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  • 1.
    Bartoszek, Krzysztof
    Department of Mathematics, Uppsala University, Uppsala, Sweden.
    Phylogenetic effective sample size2016Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 407, s. 371-386Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this paper I address the question—how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes-the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations.

  • 2.
    Bartoszek, Krzysztof
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Statistik och maskininlärning. Linköpings universitet, Filosofiska fakulteten. Uppsala University, Sweden.
    Glemin, Sylvain
    Uppsala University, Sweden; CNRS University of Montpellier IRD EPHE, France.
    Kaj, Ingemar
    Uppsala University, Sweden.
    Lascoux, Martin
    Uppsala University, Sweden.
    Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations2017Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 429, s. 35-45Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Ornstein-Uhlenbeck (OU) process plays a major role in the analysis of the evolution of phenotypic traits along phylogenies. The standard OU process includes random perturbations and stabilizing selection and assumes that species evolve independently. However, evolving species may interact through various ecological process and also exchange genes especially in plants. This is particularly true if we want to study phenotypic evolution among diverging populations within species. In this work we present a straightforward statistical approach with analytical solutions that allows for the inclusion of adaptation and migration in a common phylogenetic framework, which can also be useful for studying local adaptation among populations within the same species. We furthermore present a detailed simulation study that clearly indicates the adverse effects of ignoring migration. Similarity between species due to migration could be misinterpreted as very strong convergent evolution without proper correction for these additional dependencies. Finally, we show that our model can be interpreted in terms of ecological interactions between species, providing a general framework for the evolution of traits between "interacting" species or populations.(C) 2017 Elsevier Ltd. All rights reserved.

  • 3.
    Bartoszek, Krzysztof
    et al.
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Jones, Graham
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden / Department of Biological and Environmental Science, University of Gothenburg, Gothenburg, Sweden.
    Oxelman, Bengt
    Department of Biological and Environmental Science, University of Gothenburg, Gothenburg, Sweden.
    Sagitov, Serik
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Time to a single hybridization event in a group of species with unknown ancestral history2013Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 322, s. 1-6Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We consider a stochastic process for the generation of species which combines a Yule process with a simple model for hybridization between pairs of co-existent species. We assume that the origin of the process, when there was one species, occurred at an unknown time in the past, and we condition the process on producing n species via the Yule process and a single hybridization event. We prove results about the distribution of the time of the hybridization event. In particular we calculate a formula for all moments, and show that under various conditions, the distribution tends to an exponential with rate twice that of the birth rate for the Yule process.

  • 4.
    Bartoszek, Krzysztof
    et al.
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Pienaar, Jason
    Department of Genetics, University of Pretoria, Pretoria 0002, South Africa.
    Mostad, Petter
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Andersson, Staffan
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Hansen, Thomas F.
    CEES, Department of Biology, University of Oslo, Oslo, Norway.
    A phylogenetic comparative method for studying multivariate adaptation2012Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 314, s. 204-215Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phylogenetic comparative methods have been limited in the way they model adaptation. Although some progress has been made, there are still no methods that can fully account for coadaptationbetween traits. Based on Ornstein-Uhlenbeck (OU) models of adaptive evolution, we present a method,with R implementation, in which multiple traits evolve both in response to each other and, as inprevious OU models, to fixed or randomly evolving predictor variables. We present the interpretation ofthe model parameters in terms of evolutionary and optimal regressions enabling the study of allometric and adaptive relationships between traits. To illustrate the method we reanalyze a data set of antlerand body-size evolution in deer (Cervidae).

  • 5.
    Bartoszek, Krzysztof
    et al.
    Uppsala universitet, Tillämpad matematik och statistik.
    Sagitov, Serik
    A consistent estimator of the evolutionary rate2015Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 371, s. 69-78Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate 2, conditioned on the observed number of particles to be equal to n. Particles are assumed to move independently on the real line according to the Brownian motion with the local variance sigma(2). In this paper we treat n particles as a sample of related species. The spatial Brownian motion of a particle describes the development of a trait value of interest (e.g. log-body-size). We propose an unbiased estimator 4 of the evolutionary rate rho(2) - sigma(2)/lambda. The estimator R-n(2) is proportional to the sample variance S-n(2) computed from n trait values. We find an approximate formula for the standard error of R-n(2), based on a neat asymptotic relation for the variance of S-n(2). (C) 2015 Elsevier Ltd. All rights reserved.

  • 6.
    Christianou, Maria
    et al.
    University of the Aegean.
    Kokkoris, Giorgos D.
    University of the Aegean.
    Complexity does not affect stability in feasible model communities2008Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 253, nr 1, s. 162-169Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The complexity–stability relation is a central issue in ecology. In this paper, we show how the sampling method most often used to parameterize an ecological community, can affect the conclusions about whether or not complexity promotes stability and we suggest a sampling algorithm that overcomes the problem. We also illustrate the importance of treating feasibility separately from stability when constructing model communities. Using model Lotka–Volterra competition communities we found that probability of feasibility decreases with increasing interaction strength and number of species in the community. However, for feasible systems we found that local stability probability and resilience do not significantly differ between communities with few or many species, in contrast with earlier studies that, did not account for feasibility and concluded that species-poor communities had higher probability of being locally stable than species-rich communities.

  • 7.
    Granlund, Gösta H.
    Linköpings universitet, Institutionen för systemteknik, Bildbehandling. Linköpings universitet, Tekniska högskolan.
    The Use of Distribution Functions to Describe Integrated Density Profiles of Human Chromosomes1973Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 40, nr 3, s. 573-589Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The advent of new stains for chromosomes has increased the possibilities that useful automated chromosome analysis can be implemented. The search for appropriate descriptors to use in this process is an important task. Data compression using integrated intensity and density profiles has already shown itself to be valuable. A method is proposed in this paper to describe these profiles as a sum of distribution functions. Every distribution function can be described by a triplet stating peak height, position, and width and it appears that these parameters are directly related to physical processes. The importance of such parameters in statistical chromosome analysis is emphasized. A classification experiment is described in which 240 chromosomes 1 to 22, X and Y have been classified with an accuracy of 96%.

  • 8.
    Hauzy, Céline
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi. Linköpings universitet, Tekniska högskolan.
    Gauduchon, Mathias
    Laboratoire Université Pierre et Marie Curie, France.
    D Hulot, Florence
    Laboratoire Bioemco, Ecole Normale Supérieure, France.
    Loreau, Michel
    Department of Biology, McGill University, Canada.
    Density-dependent dispersal and relative dispersal affect the stability of predator-prey metacommunities2010Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 266, nr 3, s. 458-469Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Although density-dependent dispersal and relative dispersal (the difference in dispersal rates between species) have been documented in natural systems, their effects on the stability of metacommunities are poorly understood. Here we investigate the effects of intra- and interspecific density-dependent dispersal on the regional stability in a predator-prey metacommunity model. We show that, when the dynamics of the populations reach equilibrium, the stability of the metacommunity is not affected by density-dependent dispersal. However, the regional stability, measured as the regional variability or the persistence, can be modified by density-dependent dispersal when local populations fluctuate over time. Moreover these effects depend on the relative dispersal of the predator and the prey. Regional stability is modified through changes in spatial synchrony. Interspecific density-dependent dispersal always desynchronizses local dynamics, whereas intraspecific density-dependent dispersal may either synchronize or desynchronize it depending on dispersal rates. Moreover, intra- and interspecific density-dependent dispersal strengthen the top-down control of the prey by the predator at intermediate dispersal rates. As a consequence the regional stability of the metacommunity is increased at intermediate dispersal rates. Our results show that density-dependent dispersal and relative dispersal of species are keys to understanding the response of ecosystems to fragmentation.

  • 9.
    Jansson, Fredrik
    Linköpings universitet, Institutet för analytisk sociologi, IAS. Linköpings universitet, Filosofiska fakulteten. Centrum för evolutionär kulturforskning, Stockholms universitet; Centre for the Study of Cultural Evolution, Stockholm University.
    What Games Support the Evolution of an Ingroup Bias?2015Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 373, s. 100-110Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    There is an increasing wealth of models trying to explain the evolution of group discrimination and an ingroup bias. This paper sets out to systematically investigate the most fundamental assumption in these models: in what kind of situations do the interactions take place? What strategic structures – games – support the evolution of an ingroup bias? More specifically, the aim here is to find the prerequisites for when a bias also with respect to minimal groups – arbitrarily defined groups void of group-specific qualities – is selected for, and which cannot be ascribed to kin selection.

    Through analyses and simulations of minimal models of two-person games, this paper indicates that only some games are conducive to the evolution of ingroup favouritism. In particular, this class does not contain the prisoners' dilemma, but it does contain anti-co-ordination and co-ordination games. Contrasting to the prisoners' dilemma, these are games where it is not a matter of whether to behave altruistically, but rather one of predicting what the other person will be doing, and where I would benefit from you knowing my intentions.

    In anti-co-ordination games, on average, not only will agents discriminate between groups, but also in such a way that their choices maximise the sum of the available payoffs towards the ingroup more often than towards the outgroup. And in co-ordination games, even if agents do manage to co-ordinate with the whole population, they are more likely to co-ordinate on the socially optimal equilibrium within their group. Simulations show that this occurs most often in games where there is a component of risk-taking, and thus trust, involved. A typical such game is the stag hunt or assurance game.

  • 10.
    Jonsson, A.
    et al.
    Rockefeller University, 20, 1230 York Avenue, New York, NY 10021, United States.
    Ebenman, Bo
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk Biologi.
    Are certain life histories particularly prone to local extinction?2001Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 209, nr 4, s. 455-463Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Using stochastic simulations and elasticity analysis, we show that there are inherent differences in the risk of extinction between life histories with different demographies. Which life history is the most vulnerable depends on which vital rate varies. When juvenile survival varies semelparous organisms with delayed reproduction are the most vulnerable ones, while a varying developmental rate puts a greater threat to semelparous organisms with rapid development. Iteroparous organisms are the most vulnerable ones when adult survival varies. Generally, we do not expect to observe organisms in nature having variation in vital rates that produce a high risk of extinction. Given the results here we therefore predict that iteroparous organisms should show low variation in adult survival. Moreover, we predict that semelparous organisms should show low variation in juvenile survival and low variation in developmental rate. The effect of temporal correlation on extinction risk is most pronounced in organisms with semelparous life histories. © 2001 Academic Press.

  • 11.
    Pienaar, Elsje
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Hälsouniversitetet.
    Lerm, Maria
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Hälsouniversitetet.
    A mathematical model of the initial interaction between Mycobacterium tuberculosis and macrophages2014Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 342, s. 23-32Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    There is a large body of literature describing molecular level interactions between Mycobacterium tuberculosis (Mtb) and macrophages. Macrophages initiate a range of anti-bacterial mechanisms in response to infection, and Mtb is capable of surviving and circumventing many of these responses. We apply a computational approach to ask: what are the effects on the cellular level of these opposing interactions? The model considers the interplay between bacterial killing and the pathogen's interference with macrophage function. The results reveal an oscillating balance between host and pathogen, but the balance is transient and varies in length, indicating that stochasticity in the bacterial population or host response could contribute to the diverse incubation periods observed in exposed individuals. The model captures host and strain variation and gives new insight into host-pathogen compatibility and co-evolution.

  • 12.
    Pienaar, Elsje
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin. Linköpings universitet, Hälsouniversitetet.
    Lerm, Maria
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Hälsouniversitetet.
    Correction: A mathematical model of the initial interaction between Mycobacterium tuberculosis and macrophages (vol 342, pg 23, 2014) in JOURNAL OF THEORETICAL BIOLOGY vol 349 pg 1722014Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 349, s. 1s. 172-172Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    n/a

  • 13.
    Sagitov, Serik
    et al.
    Chalmers University of Technology and the University of Gothenburg.
    Bartoszek, Krzysztof
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg.
    Interspecies correlation for neutrally evolving traits2012Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 309, s. 11-19Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A simple way to model phenotypic evolution is to assume that after splitting, the trait values of the sister species diverge as independent Brownian motions. Relying only on a prior distribution for the underlying species tree (conditioned on the number, n, of extant species) we study the random vector (X1,…,Xn) of the observed trait values. In this paper we derive compact formulae for the variance of the sample mean and the mean of the sample variance for the vector (X1,…,Xn).

    The key ingredient of these formulae is the correlation coefficient between two trait values randomly chosen from (X1,…,Xn). This interspecies correlation coefficient takes into account not only variation due to the random sampling of two species out of n and the stochastic nature of Brownian motion but also the uncertainty in the phylogenetic tree. The latter is modeled by a (supercritical or critical) conditioned branching process. In the critical case we modify the Aldous-Popovic model by assuming a proper prior for the time of origin.

  • 14.
    Sharifimajd, Babak
    et al.
    Linköpings universitet, Institutionen för ekonomisk och industriell utveckling, Mekanik. Linköpings universitet, Tekniska högskolan.
    Stålhand, Jonas
    Linköpings universitet, Institutionen för ekonomisk och industriell utveckling, Mekanik. Linköpings universitet, Tekniska högskolan.
    A continuum model for excitation–contraction of smooth muscle under finite deformations2014Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 355, s. 1-9Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The main focus in most of continuum based muscle models is the muscle contraction dynamics while other physiological processes governing muscle contraction, e.g., the cell membrane excitation and the activation, are ignored. These latter processes are essential to initiate contraction and to determine the amount of generated force, and by excluding them, the developed model cannot replicate the true behavior of the muscle in question. The aim of this study is to establish a thermodynamically and physiologically consistent framework which allows to model smooth muscle contraction by including cell membrane excitability and kinetics of myosin phosphorylation, along with dynamics of smooth muscle contraction. The model accounts for these processes through a set of coupled dissipative constitutive equations derived by applying the first principles. To show the performance of the derived model, it is evaluated for two different cases: a mechanochemical study of pig taenia coli cells where the excitation process is excluded, and a complete excitation–contraction process of rat myometrium. The results show that the model is able to replicate important aspects of the smooth muscle EC process acceptably.

  • 15.
    Stålhand, Jonas
    et al.
    Linköpings universitet, Institutionen för ekonomisk och industriell utveckling, Mekanik och hållfasthetslära. Linköpings universitet, Tekniska fakulteten.
    Holzapfel, Gerhard A.
    Graz University of Technology, Austria.
    Length adaptation of smooth muscle contractile filaments in response to sustained activation2016Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 397, s. 13-21Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Airway and bladder smooth muscles are known to undergo length adaptation under sustained contraction. This adaptation process entails a remodelling of the intracellular actin and myosin filaments which shifts the peak of the active force-length curve towards the current length. Smooth muscles are therefore able to generate the maximum force over a wide range of lengths. In contrast, length adaptation of vascular smooth muscle has attracted very little attention and only a handful of studies have been reported. Although their results are conflicting on the existence of a length adaptation process in vascular smooth muscle, it seems that, at least, peripheral arteries and arterioles undergo such adaptation. This is of interest since peripheral vessels are responsible for pressure regulation, and a length adaptation will affect the function of the cardiovascular system. It has, e.g., been suggested that the inward remodelling of resistance vessels associated with hypertension disorders may be related to smooth muscle adaptation. In this study we develop a continuum mechanical model for vascular smooth muscle length adaptation by assuming that the muscle cells remodel the actomyosin network such that the peak of the active stress-stretch curve is shifted towards the operating point. The model is specialised to hamster cheek pouch arterioles and the simulated response to stepwise length changes under contraction. The results show that the model is able to recover the salient features of length adaptation reported in the literature.

  • 16.
    Stålhand, Jonas
    et al.
    Linköpings universitet, Institutionen för ekonomisk och industriell utveckling, Mekanik. Linköpings universitet, Tekniska högskolan.
    Klarbring, Anders
    Linköpings universitet, Institutionen för ekonomisk och industriell utveckling, Mekanik. Linköpings universitet, Tekniska högskolan.
    Holzapfel, Gerhard A
    Graz University of Technology, Institute of Biomechanics, Center of Biomedical Engineering / Royal Institute of Technology, Department of Solid Mechanics, School of Engineering Sciences.
    A mechanochemical 3D continuum model for smooth muscle contraction under finite strains2011Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 268, nr 1, s. 120-130Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper presents a modelling framework in which the mechanochemical properties of smooth muscle cells may be studied. The activation of smooth muscles is considered in a three-dimensional continuum model which is key to realistically capture the function of hollow organs such as blood vessels. On the basis of a general thermodynamical framework the mechanical and chemical phases are specialized in order to quantify the coupled mechanochemical process. A free-energy function is proposed as the sum of a mechanical energy stored in the passive tissue, a coupling between the mechanical and chemical kinetics and an energy related purely to the chemical kinetics and the calcium ion concentration. For the chemical phase it is shown that the cross-bridge model of Hai and Murphy [1988. Am. J. Physiol. Cell Physiol. 254, C99–C106] is included in the developed evolution law as a special case. In order to show the specific features and the potential of the proposed continuum model a uniaxial extension test of a tissue strip is analysed in detail and the related kinematics and stress–stretch relations are derived. Parameter studies point to coupling phenomena; in particular the tissue response is analysed in terms of the calcium ion level. The model for smooth muscle contraction may significantly contribute to current modelling efforts of smooth muscle tissue responses.

  • 17.
    Zook, Alexander E
    et al.
    Department of Ecology and Evolution, University of Chicago, United States.
    Eklöf, Anna
    Department of Ecology and Evolution, University of Chicago, United States.
    Jacob, Ute
    Institute for Hydrobiologie and Fisheries Science, University Hamburg, Germany.
    Allesina, Stefano
    Department of Ecology and Evolution, University of Chicago, United States; Computation Institute, University of Chicago, United States.
    Food webs: ordering species according to body size yields high degree of intervality2011Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 271, nr 1, s. 106-113Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Food webs, the networks describing "who eats whom" in an ecosystem, are nearly interval, i.e. there is a way to order the species so that almost all the resources of each consumer are adjacent in the ordering. This feature has important consequences, as it means that the structure of food webs can be described using a single (or few) species' traits. Moreover, exploiting the quasi-intervality found in empirical webs can help build better models for food web structure. Here we investigate which species trait is a good proxy for ordering the species to produce quasi-interval orderings. We find that body size produces a significant degree of intervality in almost all food webs analyzed, although it does not match the maximum intervality for the networks. There is also a great variability between webs. Other orderings based on trophic levels produce a lower level of intervality. Finally, we extend the concept of intervality from predator-centered (in which resources are in intervals) to prey-centered (in which consumers are in intervals). In this case as well we find that body size yields a significant, but not maximal, level of intervality. These results show that body size is an important, although not perfect, trait that shapes species interactions in food webs. This has important implications for the formulation of simple models used to construct realistic representations of food webs.

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