2024 Pairwise homoplasy index phi

Pairwise homoplasy index phi

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August undefined, 2024

WebJan 25, 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. WebAug 26, 2024 · The pairwise homoplasy index (PHI) [54] is a model test based on the fact that multiple gene phylogenies will be concordant between species and discor-dant due to recombination and mutations within a species. The data were analyzed by the pairwise homoplasy index (PHI) test [54].

Use of Whole-Genus Genome Sequence Data To Develop a …

WebJul 7, 2024 · A pairwise homoplasy index (PHI) test was performed in SplitsTree (version 4.1.4.4) using the Kimura’s two parameter (K2P) models for low genetic distance datasets. LogDet transformation were applied for the average of nucleotide frequencies and splits decomposition graph options ... WebThe 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 distance from jakarta to bali

Population-level deep sequencing reveals the interplay of clonal …

WebMay 9, 2024 · Low clonality and evidence of genetic recombination were detected from the analysis of linkage disequilibrium and the pairwise homoplasy index (PHI) test for clonality. We show evidence that even if rare (possibly due to losses of sex and meiosis-associated genes) C. graminicola can undergo sexual recombination based on lab assays and … WebThe results of the pairwise homoplasy index (PHI) test revealed no significant genetic recombination (Φw = 1.0) between the closely related C. daliensis and C. poutoensis. The … WebJun 1, 2024 · PHI = Pairwise Homoplasy Index over 40 loci (sig. < 0.05). NA = not applicable.MRCA = Most recent common ancestor (calibrated to 5 million years at MRCA … distance from jamnagar to bhuj

A statistical method to identify recombination in bacterial …

WebOct 6, 2024 · A pairwise homoplasy index (PHI) test revealed no significant recombination event between Cytospora phitsanulokensis and the closely related taxa, C. acaciae, C. italica and C. magnoliae . There was also no significant recombination among Cytospora chiangmaiensis, C. shoreae, C. thailandica, C. diopuiensis and C. xinglongensis . WebAug 19, 2024 · Pairwise homoplasy index (PHI) test The concept of Genealogical Concordance Phylogenetic Species Recognition (GCPSR) was used to analyze … distance from jammu to srinagarWebJul 1, 2013 · Previously, we tested some well-established indirect tests of recombination (linkage disequilibrium vs. distance using D′ and r 2, Homoplasy Test, Pairwise Homoplasy Index, Neighborhood Similarity Score, and Max χ 2) on sequence data derived from the only empirically confirmed case of human mtDNA recombination thus far and demonstrated … distance from jerusalem to gibeon

"WebAug 19, 2024 · Pairwise homoplasy index (PHI) test The concept of Genealogical Concordance Phylogenetic Species Recognition (GCPSR) was used to analyze phylogenetically related but ambiguous species. Taxonomy " - Pairwise homoplasy index phi

Pairwise homoplasy index phi

Debian -- Details of package phipack in sid

WebOct 26, 2016 · Pairwise homoplasy index (PHI) test Figure 4 The results of pairwise homoplasy index (PHI) test of closely related species using both LogDet transformation … WebOct 22, 2014 · START was also used to determine that the GC content in the MLST genes was comparable to that of the whole-genome GC content. To detect recombination within the Y. enterocolitica MLST data, SplitsTree 4.2 was used to compute the pairwise homoplasy index (PHI).

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WebMay 25, 2024 · Our pairwise homoplasy index tests suggest that, among continental datasets, European and North American sequences have shown evidence for the presence of recombination events (P-value = 0.001 and 0.007 respectively); while African, Oceanic, South American, and Asian datasets have shown no recombination events. WebNov 6, 2024 · Pairwise homoplasy index (PHI) test. Application of the PHI test to the concatenated 5-locus sequences (ITS, ACT, GAPDH, CHS-1, and TUB2) revealed that no significant recombination event was observed between C. wanningense and C. cairnsense (Φ W W < 0.0001) was detected among the 26 C. siamense isolates tested in this study …

WebThe PHI recombination test of all the SuHV-1 strains showed (Table 1) statistically significant recombination within the dataset (p = <0.001). ... View in full-text Context 7 WebMay 29, 2014 · The presence or absence of recombination was determined using the pairwise homoplasy index (PHI) implemented in SplitsTree. The level of heterozygosity among individuals within populations (localities) …

WebAug 11, 2024 · A pairwise homoplasy index (PHI or ϕw) below 0.05 provides evidence for the presence of significant recombination within a dataset. According to our analysis, our dataset showed a PHI of 0.99, indicating no significant genetic recombination between D. chiangraiensis and its sister taxa, D. rufocornea and D. irregularis . WebFeb 5, 2016 · Using the alignment of the concatenated genes of each of the five clusters in the second data set as input, we also ran the Pairwise Homoplasy Index (PHI) test for recombination implemented in ...

WebApr 29, 2024 · Indeed, four, highly significant (pairwise homoplasy index test, P < 0.00001) signals of recombination have been revealed at coordinates closely corresponding to the …

WebOct 26, 2016 · Pairwise homoplasy index (PHI) test Figure 4 The results of pairwise homoplasy index (PHI) test of closely related species using both LogDet transformation and splits decomposition. bebe malucoWebDec 28, 2012 · Genetic diversity was largely due to recombination, as demonstrated by a pairwise homoplasy index (PHI=5.35×10(-9)) significantly different from zero (p<0.05). The evolution of standardized association index (I(A)(S)) (all isolates: 0.6088, p<0.05; single representative of STs: 0.4567, p<0.05; and clusters of STs: 0.084, p>0.05), showed an … bebe malote bebe malvado memeWebJun 14, 2024 · Intra and inter-continental migration was predicted between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality and evidence of genetic recombination were detected from the analysis of linkage disequilibrium and the pairwise homoplasy index (PHI) test for clonality. bebe maltraiterWebPHI test and other tests of recombination. The PhiPack software package implements a few tests for recombination and can produce refined incompatibility matrices as well. … distance from jeddah to al ula saudi arabiaWebMay 6, 2024 · A pairwise homoplasy index (PHI) (Bruen et al. 2006) test was performed in SplitsTree4 (Huson 1998; Huson and Bryant 2006) as described by Quaedvlieg et al. . This … distance from jerusalem to judeaWebOct 1, 2024 · The predominantely star-like shape with little reticulation is in principle consistent with a clonally reproducing population. However, the high effective population size, the rapid decay in linkage disequilibrium and the pairwise homoplasy index (Phi; P<0.0001) show strong signatures of recombination distance from jerusalem to hebron