The pairwise homoplasy index
Webb30 jan. 2015 · The pairwise homoplasy index (PHI) was implemented in SplitsTree to test for significant recombination among the isolates. ClonalFrame v1.1 was used to estimate the relative contribution of recombination and mutation in generating polymorphisms among the 45 Bartonella STs. Webb1 juni 2024 · Tests for the pairwise homoplasy index calculated in SplitsTree are provided for the entire dataset and alignments of individual phylogroups. Genotypes are coloured …
The pairwise homoplasy index
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Webb9 okt. 2024 · A pairwise homoplasy index (PHI or Φw) below 0.05 provide evidence for the presence of significant recombination within a dataset. According to the GCPSR analysis, our dataset showed PHI of 1.0, indicating no significant genetic recombination between C. vitis and its sister taxa, C. diplodiella and C. diplodiopsis ( Fig. 3 ). Webb23 juni 2015 · The pairwise homoplasy index (PHI) and split decomposition tree obtained with Splitstree four software were also indicators of recombination events. Phylogenetic analysis. The e-BURST V3 software was used to analyze the relation among STs and to divide them into groups clonal complexes (CC).
Webb1 juli 2024 · Moreover, the pairwise homoplasy index test and the comparison of morphological and ecological characters, have strengthened the fact that reproductive isolation and geographical or host plant barriers to gene flow are absent. This study has also demonstrated that the identification of species in Diaporthe might . Declaration of … Webb1 jan. 2005 · Recombination tests based on the pairwise homoplasy index (PHI, Bruen, et al. 2006), Max χ 2 (Maynard Smith and Smith 1992), and …
WebbPHI test and other tests of recombination The PhiPack software package implements a few tests for recombination and can produce refined incompatibility matrices as well. … Webb15 apr. 2009 · Three showed statistical evidence for recombination (r 2 vs. distance, the Homoplasy test, Neighborhood Similarity Score ... Neighborhood Similarity Score (NSS, Jakobsen and Easteal 1996), and the more recently developed Pairwise Homoplasy Index (PHI, Bruen et al. 2006). Of these six tests of recombination, three were not able to ...
Webb1 apr. 2006 · The term “pairwise homoplasy index” refers to the fact that the refined incompatibility score can be interpreted as the minimum number of convergent or recurrent mutations (homoplasies) necessarily present on any tree describing the …
WebbDistance matrices are used in phylogeny as non-parametric distance methods and were originally applied to phenetic data using a matrix of pairwise distances. These distances are then reconciled to produce a tree (a phylogram, with informative branch lengths).The distance matrix can come from a number of different sources, including measured … chillicothe veterans affairsWebb11 juli 2024 · A pairwise homoplasy index test using a 6-gene dataset (ACT, CAL, GAPDH, GS, ITS, and TUB2) was performed to determine the recombination level between C. ledongense and the closely related... chillicothe vfwWebbPage topic: "Genetic Diversity, Heteroplasmy, and Recombination in Mitochondrial Genomes of Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa - Oxford Academic". Created by: Leroy Patterson. Language: english. grace kelly\u0027s deathWebbTwo other measures of homoplasy may be calculated: the retention index (RI) and the rescaled consistency index (RC). The retention index is calculated as the ratio ( g – s )/( … chillicothe vs londonWebbThe pairwise homoplasy index (PHI) is a model test based on the fact that multiple gene phylogenies will be concordant between species and discordant due to recombination and mutations within a species. The data were analyzed by the pairwise homoplasy index (PHI) test . The test was performed in SplitsTree4 [55,56] as described by Quaedvlieg chillicothe vocational schoolWebbThe results of the pairwise homoplasy index (PHI) test for closely related species of Coniella vitis using both LogDet transformation and splits decomposition. PHI test … chillicothe visitor guideWebbConsistency Index (CI) minimum number of changes divided by the number required on the tree. CI=1 if there is no homoplasy negatively correlated with the number of species sampled. Retention Index (RI) RI = MaxSteps ObsSteps ... Convert the raw data (sequences) to a pairwise distances Try to nd a tree that explains these distances. grace kelly\u0027s lovers