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In addition to assessing and testing the global congruence between trees, ParaFit can assess the contribution of each individual host-parasite association ("links") to this global congruence.
The lack of global congruence between PVs and host trees is also reflected on the existence of several polyphyletic lineages for PVs infecting the same host.
However, none of these three informative parameters (coverage, purity, ambiguity) by itself fully measures the global congruence of the two structures.
In this study, we quantified for the first time the global congruence between the structures of the GO and interactome of a eukaryotic species.
In an attempt to circumvent this argument we decided to use a global congruence [ 28] approach, where both ideologies are used and the resulting phylogenies are cross-corroborated.
However, larger sampling is more likely to decrease and not increase the global congruence between hosts and parasites if host shifts occur between moderately distant hosts as shown for Microbotryum species on Silene.
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The global-fit congruence and individual host-parasite interaction analysis were tested with 100,000 permutations using zokor distance matrix, flea distance matrix, and the zokor-flea association file.
Although the global level of congruence across experiments and populations was generally moderate, the QTL clustering was possible for 30 trait x chromosome combinations (5 traits in 19 different chromosomes) where an effective co-localization of unidirectional (similar sign of additivity) QTLs from at least 5 different data sets was observed.
Linear regression was applied to test the congruence between global clock and local clock.
First, proteins excluded from modules are not analyzed, so a fully global, statistical estimation of congruence is intrinsically impossible.
It is important to stress that congruence between global gene conservation patterns and MLST genotypes does not preclude significant differences in gene content between related strains.
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