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MDIV estimates of TMRCA and species divergence are non-overlapping with BEAST and the net divergence method.
(c) Was the population divergence method used to detect the loci under selection appropriate for the present system?
In order to reduce overlapping pixel intensity, a simple fuzzy divergence method was considered here to segment the wound area in S channel wound image [ 21, 22].
Of these, the net divergence method and the Bayesian MCMC method (as implemented in the program BEAST) gave similar temporal results.
Interestingly, and in support of a long-standing method, the much less complicated net divergence method (Table 4) has yielded very similar species divergence time estimates to the Bayesian method TMRCA.
Investigations of genes with fixed, derived substitutions exhibiting functional divergence (Method 2) or evidence of positive selection (Method 3) demonstrated enrichment in more GO terms related to NO production and regulation in polar bears than in brown bears.
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A critical point of all methods that try to detect a signature of selection using both diversity and divergence methods is the risk of false positives.
Unlike the functional divergence methods developed by Gu [ 36, 37], estimating selection using the d N / d S ratio is, by definition, dependent on the degree of divergence of the sequences under study.
Accordingly, we developed a comprehensive gene co-expression network from an independently-derived high-dimensional transcription dataset that both validated and expanded our view of potential targets of the candidate regulators of the co-expression divergence (Methods).
The population divergence methods implemented in FDIST2 have been widely used in several reports (Flint et al., 1999; Vasemägi et al., 2005; Bonin et al., 2006; Hoffman et al., 2006; Mealor and Hild, 2006; Pariset et al., 2006) and have been shown to be quite robust by simulations among various demographic scenarios (Beaumont and Balding, 2004).
The KL-divergence method based on the Bio-LDA model can identify a much larger number of association pairs.
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