| 1. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Critical case stochastic phylogenetic tree model via the Laplace transform
- 2014
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Ingår i: Demonstratio Matematicae. - : De Gruyter. - 0420-1213 .- 2391-4661. ; 47:2, s. 474-481
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Tidskriftsartikel (refereegranskat)abstract
- Birth-and-death models are now a common mathematical tool to describe branching patterns observed in real-world phylogenetic trees. Liggett and Schinazi (2009) is one such example. The authors propose a simple birth-and-death model that is compatible with phylogenetic trees of both in uenza and HIV, depending on the birth rate parameter. An interesting special case of this model is the critical case where the birth rate equals the death rate. This is a non-trivial situation and to study its asymptotic behaviour we employed the Laplace transform. With this we correct the proof of Liggett and Schinazi (2009) in the critical case.
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| 2. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Phylogenetic confidence intervals for the optimal trait value
- 2015
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Ingår i: Journal of Applied Probability. - : Cambridge University Press (CUP). - 0021-9002 .- 1475-6072. ; 52:4, s. 1115-1132
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Tidskriftsartikel (refereegranskat)abstract
- We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree is modelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein-Uhlenbeck process. As a result, the trait values of the n species form a sample with dependent observations. We establish three limit theorems for the sample mean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean is approximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.
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| 3. |
- Sagitov, Serik, 1956, et al.
(författare)
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Interspecies correlation for neutrally evolving traits
- 2012
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 309, s. 11-19
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Tidskriftsartikel (refereegranskat)abstract
- 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 (X-1, ... , X-n) 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 (X-1, ... , X-n). The key ingredient of these formulae is the correlation coefficient between two trait values randomly chosen from (X-1,X- ... , X-n). 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.
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| 4. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Asymptotic properties of quadratic stochastic operators acting on the L1 space
- 2015
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Ingår i: Nonlinear Analysis. - : Elsevier BV. - 0362-546X .- 1873-5215. ; 114, s. 26-39
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Tidskriftsartikel (refereegranskat)abstract
- Quadratic stochastic operators can exhibit a wide variety of asymptotic behaviours andthese have been introduced and studied recently in the l1 space. It turns out that inprinciple most of the results can be carried over to the L1 space. However, due to topologicalproperties of this space one has to restrict in some situations to kernel quadratic stochasticoperators. In this article we study the uniform and strong asymptotic stability of quadratic stochastic operators acting on the L1 space in terms of convergence of the associated (linear)nonhomogeneous Markov chains.
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| 5. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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A consistent estimator of the evolutionary rate
- 2015
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Ingår i: Journal of Theoretical Biology. - 0022-5193 .- 1095-8541. ; 371, s. 69-78
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Tidskriftsartikel (refereegranskat)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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| 6. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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A novel algorithm to reconstruct phylogenies using gene sequences and expression data
- 2014
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Ingår i: International Proceedings of Chemical, Biological & Environmental Engineering; Environment, Energy and Biotechnology III. ; , s. 8-12
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Konferensbidrag (refereegranskat)abstract
- Phylogenies based on single loci should be viewed with caution and the best approach for obtaining robust trees is to examine numerous loci across the genome. It often happens that for the same set of species trees derived from different genes are in conflict between each other. There are several methods that combine information from different genes in order to infer the species tree. One novel approach is to use informationfrom different -omics. Here we describe a phylogenetic method based on an Ornstein–Uhlenbeck process that combines sequence and gene expression data. We test our method on genes belonging to the histidine biosynthetic operon. We found that the method provides interesting insights into selection pressures and adaptive hypotheses concerning gene expression levels.
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| 7. |
- Bartoszek, Krzysztof, 1984, et al.
(författare)
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A phylogenetic comparative method for studying multivariate adaptation
- 2012
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 314, s. 204-215
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Tidskriftsartikel (refereegranskat)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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| 8. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Fast mvSLOUCH: Model comparison for multivariate Ornstein--Uhlenbeck-based models of trait evolution on large phylogenies
- 2023
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Annan publikationabstract
- These are the Supplementary Material, R scripts and numerical results accompanying Bartoszek, Fuentes Gonzalez, Mitov, Pienaar, Piwczyński, Puchałka, Spalik and Voje "Model Selection Performance in Phylogenetic Comparative Methods under multivariate Ornstein–Uhlenbeck Models of Trait Evolution".The four data files concern two datasets. Ungulates: measurements of muzzle width, unworn lower third molar crown height, unworn lower third molar crown width and feeding style and their phylogeny; Ferula: measurements of ratio of canals, periderm thickness, wing area, wing thickness, and fruit mass, and their phylogeny.MethodsUngulatesThe compiled ungulate dataset involves two key components: phenotypic data (Data.csv) and phylogenetic tree (Tree.tre), which consist on the following (full references for the citations presented below are provided in the paper linked to this repository, which also provides further details on the compiled dataset):The phenotypic data includes three continuous variables and one categorical variable. The continuous variables (MZW: muzzle width; HM3: unworn lower third molar crown height; WM3: unworn lower third molar crown width), measured in cm, come from Mendoza et al. (2002; J. Zool.). The categorical variable (FS, i.e. feeding style: B=browsers, G=grazers, M=mixed feeders) is based on Pérez–Barbería and Gordon (2001; Proc. R. Soc. B: Biol. Sci.). Taxonomic mismatches between these two sources were resolved based on Wilson and Reeder (2005; Johns Hopkins University Press). Only taxa with full entries for all these variables were included (i.e. no missing data allowed).The phylogenetic tree is pruned from the unsmoothed mammalian timetree of Hedges et al. (2015; MBE) to only include the 104 ungulate species for which there is complete phenotypic data available. Wilson and Reeder (2005; Johns Hopkins University Press) was used again to resolve taxonomic mismatches with the phenotypic data. The branch lengths of the tree are scaled to unit height and thus informative of relative time.Ferula1) The phenotypic data are divided into two data sets: first containing five continuous variables (no_ME) measured on mericarps (the dispersal unit of fruit in Apiaceae), whereas the second having the same variables together with measurement error (ME; see paper for computational details) for 75 species of Ferula and three species of Leutea. Three continuous variables were measured on anatomical cross sections (ratio_canals_ln – the proportion of oil ducts covering the space between median and lateral ribs [dimensionless], mean_gr_peri_ln_um – periderm (fruit wall) thickness [μm], thick_wings_ln_um – wing thickness [μm]); the remaining two on whole mericarps (Wings_area_ln_mm – wings area [mm2], Seed_mass_ln_mg – seed mass [mg])2) The phylogenetic tree was pruned from the tree obtained from the recent taxonomic revision of the genus (Panahi et al. 2018) to only include the 78 species for which the phenotypic data were generated. This tree and the associated alignment, composed of one nuclear and three plastid markers (Panahi et al. 2018), constituted an input to mcmctree software (Yang 2007) to obtain dated tree using a secondary calibration point for the root based on Banasiak et al.’s (2013) work. The branch lengths of the final tree (Ferula_fruits_tree.txt) were scaled to unit height and thus informative of relative time.The R setup for the manuscript was as follows:R version 3.6.1 (2019-09-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: openSUSE Leap 42.3The exact output can depend on the random seed. However, in the script we have the option of rerunning the analyses as it was in the manuscript, i.e.the random seeds that were used to generate the results are saved, included and can be read in.The code is divided into several directories with scripts, random seeds and result files.1) LikelihoodTestingDirectory contains the script test_rotation_invariance_mvSLOUCH.R that demonstrates that mvSLOUCH's likelihood calculations are rotation invariant. 2) CarnivoransDirectory contains files connected to the Carnivrons' vignette in mvSLOUCH. 2.1) Carnivora_mvSLOUCH_objects_Full.RDataFull output of running the R code in the vignette.With mvSLOUCH is a very bare-minimum subset of this file that allows for the creation of the vignette. 2.2) Carnivora_mvSLOUCH_objects.RData Reduced objects from Carnivora_mvSLOUCH_objects_Full.RData that are included with mvSLOUCH's vignette. 2.3) Carnivora_mvSLOUCH_objects_remove_script.R R script to reduce Carnivora_mvSLOUCH_objects_Full.RData to Carnivora_mvSLOUCH_objects.RData. 2.4) mvSLOUCH_Carnivorans.Rmd The vignette itself. 2.5) refs_mvSLOUCH.bib Bib file for the vignette. 2.6) ScaledTree.png, ScaledTree2.png, ScaledTree3.png, ScaledTree4.png Plots of phylogenetic trees for vignette.3) SimulationStudyDirectory contains all the output of the simulation study presented in the manuscript and scripts that allow for replication (the random number generator seeds are also provided) or running ones own simulation study, and scripts to generate graphs, and model comparison summary. This study was done using version 2.6.2 of mvSLOUCH. If one reruns using mvSLOUCH >= 2.7, then one will obtain different (corrected) values of R2 and an additional R2 version. 4) UngulatesDirectory contains files connected to the "Feeding styles and oral morphology in ungulates" analyses performed for the manuscript. 4.1) Data.csv The phenotypic data includes three continuous variables and one categorical variable. Continuous variables (MZW: muzzle width; HM3: unworn lower third molar crown height; WM3: unworn lower third molar crown width) from Mendoza et al. (2002), measured in cm. Categorical variable (FS, i.e. feeding style: B=browsers, G=grazers, M=mixed feeders) based on Pérez–Barbería and Gordon (2001). Phylogeny pruned from Hedges et al. (2015).Taxonomic mismatches among these sources were resolved based on Wilson and Reeder (2005). Hedges, S. B., J. Marin, M. Suleski, M. Paymer, and S. Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32:835-845. Mendoza, M., C. M. Janis, and P. Palmqvist. 2002. Characterizing complex craniodental patterns related to feeding behaviour in ungulates:a multivariate approach. Journal of Zoology 258:223-246 Pérez–Barbería, F. J., and I. J. Gordon. 2001. Relationships between oral morphology and feeding style in the Ungulata: a phylogenetically controlled evaluation. Proceedings of the Royal Society of London. Series B: Biological Sciences 268:1023-1032. Wilson, D. E., and D. M. Reeder. 2005. Mammal species of the world: A taxonomic and geographic reference. Johns Hopkins University Press, Baltimore, Maryland. 4.2) Tree.tre Ungulates' phylogeny, extracted from the mammalian phylogeny of Hedges, S. B., J. Marin, M. Suleski, M. Paymer, and S. Kumar. 2015. Tree of life reveals clock–like speciation and diversification. Mol. Biol. Evol. 32:835–845. 4.3) OUB.R, OUF.R, OUG.R R scripts for the analyses performed in the manuscript. Different files correspond to different regime setups of the feeding style variable. 4.4) OU1.txt, OUB.txt, OUF.txt, OUG.txt Outputs of the model comparison conducted under the R scripts presented above (4.3). Different files correspond to different regime setups of the feeding style variable. 5) Ferula analysesIn the models_ME directory there are input and output files from the mvSLOUCH analyzes of Ferula data with measurement error included, while in the models_no_ME directory the analyzes of data without measurement error. In each directory, one can find the following files:- input files: Data_ME.csv (with mesurment error) or Data_no_ME.csv (without measurement error) and tree file in Newick format (Ferula_fruits_tree.txt); the trait names in data files are abbreviated as follows: ration_canals – the proportion of oil ducts covering the space between median and lateral ribs, mean_gr_peri – periderm thickness, wings_area – wing area, thick_wings – wing thickness and seed_mass – seed mass,- the results for 8 analyzed models (see Fig. 2 in the main text), each in separate directory named model1, model2 and so on,- each model directory comprises the following files: two R scripts (for analyzes with diagonal and with upper triangular matrix Σyy; each model was run 1000 times), two csv files included information such as number of repetition (i), seed for preliminary analyzes generating starting point (seed_start_point), seed for the main analyses (seed) and AIC, AICc, SIC, BIC, R2 and loglik for each model run (these csv files are sorted according to AICc values), two directories containing results for 1000 analyzes, and two files extracted from these directories showing parameter estimation for the best models (with UpperTri and Diagonal matrix Σyy)
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| 9. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Identifying clusters in Czekanowski's diagram
- 2023
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Ingår i: Mathematica Applicanda. - 1730-2668 .- 2299-4009. ; 51:2, s. 183-198
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Tidskriftsartikel (refereegranskat)abstract
- Visualizing data through Czekanowski’s diagram has as its aim the illus-tration of the relationships between objects. Often, obvious clusters of observationsare directly visible. However, it is not straightforward to precisely delineate theseclusters. This paper presents the development of the package RMaCzek, which nowincludes features for cluster identification in Czekanowski diagrams.
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| 10. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Influenza differentiation and evolution
- 2010
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Ingår i: Acta Physica Polonica B Proceedings Supplement. ; 3:2, s. 417-452
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Konferensbidrag (refereegranskat)abstract
- The aim of the study is to do a very wide analysis of HA, NA and M influenza gene segments to find short nucleotide regions,which differentiate between strains (i.e. H1, H2, ... e.t.c.), hosts, geographic regions, time when sequence was found and combination of time and region using a simple methodology. Finding regions differentiating between strains has as its goal the construction of a Luminex microarray which will allow quick and efficient strain recognition. Discovery for the other splitting factors could shed lighton structures significant for host specificity and on the history of influenza evolution. A large number of places in the HA, NA and M gene segments were found that can differentiate between hosts, regions, time and combination of time and region. Also very good differentiation between different Hx strains can be seen.We link one of our findings to a proposed stochastic model of creation of viral phylogenetic trees.
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