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Septoria_krystynae_ML_1000.pdf

Version 2 2022-10-14, 15:55
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posted on 2022-10-14, 15:55 authored by Katarzyna Janik-SupersonKatarzyna Janik-Superson, Dominik Strapagiel, Małgorzata Ruszkiewicz-Michalska, Sebastian Piskorski, Ewa Zapora

Phylogenetic tree with the new Septoria krystynae fungal species, constructed by the maximum likelihood (ML) method using a concatenated alignment data set of the partial sequences of the translation elongation factor 1-α (tef1), β-tubulin (tub2), 28S nuc rRNA gene (LSU, large subunit 28S), internal transcribed spacer regions and intervening 5.8S nuc rRNA gene (ITS) of the nuc rDNA operon and actin (actA) genes. The K2+G+I (Kimura 2-parameter model with Gamma distribution and evolutionarily invariable certain fraction of sites) model that best suits the dataset has been selected. BIC scores (Bayesian Information Criterion) was 24049.04 and AICc value (Akaike Information Criterion, corrected) was 23485.62. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analysed. The evolutionary history was inferred by using the Maximum Likelihood method and Kimura 2-parameter model [ Kimura M. 1980]. The tree with the highest log likelihood (-11695.07) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (4 categories (+G, parameter = 0.8031)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 64.74% sites). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. This analysis involved 31 nucleotide sequences, with Caryophylloseptoria lychnidis CBS 109099 as a outgroup [Tab. xxx]. Codon positions included were 1st+2nd+3rd+Noncoding. There were a total of 2299 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [Kumar S, Stecher G, Li M, et al. 2018.]

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Subsidy of the Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz

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