more complex and selection is never just on the level of the individual or group alone. Here we explore how systems of collaborating agents evolve when selection is based on a mixture of group and individual performances. It has been suggested that under such situations free riders thrive and hamper evolution significantly. Here we show that free rider effects can almost be ignored. Sharing resources even with free riders benefits the evolution of cooperators, which in the long run is more beneficial than the short term cost. Copyright © ALIFE 2018.All rights reserved.

  • 38.
    Johansson, Sverker
    Högskolan för lärande och kommunikation, Högskolan i Jönköping, HLK, Ämnesforskning.
    Origins of language: Constraints on hypotheses2005Bok (Annet vitenskapelig)
    Abstract [en]

    Sverker Johansson has written an unusual book on language origins, with its emphasis on empirical evidence rather than theory-building. This is a book for the student or researcher who prefers solid data and well-supported conclusions, over speculative scenarios. Much that has been written on the origins of language is characterized by hypothesizing largely unconstrained by evidence. But empirical data do exist, and the purpose of this book is to integrate and review the available evidence from all relevant disciplines, not only linguistics but also, e.g., neurology, primatology, paleoanthropology, and evolutionary biology. The evidence is then used to constrain the multitude of scenarios for language origins, demonstrating that many popular hypotheses are untenable. Among the issues covered: (1) Human evolutionary history, (2) Anatomical prerequisites for language, (3) Animal communication and ape "language", (4) Mind and language, (5) The role of gesture, (6) Innateness, (7) Selective advantage of language, (8) Proto-language.

  • 39.
    Johansson, Sverker
    Högskolan för lärande och kommunikation, Högskolan i Jönköping, HLK, Ämnesforskning.
    Sagan om hur livet kom till Jorden1996Annet (Annet (populærvitenskap, debatt, mm))
  • 40.
    Johansson, Sverker
    Högskolan för lärande och kommunikation, Högskolan i Jönköping, HLK, Ämnesforskning.
    The Monkey Trail: On the Fossil Record of Non-Human Primates1999Rapport (Annet (populærvitenskap, debatt, mm))
  • 41.
    Johansson, Sverker
    Högskolan i Jönköping, Högskolan för lärande och kommunikation.
    What constraints does animal communication place on human language origins?2010Konferansepaper (Annet vitenskapelig)
  • 42.
    Johansson, Sverker
    Högskolan för lärande och kommunikation, Högskolan i Jönköping, HLK, Ämnesforskning.
    Är kreationismen vetenskapligt hållbar?1992Inngår i: Svensk Teologisk Kvartalsskrift, nr 68, s. 19-28Artikkel i tidsskrift (Fagfellevurdert)
  • 43. Kirkpatrick, D.
    et al.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    The role of ambient noise in the evolution of robust mental representations in cognitive systems2020Inngår i: Proceedings of the 2019 Conference on Artificial Life: How Can Artificial Life Help Solve Societal Challenges, ALIFE 2019, MIT Press , 2020, s. 432-439Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Natural environments are full of ambient noise; nevertheless, natural cognitive systems deal greatly with uncertainty but also have ways to suppress or ignore noise unrelated to the task at hand. For most intelligent tasks, experiences and observations have to be committed to memory and these representations of reality inform future decisions. We know that deep learned artificial neural networks (ANNs) often struggle with the formation of representations. This struggle may be due to the ANN's fully interconnected, layered architecture. This forces information to be propagated over the entire system, which is different from natural brains that instead have sparsely distributed representations. Here we show how ambient noise causes neural substrates such as recurrent ANNs and long short-term memory neural networks to evolve more representations in order to function in these noisy environments, which also greatly improves their functionality. However, these systems also tend to further smear their representations over their internal states making them more vulnerable to internal noise. We also show that Markov Brains (MBs) are mostly unaffected by ambient noise, and their representations remain sparsely distributed (i.e. not smeared). This suggests that ambient noise helps to increase the amount of representations formed in neural networks, but also requires us to find additional solutions to prevent smearing of said representations. Copyright © ALIFE 2019.All rights reserved.

  • 44. Labar, T.
    et al.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    Adami, C.
    Evolvability tradeoffs in emergent digital replicators2016Inngår i: Artificial Life, ISSN 1064-5462, E-ISSN 1530-9185, Vol. 22, nr 4, s. 483-498Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The role of historical contingency in the origin of life is one of the great unknowns in modern science. Only one example of life exists - one that proceeded from a single self-replicating organism (or a set of replicating hypercycles) to the vast complexity we see today in Earth's biosphere. We know that emergent life has the potential to evolve great increases in complexity, but it is unknown if evolvability is automatic given any self-replicating organism. At the same time, it is difficult to test such questions in biochemical systems. Laboratory studies with RNA replicators have had some success with exploring the capacities of simple self-replicators, but these experiments are still limited in both capabilities and scope. Here, we use the digital evolution system Avida to explore the interplay between emergent replicators (rare randomly assembled self-replicators) and evolvability. We find that we can classify fixed-length emergent replicators in Avida into two classes based on functional analysis. One class is more evolvable in the sense of optimizing the replicators' replication abilities. However, the other class is more evolvable in the sense of acquiring evolutionary innovations. We tie this tradeoff in evolvability to the structure of the respective classes' replication machinery, and speculate on the relevance of these results to biochemical replicators. © 2016 Massachusetts Institute of Technology.

  • 45. Lankinen, Å.
    et al.
    Maad, Johanne
    orwegian Univ Sci & Technol, Dept Biol, N-7491 Trondheim, Norway; Uppsala Univ, Dept Ecol Evolut & Plant Ecol, S-75236 Uppsala, Sweden.
    Armbruster, W. S.
    Pollen-tube growth rates in Collinsia heterophylla (Plantaginaceae): One-donor crosses reveal heritability but no effect on sporophytic-offspring fitness.2009Inngår i: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 103, nr 6, s. 941-950Artikkel i tidsskrift (Fagfellevurdert)
  • 46.
    Lee, Youngjo
    et al.
    Department of Statistics, Seoul National University, Seoul, Republic of Korea.
    Alam, Moudud
    Högskolan Dalarna, Akademin Industri och samhälle, Statistik.
    Sandström, Per
    Department of Forest Resource Management, Swedish University of Agricultural Sciences, Umeå.
    Skarin, Anna
    Department of Animal Nutrition and Management, Swedish University of Agricultural Science, Uppsala.
    Estimating zones of influence using threshold regression2020Rapport (Annet vitenskapelig)
    Abstract [en]

    In environmental impact assessments, it is important to be able to estimate influence of anthropogenic activities on animal populations. To quantify the influence, it is common to estimate how far, in distance, from a given disturbance source there is an influence on the animals’ habitat selection through estimating a zone of influence (ZOI). Usually, ZOI is estimated for one disturbance source at a time. In this work, we demonstrate how threshold regression modelling can be used for estimating ZOI from several possible sources of disturbances, simultaneously. Based on the theoretical properties of different estimation methods for the estimation of threshold regression we select a set of estimation methods and compare their merits through a simulation study and a real data example. The simulation results revealed that Adaptive Lasso, and Hierarchical likelihood (HL) methods, are two reasonable methods for dealing with the problem. HL performed better than Adaptive Lasso in that it had much higher success rate in identifying correct threshold with small sample size whereas Adaptive Lasso requires large sample to assure good performance. While Adaptive lasso needed to be aided with suitable weights, which are not easy to find, HL method did not require any prior weights. These two methods were applied to estimate the ZOI around 40 wind turbines and surrounding public roads on reindeer habitat selection in winter, by using GPS positioning data from 42 reindeer in north of Sweden in December to March (2012-2015). The results showed that both the disturbance sources have a negative effect on reindeer habitat selection in winter. The HL approach showed that the negative ZOI from the nearest wind turbine was 1.8 km (approx.), however the trend of higher selection of areas further away from the wind turbines was evident up to 4 km (approx.) from the active wind turbines.

    Fulltekst (pdf)
    fulltext
  • 47.
    Lindström, Anders
    et al.
    Högskolan Dalarna, Akademin Industri och samhälle, Träteknologi.
    Hellqvist, Claes
    Högskolan Dalarna, Akademin Industri och samhälle, Träteknologi.
    Praktisk plantering av miniplantor - resultat efter tre år i fält: Uppdrag Holmen AB2005Rapport (Annet vitenskapelig)
  • 48.
    Lindström, Anders
    et al.
    Högskolan Dalarna, Akademin Industri och samhälle, Träteknologi.
    Stattin, Eva
    Högskolan Dalarna, Akademin Industri och samhälle, Träteknologi.
    Praktisk plantering av miniplantor på Sveaskogs mark2005Rapport (Annet vitenskapelig)
  • 49.
    Maad, Johanne
    Norwegian Univ Sci & Technol, Dept Biol, NO-7491 Trondheim, Norway; Uppsala Univ, EBC, Dept Plant Ecol, SE-75236 Uppsala, Sweden.
    Fenster, C. B.
    Floral size variation in Campanula rotundifolia (Campanulaceae) along altitudinal gradients: patterns and possible selective mechanisms2013Inngår i: Nordic Journal of Botany, ISSN 0107-055X, E-ISSN 1756-1051, Vol. 31, nr 3, s. 361-371Artikkel i tidsskrift (Fagfellevurdert)
  • 50.
    Maad, Johanne
    Norwegian Univ Sci & Technol, Dept Biol, NO-7491 Trondheim, Norway.
    Incidence of geitonogamy differs between two populations in the hawkmoth-pollinated Platanthera bifolia (Orchidaceae)2004Inngår i: Canadian Journal of Botany, ISSN 0008-4026, E-ISSN 1480-3305, Vol. 82, nr 11, s. 1586-1593Artikkel i tidsskrift (Fagfellevurdert)
12 1 - 50 of 99
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