The pairwise homoplasy index

Author: vajl

August undefined, 2024

Webb26 okt. 2016 · Pairwise homoplasy index (PHI) test. C. camelliae). No significant recombination events were observed between C. wuxiense and phylogenetically related … 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 …

How to count the homoplasy event given a tree? ResearchGate

Webb14 juni 2024 · Intra and inter-continental migration was predicted between Europe and South America, likely associated with the movement of contaminated germplasm. Low … Webb17 dec. 2024 · Recombination within FOSC was tested using the pairwise homoplasy index and divergence ages were estimated by molecular dating. We called SNPs from … real and fiction

Diaporthe amygdali, a species complex or a complex species?

Webb28 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 … 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. … 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 how to tame a mesopithecus

Fusarium rosicola sp. nov. causing vascular wilt on Rosa chinensis

Results of the pairwise homoplasy index (PHI) test of closely …

WebbMorphological studies and multi-locus phylogenetic analyses with the concatenated sequences of internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), chitin synthase (CHS-1), actin (ACT), beta-tubulin (TUB2), calmodulin (CAL), and the intergenic region between Apn2 and Mat1-2-1 (ApMat) as well … 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. real and fancied differentiationWebbGlobal genome pairwise sequence alignments were prepared with mVista LAGAN [45] and multi-reticulate analyses performed using SplitsTree4 [46] with an uncorrected P characters transformation model, excluding all gap sites. The multi-reticulate networks indicate recombination events. A recombination pairwise homoplasy index ... how to tame a lava cat in minecraft

"Webb29 apr. 2024 · When the HD regions are considered separately, the pairwise distances vary in a broader range: from zero to 11.6% ( ND4 and ND5 regions), between 0.7–6.4% ( COI region), and up to 12.9% (CR region) ( Table 1 ). On the interspecific level, the pairwise distance fluctuations are even more pronounced. " - The pairwise homoplasy index

The pairwise homoplasy index

ISSN (print) 0093-4666 © 2015. Mycotaxon, Ltd. ISSN (online

Webb19 aug. 2024 · Pairwise homoplasy index (PHI) test The concept of Genealogical Concordance Phylogenetic Species Recognition (GCPSR) was used to analyze … 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 ...

Did you know?

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. Webb4 apr. 2024 · Pairwise values of both indices were low or moderately high, ranging from 0 to 0.163 (F ST). Many comparisons were statistically significant even after correction for multiple testing, mainly those involving Lev and Nor. Low and not significant values for comparisons, especially involving Sardinian samples, highlighted the lack of significant …

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 … 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 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 ). 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.

Webbpairwise homoplasy index; PDA potato dextrose agar; SSU small subunit ribosomal RNA gene; YMA yeast malt agar. Table 3. Data used for phylogenetic analysis in this study and their corresponding GenBank accession numbers. Type species are denoted by T. Sequences derived in this study are shown in bold.

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 ). real and fiction kölnWebbPathogenicity 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. how to tame a mek arkWebbPathogenicity 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. In addition, our study demonstrated that the combined how to tame a megaloceros in arkWebbDistance 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 … real and fake gameWebbRecombination 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. … real and imaginary partsWebbThe 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 how to tame a megaloceros arkWebb11 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... how to tame a moschops