The pairwise homoplasy index

Author: gnao

August undefined, 2024

WebbPathogenicity tests and the pairwise homoplasy index test suggest that C. jiangxiense and C. kahawae subsp. kahawae are two independent species. This study represents the first report of C. alienum and C. cliviae occurring on Camellia sinensis. WebbResults of the pairwise homoplasy index (PHI) test of closely related species using both LogDet transformation and splits decomposition. PHI test results (Φw) <0.05 indicate …

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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 ). WebbThe Consistency Index is nothing else than the Minimum number of steps given your dataset divided by the actual number on your tree (observed steps) (so CI=1 means you … green mountain insurance vt

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Webb25 jan. 2024 · Indeed, the pairwise homoplasy index (PHI) test for recombination was highly significant ( p value <0.001) when we performed split-decomposition network analysis using Split tree (Huson 1998 ). This indicates conflicting phylogenetic signals that are possibly attributed to recombination among viral genomes. WebbThe offspring displayed clear evidence of recombination on a genetic level as shown in the variations observed between banding patterns in the amplified fragment length polymorphism. Also a net-like and reticulated NeighborNet was observed and the pairwise homoplasy index test for recombination supported the presence of recombination (P = 0 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 … flying witch on broom halloween decoration

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WebbTwo 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 )/( … Webb9 maj 2024 · pairwise homoplasy index RAD-Seq restriction site-associated DNA sequencing pairwise homoplasy index SNPs single-nucleotide polymorphisms WGS whole-genome sequencing. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. green mountain investments llcWebb14 feb. 2024 · Morphological studies and multilocus phylogenetic analyses with the concatenated sequences of the internal transcribed spacer, glyceraldehyde-3-phosphate dehydrogenase, chitin synthase, actin, beta-tubulin, calmodulin, and the intergenic region between Apn2 and Mat1-2-1, as well as a pairwise homoplasy index, test placed the … green mountain insurance company ma

"Webb28 feb. 2024 · Results of the pairwise homoplasy index (PHI) test indicated significant recombination between P. byssoides and P. celtidis. Therefore, P. celtidis has been synonymized under P. byssoides. In addition, we re-illustrated and studied the type specimen of the sexual genus Bambusistroma. " - The pairwise homoplasy index

The pairwise homoplasy index

Webb14 juni 2024 · Intra and inter-continental migration was predicted between Europe and South America, likely associated with the movement of contaminated germplasm. Low … WebbMolecular Evolutionary Analysis of Potato Virus Y Infecting Potato Based on the VPg Gene. 杂志Frontiers in Microbiology，IF：5.640/Q1. 摘要：马铃薯Y病毒（PVY）是一种重要的植物病原体，感染茄科作物，对全球马铃薯和烟草生产造成重大损失。PVY的植物病理学和分子生物学的某些方面已得到深入研究，但对该病毒的进化动力学 ...

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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). Webb11 mars 2024 · 采用两个重组方法分析，先应用SplitsTree 构建系统发育网络并计算成对同质性指数（pairwise homoplasy index, PHI查)，随后应用RDP软件包中的7种方 …

Webb2013; Chan et al. 2013). Index Fungorum (www.indexfungorum.org) has listed 126 names under this genus. In China, taxonomic research on Amauroderma began with Teng, who recorded 10 species (Teng 1936, 1939, 1963). Later Zhao et al. (1979, 1983, 1984) and Zhao & Zhang (1986, 1987a,b, 2000) reported 20 species, nine of which were new. WebbRecombination analyses To detect recombination within housekeeping genes the FW References test (pairwise homoplasy index) was performed using Split- sTree program (Huson and Bryant, 2006). To evaluate the Bruen, T.C., Philippe, H., and Bryant, D. …

Webb5 dec. 2024 · Pairwise homoplasy index test. Application of the PHI test of the concatenated six-locus sequences revealed that no significant recombination event was observed between M. xinjiangensis and M. perniciosa (Фw = 0.99). Taxonomy. The isolates were assigned to three species depending on morphology and multilocus phylogeny. Webb1 juli 2013 · The Homoplasy Test is used to examine whether there are more homoplasies on a phylogenetic tree than expected under a model of clonal inheritance, where a homoplasy is the co-occurrence of a polymorphism on separate branches of the tree ( Smith and Smith 1998 ).

Webb11 mars 2014 · The dataset was evaluated for the presence of recombination using the pairwise homoplasy index (PHI) test (Bruen et al. 2006) implemented by SplitsTree, where the minimum number of homoplasies required to describe the genealogical history between sites was calculated.

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. flying witch weathervaneWebb17 dec. 2024 · Recombination within FOSC was tested using the pairwise homoplasy index and divergence ages were estimated by molecular dating. We called SNPs from … flying witch wikiWebb16 aug. 2016 · The Pairwise Homoplasy Index (PHY) test implemented in SplitsTree v. 4.13.1 and the pairwise linkage disequilibrium (D) available in the software DnaSP v. 5.10 were also used to detect the presence of recombination. … green mountain internationalWebb15 sep. 2024 · A more extreme problem of interpretation of pairwise homoplasies arises in some methods for analyzing electrophoretic data. Suppose that each of three terminal taxa A, B, and C is fixed for a different allele at some locus, and that these taxa are related through an unresolved tree with common ancestor X. flying with 20k cashWebb1 juni 2024 · Recombination within FOSC was tested using the pairwise homoplasy index and divergence ages were estimated by molecular dating. We called SNPs from assembled genomes using a k-mer approach and tested for significant linkage disequilibrium as an indication of PCE. green mountain island coconut coffee baggedWebbThe 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 green mountain iowa real estateWebb28 sep. 2011 · Statistical significance of the proportion of variance associated with the fixation index, F ST was determined through permutation tests against a null distribution generated from the data in GenAlEx. The number of migrants (N m) between each population pair was calculated from genetic distances through the equation N m = (1 − F … green mountain iowa map