| 1. |
- Bartoszek, Krzysztof, et al.
(författare)
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Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling
- 2018
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Ingår i: PloS Computational Biology. - : PUBLIC LIBRARY SCIENCE. - 1553-734X .- 1553-7358. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The Binary State Speciation and Extinction (BiSSE) model is a branching process based model that allows the diversification rates to be controlled by a binary trait. We develop a general approach, based on the BiSSE model, for predicting pathogenicity in bacterial populations from microsatellites profiling data. A comprehensive approach for predicting pathogenicity in E. coli populations is proposed using the state-dependent branching process model combined with microsatellites TRS-PCR profiling. Additionally, we have evaluated the possibility of using the BiSSE model for estimating parameters from genetic data. We analyzed a real dataset (from 251 E. coli strains) and confirmed previous biological observations demonstrating a prevalence of some virulence traits in specific bacterial sub-groups. The method may be used to predict pathogenicity of other bacterial taxa.
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| 2. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations
- 2017
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 429, s. 35-45
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Tidskriftsartikel (refereegranskat)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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| 3. |
- Görgens, Maik, 1984-, et al.
(författare)
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Gaussian processes, bridges and membranes extracted from selfsimilar random fields
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We consider the class of selfsimilar Gaussian generalized random fields introduced by Dobrushin in 1979. These fields are indexed by Schwartz functions on Rd and parametrized by a self-similarity index and the degree of stationarity of their increments. We show that such Gaussian fields arise in explicit form by letting Gaussian white noise, or Gaussian random balls white noise, drive a shift and scale shot-noise mechanism on Rd, covering both isotropic and anisotropic situations. In some cases these fields allow indexing with a wider class of signed measures, and by using families of signed measures parametrized by the points in euclidean space we are able to extract pointwise defined Gaussian processes, such as fractional Brownian motion on Rd. Developing this method further, we construct Gaussian bridges and Gaussian membranes on a finite domain, which vanish on the boundary of the domain.
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| 4. |
- Hart, Michael W., et al.
(författare)
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Positive selection on human gamete-recognition genes
- 2018
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Coevolution of genes that encode interacting proteins expressed on the surfaces of sperm and eggs can lead to variation in reproductive compatibility between mates and reproductive isolation between members of different species. Previous studies in mice and other mammals have focused in particular on evidence for positive or diversifying selection that shapes the evolution of genes that encode sperm-binding proteins expressed in the egg coat or zona pellucida (ZP). By fitting phylogenetic models of codon evolution to data from the 1000 Genomes Project, we identified candidate sites evolving under diversifying selection in the human genes ZP3 and ZP2. We also identified one candidate site under positive selection in C4BPA, which encodes a repetitive protein similar to the mouse protein ZP3R that is expressed in the sperm head and binds to the ZP at fertilization. Results from several additional analyses that applied population genetic models to the same data were consistent with the hypothesis of selection on those candidate sites leading to coevolution of sperm- and egg-expressed genes. By contrast, we found no candidate sites under selection in a fourth gene (ZP1) that encodes an egg coat structural protein not directly involved in sperm binding. Finally, we found that two of the candidate sites (in C4BPA and ZP2) were correlated with variation in family size and birth rate among Hutterite couples, and those two candidate sites were also in linkage disequilibrium in the same Hutterite study population. All of these lines of evidence are consistent with predictions from a previously proposed hypothesis of balancing selection on epistatic interactions between C4BPA and ZP3 at fertilization that lead to the evolution of co-adapted allele pairs. Such patterns also suggest specific molecular traits that may be associated with both natural reproductive variation and clinical infertility.
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| 5. |
- Kaj, Ingemar, 1957-, et al.
(författare)
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A Wright-Fisher graph model and the impact of directional selection on genetic variation
- 2024
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Ingår i: Theoretical Population Biology. - : Elsevier. - 0040-5809 .- 1096-0325. ; 159, s. 13-24
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Tidskriftsartikel (refereegranskat)abstract
- We introduce a multi-allele Wright-Fisher model with mutation and selection such that allele frequencies at a single locus are traced by the path of a hybrid jump-diffusion process. The state space of the process is given by the vertices and edges of a topological graph, i.e. edges are unit intervals. Vertices represent monomorphic population states and positions on the edges mark the biallelic proportions of ancestral and derived alleles during polymorphic segments. In this setting, mutations can only occur at monomorphic loci. We derive the stationary distribution in mutation-selection-drift equilibrium and obtain the expected allele frequency spectrum under large population size scaling. For the extended model with multiple independent loci we derive rigorous upper bounds for a wide class of associated measures of genetic variation. Within this framework we present mathematically precise arguments to conclude that the presence of directional selection reduces the magnitude of genetic variation, as constrained by the bounds for neutral evolution.
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| 6. |
- Kaj, Ingemar, 1957-, et al.
(författare)
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Analysis of diversity-dependent species evolution using concepts in population genetics
- 2021
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Ingår i: Journal of Mathematical Biology. - : Springer Nature. - 0303-6812 .- 1432-1416. ; 82:4
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Tidskriftsartikel (refereegranskat)abstract
- In this work, we consider a two-type species model with trait-dependent speciation, extinction and transition rates under an evolutionary time scale. The scaling approach and the diffusion approximation techniques which are widely used in mathematical population genetics provide modeling tools and conceptual background to assist in the study of species dynamics, and help exploring the analogy between trait-dependent species diversification and the evolution of allele frequencies in the population genetics setting. The analytical framework specified is then applied to models incorporating diversity-dependence, in order to infer effective results from processes in which the net diversification of species depends on the total number of species. In particular, the long term fate of a rare trait may be analyzed under a partly symmetric scenario, using a time-change transform technique.
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| 7. |
- Kaj, Ingemar, 1957-, et al.
(författare)
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Convergence to fractional Brownian motion and to the Telecom process : the integral representation approach
- 2008
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Ingår i: In and Out of Equilibrium 2. - Basel : Birkhäuser Verlag. - 9783764387853 ; , s. 383-427
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Bokkapitel (refereegranskat)abstract
- It has become common practice to use heavy-tailed distributions in order to describe the variations in time and space of network traffic workloads. The asymptotic behavior of these workloads is complex; different limit processes emerge depending on the specifies of the work arrival structure and the nature of the asymptotic scaling. We focus on two variants of the infinite source Poisson model and provide a coherent and unified presentation of the scaling theory by using integral representations. This allows us to understand physically why the various limit processes arise.
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| 8. |
- Kaj, Ingemar, 1957-
(författare)
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Probabilistic analysis of hierarchical cluster protocols for wireless sensor networks
- 2009
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Ingår i: Network Control and Optimization. - Berlin Heidelberg : Springer Verlag. - 9783642104053 ; , s. 137-151
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Konferensbidrag (refereegranskat)abstract
- Wireless sensor networks are designed to extract data from the deployment environment and combine sensing, data processing and wireless communication to provide useful information for the network users. Hundreds or thousands of small embedded units, which operate under low-energy supply and with limited access to central network control, rely on interconnecting protocols to coordinate data aggregation and transmission. Energy efficiency is crucial and it has been proposed that cluster based and distributed architectures such as LEACH are particularly suitable. We analyse the random cluster hierarchy in this protocol and provide a solution for low-energy and limited-loss optimization. Moreover, we extend these results to a multi-level version of LEACH, where clusters of nodes again self-organize to form clusters of clusters, and so on.
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| 9. |
- Kaj, Ingemar, 1957-, et al.
(författare)
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Retransmission performance in a stochastic geometric cellular network model
- 2024
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Ingår i: Performance evaluation (Print). - : Elsevier. - 0166-5316 .- 1872-745X. ; 165
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Tidskriftsartikel (refereegranskat)abstract
- Suppose sender-receiver transmission links in a downlink network at a given data rate are subject to fading, path loss, and inter -cell interference, and that transmissions either pass, suffer loss, or incur retransmission delay. We introduce a method to obtain the average activity level of the system required for handling the buffered work and from this derive the resulting coverage probability and key performance measures. The technique involves a family of stationary buffer distributions which is used to solve iteratively a nonlinear balance equation for the unknown busy -link probability and then identify throughput, loss probability, and delay. The results allow for a straightforward numerical investigation of performance indicators, are in special cases explicit and may be easily used to study the trade-off between reliability, latency, and data rate.
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| 10. |
- Kaj, Ingemar, 1957-, et al.
(författare)
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Stochastic equations and limit results for some two-type branching models
- 2019
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Ingår i: Statistics and Probability Letters. - : Elsevier BV. - 0167-7152 .- 1879-2103. ; 150, s. 35-46
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Tidskriftsartikel (refereegranskat)abstract
- A class of binary state, asymmetric, continuous time Markov branching processes are analyzed under supercritical conditions. Stochastic equations are provided, and limit results for the long time asymptotics as well as for the behavior of the model under rescaling are reviewed. Extensions are presented for model variations, such as population size dependence, with the purpose of promoting further use of these models for applications.
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