Phylogenetic complexity of the Kimura 3-parameter model

Michałek, Mateusz; Ventura, Emanuele

doi:10.1016/j.aim.2018.11.021

Cited by 7 publications

(4 citation statements)

References 41 publications

(53 reference statements)

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“…1.10 (Guindon and Gascuel, 2003;Darriba et al, 2012). The three-parameter model 2 with gamma distribution (TPM2+G) (Michalek and Ventura, 2019) was chosen for the 18S rDNA sequences and Tamura-Nei with gamma distribution (TrN +G) (Tamura and Nei, 1993) for the cox1. Phylogenetic trees were generated using the package Bayesian Evolutionary Analysis by Sampling Trees (BEAST v1.10.4) (Bouckaert et al, 2019), and an.xml input file was created with Bayesian Evolutionary Analysis Utility (BEAUti v1.10.4) with 10 7 Markov chain Monte Carlo (MCMC) generations and a burn-in length of 10 3 .…”

Section: Phylogenetic and Species Delimitation Analysesmentioning

confidence: 99%

Elucidating Spirocerca lupi spread in the Americas by using phylogenetic and phylogeographic analyses

Alfaro-Segura,

Robleto-Quesada,

Montenegro-Hidalgo

et al. 2023

Front. Parasitol.

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Spirocerca lupi is a parasitic nematode of domestic and wild canids of the world. This nematode induces esophageal spirocercosis and may eventually lead to carcinomas, aortic aneurisms, and death of the animal. Two genotypes of S. lupi have been described based on specimens from Europe, Asia, Africa, and Oceania, but no profound analysis has been conducted with S. lupi from the Americas. To study this, S. lupi specimens isolated from domestic dogs from Mexico, Costa Rica, and the United States, were molecularly characterized using 18S rDNA and cox1 fragments. Bayesian inference (BI) phylogenetic trees, Templeton-Crandall-Sing (TCS) haplotype networks and Principal coordinate analysis on nucleotide distances were constructed for each locus separately. In addition, a phylogeographic study using a fragment of the cox1 gene was used to infer the evolutionary history of the genus. BI cox1 trees grouped S. lupi from the Americas in genotype 1, together with Israeli specimens, and showed a high nucleotide identity with those worms. In the TCS network, American specimens clustered next to Israeli S. lupi. Furthermore, the 18S rDNA gene fragment separated Costa Rican worms from African, Asian, and European specimens and other species of the family Spiruridae. Interestingly, the phylogeographic analysis suggested that the origin of S. vulpis was in Europe, and it later diverged into S. lupi that spread first to Africa, then to Asia and finally to the Americas. Therefore, we suggest that the worms from the American continent might have originated from Asia by dispersion of infected intermediate, paratenic or definitive hosts.

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Section: Phylogenetic and Species Delimitation Analysesmentioning

confidence: 99%

Elucidating Spirocerca lupi spread in the Americas by using phylogenetic and phylogeographic analyses

Alfaro-Segura,

Robleto-Quesada,

Montenegro-Hidalgo

et al. 2023

Front. Parasitol.

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“…Codon positions included in the analyses were 1st + 2nd + 3rd + Noncoding. During phylogenetic analysis of the three genes, Kimura 3 parameter and Jukes-Cantor evolutionary models were followed [36,37]. The models assumed the rates and patterns of substitution were uniform among the four nucleotide sites.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Molecular Phylogeny of Selected Kenyan Eucalyptus Species Inferred from MatK, rbcL and TrnL-F Genes and Their Suitability for Power Transmission Poles

et al. 2022

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Genus Eucalyptus belongs to the family Myrtaceae and consists of more than 900 species, various hybrids and varieties. The major species that are grown in Kenya are Eucalyptus grandis, E. globulus, E. saligna and E. camaldulensis. Most Eucalyptus species are highly dependent on rainfall and this is challenged by climatic changes owing to global warming making it difficult to effectively match the availability of mature trees and the market demand especially for use as power transmission poles. With the widespread availability of other naturally occurring Eucalyptus species such as E. camaldulensis and E. globulus, it becomes important to determine the genetic diversity and to analyze the phenotypic traits of these species for suitability as power transmission poles in order to counter the overdependence on E. grandis. Phenotypic traits investigated included measuring total tree height and diameter at breast height (DBH), while molecular data were obtained from sequencing MatK, rbcL and TrnL-F genes from selected species and evolutionary analyses such as nucleotide substitution rates, base composition disparity indices, evolutionary divergence, nucleotide diversity indices and phylogeny construction were conducted in MEGA 11. Significant differences in DBH and height among Eucalyptus species were observed when the phenotypic data were subjected to ANOVA. In this study, E. robusta, E. paniculata, E. maculata, E. dunnii, E. camaldulensis and E. citriodora are fit to be used as power transmission poles but they are limited by their short height. However, E. tereticornis and E. glaucina have the desired DBH and height and hence can be used as substitutes for E.grandis. Generally, the molecular phylogeny study has shown that the studied Eucalyptus species are closely related and form various monophyletic clades which can be attributed to the short genetic distances, low substitution rates, low nucleotide bias disparity indices and low diversity scores. Further phylogenetic and gene expression studies involving more Eucalyptus species are needed to better understand Eucalyptus phylogeny, and diversity and identify species with similar genetic make-up to that of E. grandis which has been used extensively for the provision of electricity transmission poles.

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“…As described above, we are interested in the geometry of network-based Markov models, in particular, their dimensions. Such work is along the lines of Sturmfels and Sullivant ( 2005 ), Eriksson et al ( 2005 ), Allman and Rhodes ( 2007 ), Allman and Rhodes ( 2008 ), Casanellas and Fernández-Sánchez ( 2008 ), Zwiernik and Smith ( 2011 ), Casanellas and Fernández-Sánchez ( 2011 ), Michałek ( 2011 ), Casanellas et al ( 2017 ), Michałek and Ventura ( 2019 ), and Casanellas et al ( 2021 ), which study the geometry of tree-based Markov models. Indeed, by moving to and taking Zariski closures, images of the parameterization maps correspond to algebraic varieties whose study can aid in model selection (see Pachter and Strumfels ( 2005 ), Drton et al ( 2009 ), and Sullivant ( 2018 ) for discussions).…”

Section: Introductionmentioning

confidence: 99%

Dimensions of Level-1 Group-Based Phylogenetic Networks

Gross,

Krone,

Martin

2024

Bull Math Biol

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Phylogenetic networks represent evolutionary histories of sets of taxa where horizontal evolution or hybridization has occurred. Placing a Markov model of evolution on a phylogenetic network gives a model that is particularly amenable to algebraic study by representing it as an algebraic variety. In this paper, we give a formula for the dimension of the variety corresponding to a triangle-free level-1 phylogenetic network under a group-based evolutionary model. On our way to this, we give a dimension formula for codimension zero toric fiber products. We conclude by illustrating applications to identifiability.

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Phylogenetic complexity of the Kimura 3-parameter model

Abstract: In algebraic statistics, the Kimura 3-parameter model is one of the most interesting and classical phylogenetic models. We prove that the ideals associated to this model are generated in degree four, confirming a conjecture by Sturmfels and Sullivant.

Cited by 7 publications

References 41 publications

Elucidating Spirocerca lupi spread in the Americas by using phylogenetic and phylogeographic analyses

Elucidating Spirocerca lupi spread in the Americas by using phylogenetic and phylogeographic analyses

Molecular Phylogeny of Selected Kenyan Eucalyptus Species Inferred from MatK, rbcL and TrnL-F Genes and Their Suitability for Power Transmission Poles

Dimensions of Level-1 Group-Based Phylogenetic Networks

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