| 1. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
-
Fast mvSLOUCH: Model comparison for multivariate Ornstein--Uhlenbeck-based models of trait evolution on large phylogenies
- 2023
-
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)
|
|
| 2. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
-
Model Selection Performance in Phylogenetic Comparative Methods Under Multivariate Ornstein–Uhlenbeck Models of Trait Evolution
- 2023
-
Ingår i: Systematic Biology. - : OXFORD UNIV PRESS. - 1063-5157 .- 1076-836X. ; 72:2, s. 275-293
-
Tidskriftsartikel (refereegranskat)abstract
- The advent of fast computational algorithms for phylogenetic comparative methods allows for considering multiple hypotheses concerning the co-adaptation of traits and also for studying if it is possible to distinguish between such models based on contemporary species measurements. Here we demonstrate how one can perform a study with multiple competing hypotheses using mvSLOUCH by analyzing two data sets, one concerning feeding styles and oral morphology in ungulates, and the other concerning fruit evolution in Ferula (Apiaceae). We also perform simulations to determine if it is possible to distinguish between various adaptive hypotheses. We find that Akaikes information criterion corrected for small sample size has the ability to distinguish between most pairs of considered models. However, in some cases there seems to be bias towards Brownian motion or simpler Ornstein-Uhlenbeck models. We also find that measurement error and forcing the sign of the diagonal of the drift matrix for an Ornstein-Uhlenbeck process influences identifiability capabilities. It is a cliche that some models, despite being imperfect, are more useful than others. Nonetheless, having a much larger repertoire of models will surely lead to a better understanding of the natural world, as it will allow for dissecting in what ways they are wrong. [Adaptation; AICc; model selection; multivariate Ornstein-Uhlenbeck process; multivariate phylogenetic comparative methods; mvSLOUCH.]
|
|
| 3. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
-
Identifying clusters in Czekanowski's diagram
- 2023
-
Ingår i: Mathematica Applicanda. - Warsaw, Poland : Polskie Towarzystwo Matematyczne. - 1730-2668 .- 2299-4009. ; 51:2, s. 183-198
-
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.
|
|
| 4. |
- Bartoszek, Krzysztof, 1984-
(författare)
-
Limit distribution of the quartet balance index for Aldous’s $(\beta \ge 0)$-model
- 2020
-
Ingår i: Applicationes Mathematicae. - : Institute of Mathematics, Polish Academy of Science. - 1233-7234 .- 1730-6280. ; 6, s. 29-44
-
Tidskriftsartikel (refereegranskat)abstract
- This paper builds on T. Martínez-Coronado, A. Mir, F. Rosselló and G. Valiente’s 2018 work, introducing a new balance index for trees. We show that this balance index, in the case of Aldous’s $(\beta \ge 0)$-model, converges weakly to a distribution that can be characterized as the fixed point of a contraction operator on a class of distributions.
|
|
| 5. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
-
“Old Techniques for New Times”: the RMaCzek package for producing Czekanowski’s diagrams
- 2020
-
Ingår i: Biometrical Letters. - : Polskie Towarzystwo Biometryczne. - 1896-3811. ; 57:2, s. 89-118
-
Tidskriftsartikel (refereegranskat)abstract
- Inspired by the MaCzek Visual Basic program we provide an R package, RMaCzek, that produces Czekanowski’s diagrams. Our package permits any seriation and distance method the user provides. In this paper we focus on the "OLO" and "QAP_2SUM" methods from the seriation package. We illustrate the possibilities of our package with three anthropological studies, one socioeconomic study and a phylogenetically motivated simulation study.
|
|
| 6. |
- Bartoszek, Krzysztof, 1984-
(författare)
-
Revisiting the Nowosiółka skull with RMaCzek
- 2023
-
Ingår i: Mathematica Applicanda. - : Polish Mathematical Society. - 1730-2668 .- 2299-4009. ; 50:2, s. 255-266
-
Tidskriftsartikel (refereegranskat)abstract
- One of the first fully quantitative distance matrix visualization methods was proposed by Jan Czekanowski at the beginning of the previous century. Recently, a software package, RMaCzek, was made available that allows for producing such diagrams in R. Here we reanalyze the original data that Czekanowski used for introducing his method, and in the accompanying code show how the user can specify their own custom distance functions in the package.
|
|
| 7. |
|
|
| 8. |
- Kiang, Woodrow Hao Chi, 1993-
(författare)
-
Uncertainty Estimation in Models of Multivariate Trait Evolution on Given Phylogenies
- 2024
-
Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Phylogenetic comparative methods are a set of statistical methods that model the evolutionary history of species, especially in the context where one has data on certain traits of related extant species that have evolved over a phylogenetic tree in accordance to an underlying stochastic process. This thesis presents a Hessian-based closed-form asymptotic confidence region that covers a wide family of Gaussian continuous-trait evolution models; the result has been implemented in an R package. Also, some analyses have been done on the simpler Brownian Motion and Ornstein-Uhlenbeck process cases; and this leads to novel exact confidence regions for the Brownian Motion’s parameters and a closed-form ’partial’ unbiased estimator for the Ornstein-Uhlenbeck process’ varaince-covariance matrix when other parameters are given. The thesis contains two papers. Paper I is an applied work that uses discrete-trait speciation and extinction model to investigate early spread of COVID-19; it shows that it is possible to detect statistical signals of inter-continental spread of the virus from a very noisy world-wide phylogeny. Paper II is a more mathematical work that derived the closed-form formulae for the Hessian matrix of a wide family of Gaussian-process-based multivariate continuous-trait PCM models; accompanying with the Paper I have developed an R package called glinvci, publicly available on The Comprehensive R Archive Network (CRAN), that can compute Hessian-based confidence regions for these models while at the same time allowing users to have missing data and multiple evolutionary regimes.
|
|
| 9. |
- Tahir, Daniah, et al.
(författare)
-
Using multitype branching models to analyze bacterial pathogenicity
- 2020
-
Ingår i: Mathematica Applicanda. - Warsaw, Poland : Polskie Towarzystwo Matematyczne. - 1730-2668 .- 2299-4009. ; 48:1, s. 59-86
-
Tidskriftsartikel (refereegranskat)abstract
- We apply multitype, continuous time, Markov branching models to study pathogenicity in E. coli, a bacterium belonging to the genus Escherichia. First, we examine briefly, the properties of multitype branching processes and we also survey some fundamental limit theorems regarding the behavior of such models under various conditions. These theorems are then applied to discrete, state dependent models, in order to analyze pathogenicity in a published clinical data set consisting of 251 strains of E. coli. We use well established methods, incorporating maximum likelihood techniques, to estimate speciation rates as well as the rates of transition between different states of the models. From the analysis, we not only derive new results, but we also verify some preexisting notions about virulent behavior in bacterial strains.
|
|
