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The between-dataset discordance arises due to the algorithmic characteristics of the two methods.
The 35% discordance arises when our method estimated the presence of multiple genotypes, whereas the MSP typing reported single infections.
This discordance arises from an important difference in the approaches taken for diagnosis of neurocognitive disorders on the one hand, and for measurement of cognition on the other.
Note that Mendelian discordance arises from two possibilities: observation errors of copy numbers of a child or parents, and copy number change that occurs in a child's chromosomes when the chromosomes are transmitted from parents to a child.
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The 24 tumors for which judgment discordance arose for 3 × 3 categories are shown in Table 1.
For these simulated gene trees, we calculated the 'number of deep coalescences' (nDC), a measure of gene tree-population tree discordance arising from incomplete lineage sorting [ 91].
A second explanation is that these discordances arise from the contrasting modes of transmission, evolution, and resolution of these marker-types; this could plausibly explain a lack of isolation-by-distance in the mtDNA, but isolation-by-distance in the allozymes.
STI discordance could arise in a couple as a result of one partner clearing the infection while the other remains infected or in couples where the infection has not yet been transmitted within the couple, or it could be an artifact of failure of the assay to detect infection in one partner.
However, discordance can arise even from the simple fact that some gene is missing in some specific species, resulting in a contraction of internal nodes.
Such discordance may arise from measurement variability, change over time, or because A1C, FPG, and postchallenge glucose each measure different physiological processes.
Such discordance may arise from incomplete lineage sorting, horizontal gene transfer or hybridization, and was observed in our data set when using classical phylogenomics methods such as superalignment strategy or consensus supertree methods.
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