| 1. |
- Jagers, Peter, 1941, et al.
(author)
-
Random variation and concentration effects in PCR
- 2003
-
In: J. Theoret. Biol. 224, 299-304 (2003). - 0022-5193 .- 1095-8541. ; 224, s. 299-304
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Journal article (peer-reviewed)abstract
- Even though the efficiency of the PCR reaction decreases, analyses are made in terms of Galton-Watson processes, or simple deterministic models with constant replication probability (efficiency).Recently Schnell and Mendoza have suggested that the form of the efficiency can be derived from enzyme kinetics. This results in the sequence of molecules numbers forming a stochastic process with the properties of a branching process with population size dependence, which is supercritical, but has a mean reproductionnumber that approaches one. Such processes display ultimate linear growth, after an initial exponential phase, as is the case in PCR. It is also shown that the resulting stochastic process for a large Michaelis Menten constant behaves like the deterministic sequence x_n arising by iterations of the function f(x) = x+x/(1+x).
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| 2. |
- Borodich, A, et al.
(author)
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Segregation of the photosystems in higher plant thylakoids and short- and long-term regulation by a mesoscopic approach
- 2003
-
In: Journal of Theoretical Biology. - 0022-5193 .- 1095-8541. ; 225:4, s. 431-441
-
Journal article (peer-reviewed)abstract
- In this paper we consider the relationship between the lateral segregation of photosystems I and II in the grana and characteristics of the short- and long-term regulation in thylakoids following the mesoscopic approach. Our study is thermodynamic; it is based on the Flory-Huggins theory for binary mixtures and the McMillan-Mayer theory of heterogeneous solutions. We demonstrate that state transitions promote rearrangement of photosystems by either favoring their mixing after LHCII phosphorylation or enhancing their segregation after LHCII dephosphorylation. This regulation influences the entire system properties locally. We also demonstrate that the variations of the photosystem ratio promote rearrangement of the photosystems preserving their segregation. This regulation influences the entire system properties globally. The studies presented are another indication of the importance of the segregation of the photosystems in the grana thylakoids of higher plants. Segregation of PSIs and PSIIs is a signature of the spinodal decomposition, which is a fine regulatory mechanism, related to both the short- and long-term adaptations of the photosynthetic apparatus in higher plant thylakoids. (C) 2003 Elsevier Ltd. All rights reserved.
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| 3. |
- Granlund, Gösta H.
(author)
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The Use of Distribution Functions to Describe Integrated Density Profiles of Human Chromosomes
- 1973
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In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 40:3, s. 573-589
-
Journal article (peer-reviewed)abstract
- 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%.
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| 4. |
- Agliari, Elena, et al.
(author)
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Anergy in self-directed B lymphocytes : A statistical mechanics perspective
- 2013
-
In: Journal of Theoretical Biology. - : Elsevier. - 0022-5193 .- 1095-8541. ; 375, s. 21-31
-
Journal article (peer-reviewed)abstract
- Self-directed lymphocytes may evade clonal deletion at ontogenesis but still remain harmless due to a mechanism called clonal anergy. For B-lymphocytes, two major explanations for anergy developed over the last decades: according to Varela theory, anergy stems from a proper orchestration of the whole B-repertoire, such that self-reactive clones, due to intensive feed-back from other clones, display strong inertia when mounting a response. Conversely, according to the model of cognate response, self-reacting cells are not stimulated by helper lymphocytes and the absence of such signaling yields anergy. Through statistical mechanics we show that helpers do not prompt activation of a sub-group of B-cells: remarkably, the latter are just those broadly interacting in the idiotypic network. Hence Varela theory can finally be reabsorbed into the prevailing framework of the cognate response model. Further, we show how the B-repertoire architecture may emerge, where highly connected clones are self-directed as a natural consequence of ontogenetic learning.
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| 5. |
- Aikio, S, et al.
(author)
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Seed bank in annuals: Competition between banker and non-banker morphs
- 2002
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 217:3, s. 341-349
-
Journal article (peer-reviewed)abstract
- Seed bank is a plant life history strategy against the unpredictability of the biotic and the abiotic environment. We simulated competition between a seed banking and a non-banking morph of an annual plant. A constant fraction of the banker morph seeds was allocated to the seed bank, where they had a constant mortality and germination rate. All surviving seeds of the non-banker morph germinated in the next generation. The seedlings of both morphs experienced similar density-dependent mortality. Whether one of the morphs wins or the morphs coexist was evaluated from parameter space plots and statistically with logistic regression analysis. All parameters of the model had a significant, nonlinear effect on the persistence of the morphs, supporting our approach of numerically covering a wide range of parameter values. The seed production of a focal morph increased its survival and decreased the survival of the other morph. Otherwise, the morphs showed opposite response to changes in the model parameters. The banker morph was usually the winning strategy when it had a higher seed production than the non-banker morph. The banker morph benefitted from high germination probability, while the non-banker benefitted from high allocation to seed bank and high seed mortality. The coexistence of the morphs was inhibited by high banker morph seed production and seed mortality and promoted by high values of all other parameters. The system showed complex dynamics when banking was the winning strategy or the morphs coexisted. In addition, a part of the parameter space where the non-banker morph wins showed complex dynamics. Our results suggest that seed banking is a beneficial strategy if seed number is increased consequently, e.g. due to a decreased seed size. If banking decreases seed number, the non-banker morph wins or the two morphs coexist. (C) 2002 Elsevier Science Ltd. All rights reserved.
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| 6. |
- Alerstam, Thomas
(author)
-
Detours in bird migration
- 2001
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 209:3, s. 319-331
-
Journal article (peer-reviewed)abstract
- Bird migration routes often follow detours where passages across ecological barriers are reduced in extent. This occurs in spite of the fact that long barrier crossings are within the birds' potential flight range capacity. Long-distance flights are associated with extra energy costs for transport of the heavy fuel loads required. This paper explores how important the fuel transport costs, estimated on the basis of flight mechanics, map be to explain detours for birds migrating by flapping flight, Maximum detours in relation to expanse of the barrier are predicted for cases where birds travel along the detour by numerous short flights and small fuel reserves, divide the detour into a limited number of flight steps, and where a reduced barrier passage is included in the detour. The principles for determining the optimum route, often involving a shortcut across part of the barrier, are derived. Furthermore, the effects of differences in fuel deposition rates and in transport costs for the profitability of detours are briefly considered. An evaluation of a number of observed and potential detours in relation to the general predictions of maximum detours, indicates that reduction of fuel transport costs may well be a factor of widespread importance for the evolution of detours in bird migration at wide ecological barriers. (C) 2001 Academic Press.
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| 7. |
- Alerstam, Thomas
(author)
-
Flight by night or day? Optimal daily timing of bird migration.
- 2009
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 258:4, s. 530-536
-
Journal article (peer-reviewed)abstract
- Many migratory bird species fly mainly during the night (nocturnal migrants), others during daytime (diurnal migrants) and still others during both night and day. Need to forage during the day, atmospheric structure, predator avoidance and orientation conditions have been proposed as explanations for the widespread occurrence of nocturnal migration. However, the general principles that determine the basic nocturnal-diurnal variation in flight habits are poorly known. In the present study optimal timing of migratory flights, giving the minimum total duration of the migratory journey, is evaluated in a schematic way in relation to ecological conditions for energy gain in foraging and for energy costs in flight. There exists a strong and fundamental advantage of flying by night because foraging time is maximized and energy deposition can take place on days immediately after and prior to the nocturnal flights. The increase in migration speed by nocturnal compared with diurnal migration will be largest for birds with low flight costs and high energy deposition rates. Diurnal migration will be optimal if it is associated with efficient energy gain immediately after a migratory flight because suitable stopover/foraging places have been located during the flight or if energy losses during flight are substantially reduced by thermal soaring and/or by fly-and-forage migration. A strategy of combined diurnal and nocturnal migration may be optimal when birds migrate across regions with relatively poor conditions for energy deposition (not only severe but also soft barriers). Predictions about variable timing of migratory flights depending on changing foraging and environmental conditions along the migration route may be tested for individual birds by analysing satellite tracking results with respect to daily travel routines in different regions. Documenting and understanding the adaptive variability in daily travel schedules among migrating animals constitute a fascinating challenge for future research.
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| 8. |
- Alger, Ingela, et al.
(author)
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A generalization of Hamilton's rule-Love others how much?
- 2012
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 299, s. 42-54
-
Journal article (peer-reviewed)abstract
- According to Hamilton's (1964a, b) rule, a costly action will be undertaken if its fitness cost to the actor falls short of the discounted benefit to the recipient, where the discount factor is Wright's index of relatedness between the two. We propose a generalization of this rule, and show that if evolution operates at the level of behavior rules, rather than directly at the level of actions, evolution will select behavior rules that induce a degree of cooperation that may differ from that predicted by Hamilton's rule as applied to actions. In social dilemmas there will be less (more) cooperation than under Hamilton's rule if the actions are strategic substitutes (complements). Our approach is based on natural selection, defined in terms of personal (direct) fitness, and applies to a wide range of pairwise interactions.
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| 9. |
- Ali, Qasim, 1986, et al.
(author)
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Adaptive damage retention mechanism enables healthier yeast population
- 2019
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 473, s. 52-66
-
Journal article (peer-reviewed)abstract
- During cytokinesis in budding yeast (Saccharomyces cerevisiae) damaged proteins are distributed asymmetrically between the daughter and the mother cell. Retention of damaged proteins is a crucial mechanism ensuring a healthy daughter cell with full replicative potential and an ageing mother cell. However, the protein quality control (PQC) system is tuned for optimal reproduction success which suggests optimal health and size of the population, rather than long-term survival of the mother cell. Modelling retention of damage as an adaptable mechanism, we propose two damage retention strategies to find an optimal way of decreasing damage retention efficiency to maximize population size and minimize the damage in the individual yeast cell. A pedigree model is used to investigate the impact of small variations in the strategies over the whole population. These impacts are based on the altruistic effects of damage retention mechanism and are measured by a cost function whose minimum value provides the optimal health and size of the population. We showed that fluctuations in the cost function allow yeast cell to continuously vary its strategy, suggesting that optimal reproduction success is a local minimum of the cost function. Our results suggest that a rapid decrease in the efficiency of damage retention, at the time when the mother cell is almost exhausted, produces fewer daughters with high levels of damaged proteins. In addition, retaining more damage during the early divisions increases the number of healthy daughters in the population. (C) 2019 Elsevier Ltd. All rights reserved.
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| 10. |
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| 11. |
- Asano, Masanari, et al.
(author)
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Quantum-like model of diauxie in Escherichia coli : operational description of precultivation effect
- 2012
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 314, s. 130-137
-
Journal article (peer-reviewed)abstract
- In this paper we apply the quantum-like (QL) approach to microbiology to present an operational description of the complex process of diauxie in Escherichia coil. We take as guaranteed that dynamics in cells is adaptive, i.e., it depends crucially on the microbiological context. This very general assumption is sufficient to appeal to quantum and more general QL probabilistic models. The next step is to find the operational representation - by operators in complex Hilbert space (as in quantum physics). To determine QL operators, we used the statistical data from Inada et al. (1996). To improve the QL-representation, we needed better experimental data. Corresponding experiments were recently done by two of the authors and in this paper we use these new data. In these data we found that biochemical context of precultivation of populations of E. coli plays a crucial role in E. coli preferences with respect to sugars. Hence, the form of the QL operator representing lactose operon activation also depends crucially on precultivation. One of our results is decomposition of the lactose operon activation operator to extract the factor determined by precultivation. The QL operational approach developed in this paper can be used not only for description of the process of diauxie in E. coli, but also other processes of gene expression. However, new experimental statistical data are demanded. (C) 2012 Elsevier Ltd. All rights reserved.
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| 12. |
- Bach, Lars, et al.
(author)
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The evolution of n-player cooperation—threshold games and ESS bifurcations
- 2006
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 238:2, s. 426-434
-
Journal article (peer-reviewed)abstract
- An evolutionary game of individuals cooperating to obtain a collective benefit is here modelled as an n-player Prisoner's Dilemma game. With reference to biological situations, such as group foraging, we introduce a threshold condition in the number of cooperators required to obtain the collective benefit. In the simplest version, a three-player game, complex behaviour appears as the replicator dynamics exhibits a catastrophic event separating a parameter region allowing for coexistence of cooperators and defectors and a region of pure defection. Cooperation emerges through an ESS bifurcation, and cooperators only thrive beyond a critical point in cost-benefit space. Moreover, a repelling fixed point of the dynamics acts as a barrier to the introduction of cooperation in defecting populations. The results illustrate the qualitative difference between two-player games and multiple player games and thus the limitations to the generality of conclusions from two-player games. We present a procedure to find the evolutionarily stable strategies in any n-player game with cost and benefit depending on the number of cooperators. This was previously done by Motro [1991. Co-operation and defection: playing the field and the ESS. J. Theor. Biol. 151, 145–154] in the special cases of convex and concave benefit functions and constant cost.
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| 13. |
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| 14. |
- Bartoszek, Krzysztof, et al.
(author)
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A consistent estimator of the evolutionary rate
- 2015
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 371, s. 69-78
-
Journal article (peer-reviewed)abstract
- 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.
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| 15. |
- Bartoszek, Krzysztof, 1984-, et al.
(author)
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A consistent estimator of the evolutionary rate
- 2015
-
In: Journal of Theoretical Biology. - 0022-5193 .- 1095-8541. ; 371, s. 69-78
-
Journal article (peer-reviewed)abstract
- We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate λ, 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 σ2. 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 Rn2 of the evolutionary rate ρ2=σ2/λ. The estimator Rn2 is proportional to the sample variance Sn2 computed from n trait values. We find an approximate formula for the standard error of Rn2 based on a neat asymptotic relation for the variance of Sn2.
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| 16. |
- Bartoszek, Krzysztof, 1984, et al.
(author)
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A phylogenetic comparative method for studying multivariate adaptation
- 2012
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 314, s. 204-215
-
Journal article (peer-reviewed)abstract
- 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 coadaptation between 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 in previous OU models, to fixed or randomly evolving predictor variables. We present the interpretation of the 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 antler and body-size evolution in deer (Cervidae).
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| 17. |
- Bartoszek, Krzysztof, 1984-
(author)
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Phylogenetic effective sample size
- 2016
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In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 407, s. 371-386
-
Journal article (peer-reviewed)abstract
- 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.
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| 18. |
- Bartoszek, Krzysztof, 1984-, et al.
(author)
-
Time to a single hybridization event in a group of species with unknown ancestral history
- 2013
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 322, s. 1-6
-
Journal article (peer-reviewed)abstract
- 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.
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| 19. |
- Bartoszek, Krzysztof, 1984-, et al.
(author)
-
Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations
- 2017
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 429, s. 35-45
-
Journal article (peer-reviewed)abstract
- 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.
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| 20. |
- Bengtsson, Bengt Olle
(author)
-
Modelling the evolution of genomes with integrated external and internal functions
- 2004
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 231:2, s. 271-278
-
Journal article (peer-reviewed)abstract
- The genomes that organisms transmit between generations contain information about different kinds of functions. The genome with the "best" mix and number of genes for these functions is the one that natural selection favours. Here I introduce a new way to model simple organisms with genes for external and internal functions, and use it to study the evolution of genome size. The external functions are exemplified by resource use and the internal functions by mutation control (repair). It is shown that even with a suitable proportion of genes for mutation control, the genomes in the organisms do not forever incorporate genes that increase resource use. Instead they evolve towards an optimal genome of limited size. The optimal proportion of genes for mutation control is shown to have an upper limit given by the ease with which transmission accuracy is improved by adding extra genes for this purpose to the genome. The model illustrates how natural selection on genomes integrates systems for the transmission of genetic information with systems relating to the external adaptation of the organism. It also opens Lip for other, more detailed theoretical investigations of genome functions.
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| 21. |
- Bengtsson, Bengt Olle, et al.
(author)
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The effective size of bryophyte populations.
- 2009
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 258:Available online 8 January 2009, s. 121-126
-
Journal article (peer-reviewed)abstract
- Bryophytes with their dominant haploid stage conform poorly to the life cycles generally treated in population genetical models. Here we make a detailed analysis of what effective sizes bryophyte model populations have as a function of their breeding system. It is found that the effective size is rarely much smaller than the scored number of haploid gametophytic individuals, even when the limited number of diploids (sporophytes) formed is taken into account. The most severe decrease in effective size occurs when unisexual gametophytic females produce only a small number of fertile diploid sporophytes in male biased populations; this effect is due to the restricted sampling of male gametophytic individuals that then occurs. It is shown that the harmonic mean of diploid sporophytes formed per haploid gametophytic individuals is the relevant measure in these calculations and not the standard (and generally larger) arithmetic mean.
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| 22. |
- Bengtsson, Göran, et al.
(author)
-
Irregular walks and loops combines in small-scale movement of a soil insect : implications for dispersal biology
- 2004
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 231:2, s. 299-306
-
Journal article (peer-reviewed)abstract
- Analysis of small-scale movement patterns of animals we may help to understand and predict movement at a larger scale, such as dispersal, which is a key parameter in spatial population dynamics. We have chosen to study the movement of a soil-dwelling Collembola, Protaphorura armata, in an experimental system consisting of a clay surface with or without physical obstacles. A combination of video recordings, descriptive statistics, and walking simulations was used to evaluate the movement pattern. Individuals were found to link periods of irregular walk with those of looping in ahomogeneous environment as well as in one structured to heterogeneity by physical obstacles. The number of loops varied between 0 and 44 per hour from one individual to another and some individuals preferred to make loops by turning right and others by turning left. P. armata spent less time at the boundary of small obstacles compared to large, presumably because of a lower probability to track the steepness of the curvature as the individual walks along a highly curved surface. Food deprived P. armata had amore winding movement and made more circular loops than those that were well fed. The observed looping behaviour is interpreted in the context of systematic search strategies and compared with similar movement patterns found in other species.
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| 23. |
- Bengtsson, Hans-Uno, et al.
(author)
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A simple model for the arterial system
- 2003
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 221:3, s. 437-443
-
Journal article (peer-reviewed)abstract
- We present a simple model for the arterial part of the cardiovascular system, based on Poiseuille flow constrained by the power dissipated into the cells lining the vessels. This, together with the assumption of a volume-filling network, leads to correct predictions for the evolution of vessel radii, vessel lengths and blood pressure in the human arterial system. The model can also be used to find exponents for allometric scaling, and gives good agreement with data on mammals.
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| 24. |
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| 25. |
- Björklund, Mats
(author)
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Optimal choice in a neural network
- 2002
-
In: Journal of Theoretical Biology. - 0022-5193 .- 1095-8541. ; 218, s. 149-154
-
Journal article (peer-reviewed)
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| 26. |
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| 27. |
- Björn, Lars Olof, et al.
(author)
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Ecological importance of the thermal emissivity of avian eggshells
- 2012
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 301, s. 62-66
-
Journal article (peer-reviewed)abstract
- Breeding birds have to divide their time between egg incubation and foraging. Particularly in cases when only one parent incubates the eggs, and especially in cold climates, the cooling of the eggs during absence from the nest may be problematic. In the present study we find that the thermal emissivity of eggshells may be ecologically important, and that an evolutionary pressure towards lower emissivity for exposed eggs in cold climates exists. We plan to experimentally compare emissivities among species in a future study. (C) 2012 Elsevier Ltd. All rights reserved.
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| 28. |
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| 29. |
- Brush, Eleanor, et al.
(author)
-
Indirect reciprocity with negative assortment and limited information can promote cooperation
- 2018
-
In: Journal of Theoretical Biology. - : Elsevier. - 0022-5193 .- 1095-8541. ; 443, s. 56-65
-
Journal article (peer-reviewed)abstract
- Cooperation is ubiquitous in biological and social systems, even though cooperative behavior is often costly and at risk of exploitation by non-cooperators. Several studies have demonstrated that indirect reciprocity, whereby some members of a group observe the behaviors of their peers and use this information to discriminate against previously uncooperative agents in the future, can promote prosocial behavior. Some studies have shown that differential propensities of interacting among and between different types of agents (interaction assortment) can increase the effectiveness of indirect reciprocity. No previous studies have, however, considered differential propensities of observing the behaviors of different types of agents (information assortment). Furthermore, most previous studies have assumed that discriminators possess perfect information about others and incur no costs for gathering and storing this information. Here, we (1) consider both interaction assortment and information assortment, (2) assume discriminators have limited information about others, and (3) introduce a cost for information gathering and storage, in order to understand how the ability of discriminators to stabilize cooperation is affected by these steps toward increased realism. We report the following findings. First, cooperation can persist when agents preferentially interact with agents of other types or when discriminators preferentially observe other discriminators, even when they have limited information. Second, contrary to intuition, increasing the amount of information available to discriminators can exacerbate defection. Third, introducing costs of gathering and storing information makes it more difficult for discriminators to stabilize cooperation. Our study is one of only a few studies to date that show how negative interaction assortment can promote cooperation and broadens the set of circumstances in which it is know that cooperation can be maintained.
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| 30. |
- Calander, Nils, 1953
(author)
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Propensity of a circadian clock to adjust to the 24 h day-night light cycle and its sensitivity to molecular noise
- 2006
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 241:4, s. 716-724
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Journal article (peer-reviewed)abstract
- The circadian clock of Drosophila melanogaster and its tendency to adjust to the day-night light cycle is simulated by deterministic and stochastic methods. The robustness of the locking to the light-cycle with respect to molecular noise is studied. It is found that within the model studied, the molecular noise in the stochastic simulation erases the finer injection-locking structures, stronger injection signals are needed and the locking has the character of prolonged locked time intervals with cycle slips in between. The simulations are compared to a simple injection-locking model with noise that seems to describe the overall behavior well. © 2006 Elsevier Ltd. All rights reserved.
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| 31. |
- Calleja-Rodriguez, Ainhoa, et al.
(author)
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Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design
- 2019
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 462, s. 283-292
-
Journal article (peer-reviewed)abstract
- In forest tree breeding, family-based Quantitative Trait Loci (QTL) studies are valuable as methods to dissect the complexity of a trait and as a source of candidate genes. In the field of conifer research, our study contributes to the evaluation of phenotypic and predicted breeding values for the identification of QTL linked to complex traits in a three-generation pedigree population in Scots pine (Pinus sylvestris L.). A total of 11 470 open pollinated F-2-progeny trees established at three different locations, were measured for growth and adaptive traits. Breeding values were predicted for their 360 mothers, originating from a single cross of two grand-parents. A multilevel LASSO association analysis was conducted to detect QTL using genotypes of the mothers with the corresponding phenotypes and Estimated Breeding Values (EBV). Different levels of genotype-by-environment (G x E) effects among sites at different years, were detected for survival and height. Moderate-to-low narrow sense heritabilities and EBV accuracies were found for all traits and all sites. We identified 18 AFLPs and 12 SNPs to be associated with QTL for one or more traits. 62 QTL were significant with percentages of variance explained ranging from 1.7 to 18.9%. In those cases where the same marker was associated to a phenotypic or an ebvQTL, the ebvQTL always explained higher proportion of the variance, maybe due to the more accurate nature of Estimated Breeding Values (EBV). Two SNP-QTL showed pleiotropic effects for traits related with hardiness, seed, cone and flower production. Furthermore, we detected several QTL with significant effects across multiple ages, which could be considered as strong candidate loci for early selection. The lack of reproducibility of some QTL detected across sites may be due to environmental heterogeneity reflected by the genotype- and QTL-by-environment effects. (C) 2018 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.
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| 32. |
- Cartling, Bo
(author)
-
Control of neural information transmission by synaptic dynamics
- 2002
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 214:2, s. 275-292
-
Journal article (peer-reviewed)abstract
- The computational processing of a neural system is strongly influenced by the dynamical characteristics of the information transmission between neurons. In this work, the control of neural information transmission by synaptic dynamics is investigated by means of a master-equation-based stochastic model of pre-synaptic release of neurotransmitter-containing vesicles. The model incorporates facilitation of vesicle fusion with the pre-synaptic membrane due to intracellular calcium ions and depletion of readily releasable vesicles. The message to be transmitted is coded by the pre-synaptic firing sequence, and the received signal corresponds to the post-synaptic membrane potential response. At the sending end, the stochastic character of the vesicle release contributes to the entropy of the probability distribution of the number of vesicles released and represents noise with respect to information transmission. At the receiving end, the generation of post-synaptic membrane potentials is influenced by the temporal behaviour of ionic currents and membrane charging and is determined by means of a low-dimensional model. The rate and temporal types of neural coding are compatible with limiting cases of the synaptic information transmission as a function of initial vesicle release probability and pre-synaptic firing rate. The effects of the nonlinear dependencies of the vesicle release probability on intracellular calcium concentration and number of available vesicles are analysed. The model is compared with phenomenological and reduced models, a principal advantage being the capability of also determining fluctuations of dynamic variables.
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| 33. |
- Christianou, Maria, 1974-, et al.
(author)
-
Complexity does not affect stability in feasible model communities
- 2008
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 253:1, s. 162-169
-
Journal article (peer-reviewed)abstract
- 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.
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| 34. |
- de Borst, Karin, et al.
(author)
-
Structure-€“function relationships in hardwood : Insight from micromechanical modelling
- 2014
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 345, s. 78-91
-
Journal article (peer-reviewed)abstract
- Abstract A micromechanical model is presented that predicts the stiffness of wood tissues in their three principal anatomical directions, across various hardwood species. The wood polymers cellulose, hemicellulose, and lignin, common to all wood tissues, serve as the starting point. In seven homogenisation steps, the stiffnesses of these polymers are linked to the macroscopic stiffness. The good agreement of model predictions and corresponding experimental data for ten different European and tropical species confirms the functionality and accuracy of the model. The model enables investigating the influence of individual microstructural features on the overall stiffness. This is exploited to elucidate the mechanical effects of vessels and ray cells. Vessels are shown to reduce the stiffness of wood at constant overall density. This supports that a trade-off exists between the hydraulic efficiency and the mechanical support in relation to the anatomical design of wood. Ray cells are shown to act as reinforcing elements in the radial direction.
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| 35. |
- Diehl, Stefan, et al.
(author)
-
A one-dimensional moving-boundary model for tubulin-driven axonal growth.
- 2014
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 358:Online 21 June 2014, s. 194-207
-
Journal article (peer-reviewed)abstract
- A one-dimensional continuum-mechanical model of axonal elongation due to assembly of tubulin dimers in the growth cone is presented. The conservation of mass leads to a coupled system of three differential equations. A partial differential equation models the dynamic and the spatial behaviour of the concentration of tubulin that is transported along the axon from the soma to the growth cone. Two ordinary differential equations describe the time-variation of the concentration of free tubulin in the growth cone and the speed of elongation. All steady-state solutions of the model are categorized. Given a set of the biological parameter values, it is shown how one easily can infer whether there exist zero, one or two steady-state solutions and directly determine the possible steady-state lengths of the axon. Explicit expressions are given for each stationary concentration distribution. It is thereby easy to examine the influence of each biological parameter on a steady state. Numerical simulations indicate that when there exist two steady states, the one with shorter axon length is unstable and the longer is stable. Another result is that, for nominal parameter values extracted from the literature, in a large portion of a fully grown axon the concentration of free tubulin is lower than both concentrations in the soma and in the growth cone.
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| 36. |
- Ehn, Micael, et al.
(author)
-
Adaptive strategies for cumulative cultural learning
- 2012
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 301, s. 103-111
-
Journal article (peer-reviewed)abstract
- The demographic and ecological success of our species is frequently attributed to our capacity for cumulative culture. However, it is not yet known how humans combine social and asocial learning to generate effective strategies for learning in a cumulative cultural context. Here we explore how cumulative culture influences the relative merits of various pure and conditional learning strategies, including pure asocial and social learning, critical social learning, conditional social learning and individual refiner strategies. We replicate the Rogers' paradox in the cumulative setting. However, our analysis suggests that strategies that resolved Rogers' paradox in a non-cumulative setting may not necessarily evolve in a cumulative setting, thus different strategies will optimize cumulative and non-cumulative cultural learning.
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| 37. |
- El Khalifi, Mohamed, et al.
(author)
-
SIRS epidemics with individual heterogeneity of immunity waning
- 2024
-
In: Journal of Theoretical Biology. - 0022-5193 .- 1095-8541. ; 587
-
Journal article (peer-reviewed)abstract
- In the current paper we analyse an extended SIRS epidemic model in which immunity at the individual level wanes gradually at exponential rate, but where the waning rate may differ between individuals, for instance as an effect of differences in immune systems. The model also includes vaccination schemes aimed to reach and maintain herd immunity. We consider both the informed situation where the individual waning parameters are known, thus allowing selection of vaccinees being based on both time since last vaccination as well as on the individual waning rate, and the more likely uninformed situation where individual waning parameters are unobserved, thus only allowing vaccination schemes to depend on time since last vaccination. The optimal vaccination policies for both the informed and uniformed heterogeneous situation are derived and compared with the homogeneous waning model (meaning all individuals have the same immunity waning rate), as well as to the classic SIRS model where immunity at the individual level drops from complete immunity to complete susceptibility in one leap. It is shown that the classic SIRS model requires least vaccines, followed by the SIRS with homogeneous gradual waning, followed by the informed situation for the model with heterogeneous gradual waning. The situation requiring most vaccines for herd immunity is the most likely scenario, that immunity wanes gradually with unobserved individual heterogeneity. For parameter values chosen to mimic COVID-19 and assuming perfect initial immunity and cumulative immunity of 12 months, the classic homogeneous SIRS epidemic suggests that vaccinating individuals every 15 months is sufficient to reach and maintain herd immunity, whereas the uninformed case for exponential waning with rate heterogeneity corresponding to a coefficient of variation being 0.5, requires that individuals instead need to be vaccinated every 4.4 months.
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| 38. |
- Fagerlind, Magnus G., et al.
(author)
-
Dynamic modelling of cell death during biofilm development
- 2012
-
In: Journal of Theoretical Biology. - : Academic Press. - 0022-5193 .- 1095-8541. ; 295, s. 23-36
-
Journal article (peer-reviewed)abstract
- Biofilms are currently recognised as the predominant bacterial life-style and it has been suggested that biofilm development is influenced by a number of different processes such as adhesion, detachment, mass transport, quorum sensing, cell death and active dispersal. One of the least understood processes and its effects on biofilm development is cell death. However, experimental studies suggest that bacterial death is an important process during biofilm development and many studies show a relationship between cell death and dispersal in microbial biofilms. We present a model of the process of cell death during biofilm development, with a particular focus on the spatial localisation of cell death or cell damage. Three rules governing cell death or cell damage were evaluated which compared the effects of starvation, damage accumulation, and viability during biofilm development and were also used to design laboratory based experiments to test the model. Results from model simulations show that actively growing biofilms develop steep nutrient gradients within the interior of the biofilm that affect neighbouring microcolonies resulting in cell death and detachment. Two of the rules indicated that high substrate concentrations lead to accelerated cell death, in contrast to the third rule, based on the accumulation of damage, which predicted earlier cell death for biofilms grown with low substrate concentrations. Comparison of the modelling results with experimental results suggests that cell death is favoured under low nutrient conditions and that the accumulation of damage may be the main cause of cell death during biofilm development. (C) 2011 Elsevier Ltd. All rights reserved.
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| 39. |
- Fallqvist, Björn, 1985-, et al.
(author)
-
Constitutive modelling of composite biopolymer networks
- 2016
-
In: Journal of Theoretical Biology. - : Elsevier. - 0022-5193 .- 1095-8541. ; 395, s. 51-61
-
Journal article (peer-reviewed)abstract
- The mechanical behaviour of biopolymer networks is to a large extent determined at a microstructural level where the characteristics of individual filaments and the interactions between them determine the response at a macroscopic level. Phenomena such as viscoelasticity and strain-hardening followed by strain-softening are observed experimentally in these networks, often due to microstructural changes (such as filament sliding, rupture and cross-link debonding). Further, composite structures can also be formed with vastly different mechanical properties as compared to the indivudal networks. In this present paper, we present a constitutive model presented in a continuum framework aimed at capturing these effects. Special care is taken to formulate thermodynamically consistent evolution laws for dissipative effects. This model, incorporating possible anisotropic network properties, is based on a strain energy function, split into an isochoric and a volumetric part. Generalisation to three dimensions is performed by numerical integration over the unit sphere. Model predictions indicate that the constitutive model is well able to predict the elastic and viscoelastic response of biological networks, and to an extent also composite structures.
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| 40. |
- Fallqvist, B., et al.
(author)
-
Modelling of cross-linked actin networks : influence of network parameters and cross-link compliance
- 2014
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 350, s. 57-69
-
Journal article (peer-reviewed)abstract
- A major structural component of the cell is the actin cytoskeleton, in which actin subunits are polymerised into actin filaments. These networks can be cross-linked by various types of ABPs (Actin Binding Proteins), such as Filamin A. In this paper, the passive response of cross-linked actin filament networks is evaluated, by use of a numerical and continuum network model. For the numerical model, the influence of filament length, statistical dispersion, cross-link compliance (including that representative of Filamin A) and boundary conditions on the mechanical response is evaluated and compared to experimental results. It is found that the introduction of statistical dispersion of filament lengths has a significant influence on the computed results, reducing the network stiffness by several orders of magnitude. Actin networks have previously been shown to have a characteristic transition from an initial bending-dominated to a stretching-dominated regime at larger strains, and the cross-link compliance is shown to shift this transition. The continuum network model, a modified eight-chain polymer model, is evaluated and shown to predict experimental results reasonably well, although a single set of parameters cannot be found to predict the characteristic dependence of filament length for different types of cross-links. Given the vast diversity of cross-linking proteins, the dependence of mechanical response on cross-link compliance signifies the importance of incorporating it properly in models to understand the roles of different types of actin networks and their respective tasks in the cell.
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| 41. |
- Fallqvist, Björn, et al.
(author)
-
Modelling of cross-linked actin networks - Influence of geometrical parameters and cross-link compliance
- 2014
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 350, s. 57-69
-
Journal article (peer-reviewed)abstract
- A major structural component of the cell is the actin cytoskeleton, in which actin subunits are polymerised into actin filaments. These networks can be cross-linked by various types of ABPs (Actin Binding Proteins), such as Filamin A. In this paper, the passive response of cross-linked actin filament networks is evaluated, by use of a numerical and continuum network model. For the numerical model, the influence of filament length, statistical dispersion, cross-link compliance (including that representative of Filamin A) and boundary conditions on the mechanical response is evaluated and compared to experimental results. It is found that the introduction of statistical dispersion of filament lengths has a significant influence on the computed results, reducing the network stiffness by several orders of magnitude. Actin networks have previously been shown to have a characteristic transition from an initial bending-dominated to a stretching-dominated regime at larger strains, and the cross-link compliance is shown to shift this transition. The continuum network model, a modified eight-chain polymer model, is evaluated and shown to predict experimental results reasonably well, although a single set of parameters cannot be found to predict the characteristic dependence of filament length for different types of cross-links. Given the vast diversity of cross-linking proteins, the dependence of mechanical response on cross-link compliance signifies the importance of incorporating it properly in models to understand the roles of different types of actin networks and their respective tasks in the cell.
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| 42. |
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| 43. |
- Foster, David V., et al.
(author)
-
Dynamic landscapes : A model of context and contingency in evolution
- 2013
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 334, s. 162-172
-
Journal article (peer-reviewed)abstract
- Although the basic mechanics of evolution have been understood since Darwin, debate continues over whether macroevolutionary phenomena are driven by the fitness structure of genotype space or by ecological interaction. In this paper we propose a simple model capturing key features of fitness-landscape and ecological models of evolution. Our model describes evolutionary dynamics in a high-dimensional, structured genotype space with interspecies interaction. We find promising qualitative similarity with the empirical facts about macroevolution, including broadly distributed extinction sizes and realistic exploration of the genotype space. The abstraction of our model permits numerous applications beyond macroevolution, including protein and RNA evolution.
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| 44. |
- Frey, Simone, et al.
(author)
-
How quantitative measures unravel design principles in multi-stage phosphorylation cascades.
- 2008
-
In: Journal of theoretical biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 254:1, s. 27-36
-
Journal article (peer-reviewed)abstract
- We investigate design principles of linear multi-stage phosphorylation cascades by using quantitative measures for signaling time, signal duration and signal amplitude. We compare alternative pathway structures by varying the number of phosphorylations and the length of the cascade. We show that a model for a weakly activated pathway does not reflect the biological context well, unless it is restricted to certain parameter combinations. Focusing therefore on a more general model, we compare alternative structures with respect to a multivariate optimization criterion. We test the hypothesis that the structure of a linear multi-stage phosphorylation cascade is the result of an optimization process aiming for a fast response, defined by the minimum of the product of signaling time and signal duration. It is then shown that certain pathway structures minimize this criterion. Several popular models of MAPK cascades form the basis of our study. These models represent different levels of approximation, which we compare and discuss with respect to the quantitative measures.
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| 45. |
- Fåhraeus, C, et al.
(author)
-
The K-Cl cotransporter in the lobster stretch receptor neurone-a kinetic analysis.
- 2002
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 217:3, s. 287-309
-
Journal article (peer-reviewed)abstract
- Experiments were performed to define quantitatively the substrate (K(+) and Cl(-)) dependence of the transport function (production of equally large and oppositely directed K(+)and Cl(-) flows/currents) of an earlier (Theander et al., 1999) identified electroneutral K-Cl cotransporter in the slowly adapting stretch receptor neurone of the European lobster. The experiments were based on microelectrode techniques. This allowed us to perform steady-state measurements of the so-called "instantaneous" current-voltage relationships (around a holding voltage of -65 mV after a blockage of the cell's action potential and hyperpolarization-activated currents) and intracellular ion concentrations at various settings of the extracellular K(+) and Cl(-) concentrations. From the results, we could then define steady-state values of all of the cell's non-KCl cotransporter K(+) and Cl(-) currents. Finally, the negative sums of the inferred non-KCl cotransporter K(+) and Cl(-) currents could be taken as equivalents of the K-Cl cotransporter's K(+) and Cl(-) currents for the reason that, in steady state, all membrane currents add up to zero. For the cotransporter currents, thus inferred for a range from 2.5/410.5 to 40.0/448.0 mM external K(+)/Cl(-), we found that their absolute values increased in a nonlinear fashion from about 5 nA cell(-1) at the lowest, to about 20 nA cell(-1) at the highest external K(+)/Cl(-) concentrations. Formally, this relationship could be reproduced by a Hill function-based enzyme kinetic expression simulating inward and outward transmembrane electroneutral ion transports. Following insertion of this expression into a comprehensive model of electrical membrane functions and intracellular solute and solvent control in the lobster stretch receptor neurone, the model predictions suggested that the K-Cl cotransporter does play an important role in (a) keeping intracellular Cl(-) low for a proper function of the cell's inhibitory system, and (b) enabling rapid transmembrane K(+) shifts that provide for a stabilization of the cell's membrane voltage and membrane excitability in cases of varying extracellular K(+) concentrations. The model predictions gave, however, no clear evidence that the K-Cl cotransporter is critically involved in the cell's volume regulation in conditions of varying extracellular osmolalities.
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| 46. |
- Geli, Patricia, et al.
(author)
-
A multi-type branching model with varying environment for bacterial dynamics with postantibiotic effect
- 2009
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 256:1, s. 58-64
-
Journal article (peer-reviewed)abstract
- A multi-type branching process with varying environment was used to construct a pharmacokinetic/pharmacodynamic (PK/PD) model that captures the postantibiotic effect (PAE) seen in bacterial populations after exposure of antibiotics. This phenomenon of continued inhibition of bacterial growth even after removal of the antibiotic from the growth medium is of high relevance in the context of optimizing dosing regimens. The clinical implication of long PAEs lies in the interesting possibility of increasing the intervals between drug administrations. The model structure is generalizable to most types of antibiotics and is useful both as a theoretical framework for understanding the time properties of PAE and to explore optimal antibiotic dosing regimens. Data from an in vitro study with Escherichia coli exposed to different dosing regimens of cefotaxime were used to evaluate the model.
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| 47. |
- Ghachem, Montasser
(author)
-
The institution as a blunt instrument : Cooperation through imperfect observability
- 2016
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 396, s. 182-190
-
Journal article (peer-reviewed)abstract
- Observing others enables us to indirectly reciprocate their actions. In large societies, however, reliable individual observation is hard to achieve. Societies therefore rely on institutions to aid in observing cooperative behaviour and identifying those who cooperated. Institutions are integral part of modern societies. Here, we propose an evolutionary model in which an institution aims to label cooperators with a tag to verify their trustworthiness, as is the case for financial credit ratings or quality certificates. However, errors in assigning tags inevitably arise: the institution may accidentally leave some cooperators untagged or award tags to some defectors. Taking these two specific types of errors into account, we derive simple analytical conditions under which cooperation becomes stable and is favoured by selection. We find that these two institutional errors are not weighted equally in promoting cooperation: it is more detrimental to cooperation if tags are erroneously awarded to defectors than if they are mistakenly withheld from cooperators. Institutional tagging can lead to non-uniform interaction rates among cooperators and defectors, whereby cooperators benefit disproportionally by playing more games than defectors. This work sheds light on the significant role of institutions in promoting and maintaining societal cooperation.
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| 48. |
- Green, Martin, et al.
(author)
-
The problem of estimating wind drift in migrating birds
- 2002
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 218:4, s. 485-496
-
Journal article (peer-reviewed)abstract
- Whether migrating birds compensate for wind drift or not is a fundamental question in bird migration research. The procedures to demonstrate and quantitatively estimate wind drift or compensation are fraught with difficulties and pitfalls. In this paper, we evaluate four methods that have been used in several studies over the past decades. We evaluate the methods by analysing a model migratory movement with a realistic scatter in flight directions, for the ideal cases of full drift and complete compensation. Results obtained with the different methods are then compared with the "true behaviour" of the model movement, illustrating that spurious patterns of drift and compensation arise in some cases. We also illustrate and evaluate the different methods of estimating drift for a real case, based on tracking radar measurements of bird migration in relation to winds. Calculating the linear regression of mean geographic track (resulting flight direction) and heading directions (directions of the birds' body axis) of a migratory movement under different wind conditions in relation to the angle a (the angle between mean track and heading) always provides robust and reliable results. Comparing mean flight directions between occasions with winds from the left and right of the mean flight direction of the whole migratory movement also always provides expected and correct measures of drift. In contrast, regressions of individual flight directions in relation to alpha (the angle between track and heading for the specific individuals or flocks) are liable to produce biased and spurious results, overestimating compensation/ overcompensation if following winds dominate in the analysis and overestimating drift/ overdrift if opposed winds are dominating. Comparing mean directions for cases with winds from the left and right in relation to individual flight directions also gives biased and spurious results unless there is full variation in wind directions or an equal distribution of crosswinds from left and right. The results of the methodological evaluation and the analysis of the real case indicate that some earlier analyses of wind drift may have to be re-evaluated. (C) 2002 Elsevier Science Ltd. All rights reserved.
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| 49. |
- Harding, Karin C., 1968, et al.
(author)
-
Increased migration in host–pathogen metapopulations can cause host extinction
- 2012
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 298, s. 1-7
-
Journal article (peer-reviewed)abstract
- There are at least two potentially counteracting effects of migration in host–pathogen metapopulations. On the one hand increased migration leads to increased colonization of empty habitats by healthy hosts; on the other hand migrants can carry infectious diseases to susceptible populations. Earlier metapopulation models have found that the beneficial effects of increasing migration (reduced infection) are likely to dominate, and a general recommendation for managers of endangered metapopulations has been to increase connectivity between habitat patches. We extend the model framework to simultaneously allow for (1) Allee effects in host colonization rate, (2) spillover of pathogens from a second host species, and (3) differential colonization success by infected and healthy hosts. We find that the dynamics of a host–pathogen system can be highly sensitive to increased migration rates. Allee effects make host populations vulnerable to spillover of pathogens from other hosts, and metapopulation extinction can emerge from seemingly stable situations of endemic coexistence. Increasing connectivity in endangered metapopulations can be a risky management action unless the details of the biology of the host–pathogen system are known.
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| 50. |
- Harish, Ajith, et al.
(author)
-
Mitochondria are not captive bacteria
- 2017
-
In: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 434, s. 88-98
-
Journal article (peer-reviewed)abstract
- Lynn Sagan's conjecture (1967) that three of the fundamental organelles observed in eukaryote cells, specifically mitochondria, plastids and flagella were once free-living primitive (prokaryotic) cells was accepted after considerable opposition. Even though the idea was swiftly refuted for the specific case of origins of flagella in eukaryotes, the symbiosis model in general was accepted for decades as a realistic hypothesis to describe the endosymbiotic origins of eukaryotes. However, a systematic analysis of the origins of the mitochondrial proteome based on empirical genome evolution models now indicates that 97% of modern mitochondrial protein domains as well their homologues in bacteria and archaea were present in the universal common ancestor (UCA) of the modern tree of life (ToL). These protein domains are universal modular building blocks of modern genes and genomes, each of which is identified by a unique tertiary structure and a specific biochemical function as well as a characteristic sequence profile. Further, phylogeny reconstructed from genome-scale evolution models reveals that Eukaryotes and Akaryotes (archaea and bacteria) descend independently from UCA. That is to say, Eukaryotes and Akaryotes are both primordial lineages that evolved in parallel. Finally, there is no indication of massive inter-lineage exchange of coding sequences during the descent of the two lineages. Accordingly, we suggest that the evolution of the mitochondrial proteome was autogenic (endogenic) and not endosymbiotic (exogenic).
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