The pairwise homoplasy index

Author: mzih

August undefined, 2024

Webb11 apr. 2024 · However, the pairwise homoplasy index did not indicate significant evidence for recombination (mean = 0.6, variance = 1.7E-5, p-value = 0.5), suggesting that the reticulations in the network did not have a strong influence on the evolutionary history of these genogroups. Download: PPT. PowerPoint ... Webb14 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 …

Coniella vitis sp. nov. Is the Common Pathogen of White Rot in …

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 … 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 )/( … small compost bins for sale

Population Genetic Analysis Reveals a High Genetic Diversity in …

Webb4 dec. 2008 · Pairwise Homoplasy Test of Recombination. ... [Tajima 1989] is significantly negative in G. morhua), we also calculated the pairwise homoplasy index, a simple but robust estimator of compatibility among sites (Bruen et al. 2006). In none of these tests was any evidence of recombination detected. Webb7 juli 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 … WebbGlobal 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 ... small component speakers

Unravelling species diversity and pathogenicity of

Pairwise homoplasty index (PHI) statistic test p-values for ...

WebbPairwise homoplasty index (PHI) statistic test p-values for recombination in the varicelloviruses Source publication +7 Phylogenetic and recombination analysis of the … Webb26 okt. 2016 · The results of pairwise homoplasy index (PHI) test of closely related species using both LogDet transformation and splits decomposition. PHI test results (Φw) <0.05 indicate significant... small compost bins for kitchenWebb5 feb. 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 ... sometimes too hot the eye of heaven shines

"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

Biology Free Full-Text Historical Biogeography of Earwigs

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. Webb14 juni 2024 · Intra and inter-continental migration was predicted between Europe and South America, likely associated with the movement of contaminated germplasm. Low …

Did you know?

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 … 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

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 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 ).

Webb18 feb. 2024 · Meanwhile, the pairwise homoplasy index (PHI) [ 40] statistic provided highly significant evidence for recombination within M. luteus species ( p = 0.00). Fig. 4 Recombination in M. luteus. a Phylogenetic network inferred with the concatenation of single-copy core genes. Lines between splits show where recombination has occurred. Webb9 dec. 2024 · Consistency index (ci), retention index (ri), rescaled consistency index (rc) and homoplasy index (hi) are presented for each “character” (taxon); Table S4: Apomorphy list for Figure 2. A double-lined arrow means that the change occurs in all possible reconstructions (i.e., is unambiguous); characters with such changes are uniquely …

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 …

Webb1 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. small compound bowWebb30 juli 2024 · SUPPLEMENTARY INFORMATION Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen Oscar A. MacLean 1,#, Spyros Lytras, Steven Weaver2, Joshua B. Singer1, Maciej F. Boni3, Philippe Lemey4, Sergei L. Kosakovsky Pond2,*, David L. Robertson1,* 1MRC-University of Glasgow Centre … sometimes truth needs a lieWebb25 juni 2024 · Pairwise Homoplasy Index Test and Phylogenetic Network Analysis The concatenated five loci tree was used to infer the occurrence of sexual recombination … small compost bins small gardens small compressed air cylindershttp://www.infogalactic.com/info/Distance_matrices_in_phylogeny sometimes two people need to fall apartWebb29 maj 2014 · Pairwise homoplasy index (PHI) = 3.646 −11, indicating the presence of recombination across all collections. Discussion. No apparent phylogenetic basis for observed morphological variation in F. manipularis. small composter for garden ukWebbPathogenicity 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. small compression springs home depot