Further, root divergence time estimates returned by r8s do not show confidence intervals in table 1, since r8s only assesses the sampling variance of node times due to stochastic errors in branch lengths due to finite sequence length (it does this via the bootstrap) and does not include the effect of stochastic variation of evolutionary rate.
Minor topological and distance inconsistencies may occur across segments in phylogenies even without a reassortment event, due to stochastic errors and limitations in distance estimation methods.
This is in line with expectation, since a possible advantage of kit-based DNA extraction protocols is that variation due to stochastic error should be minimized.
Although older estimates were obtained when calibrated with recent nodes, these outlying values are likely due to stochastic error associated with using shallowly placed nodes for deep extrapolations [ 26, 27].
A wide variety of analytical factors can lead to failure to accurately infer a gene tree; these can be either due to stochastic error (e.g., insufficient sequence length or taxon samples) or due to systematic error (in case of departure from model assumptions, Jeffroy et al. 2006).
In our experience with single-molecule methylation analyses (23, 43), the rate of single CpG errors which can be due to stochastic methylation errors (biological variation) or bisulfite conversion errors (technical variation) is in the order of several (0 5) percent, depending on the analyzed gene and cell type.
The average error rate among loci due to allelic dropout (E1) was estimated to be low (0.02 mean, 0.01 SD), and the error rate due to stochastic genotyping errors (E2) was even lower (0.004 mean, 0.001 SD).
Considering the enormous epigenetic variability due to stochastic methylation errors or extrinsic variations during post-zygotic genome reprogramming,,,, we cannot rule out the possibility that epimutations in the affected twin in genes other than those studied are responsible for the discordant phenotype.
In this case, it is needed to reliably identify nucleotide types that are strictly absent from a given position of the aligned sequence set, i.e. their absence is not due to stochastic sampling error.
In order to investigate possible artifacts due to stochastic or systematic errors, 12 different datasets were constituted.
A mathematical approximation of a complex biophysical system must account for multiple sources of uncertainty, due to stochastic noise, experimental error, or other possible fluctuations induced by the interaction of the system with its surrounding.
