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The alignment was then submitted to the test of substitution saturation [63] available in DAMBE [64].
Our pooling model is deliberately vague (i.e., general) in order to provide a generous test of substitution.
Thus, using Kumar and Gadagkar [ 39] disparity test of substitution pattern homogeneity rate, we showed that variations are generally low at the trnL-F intergenic spacer region.
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Tests of substitution rate differences between groups were conducted as follows.
Although tests of substitution rates in the sperm whale mitogenome have been conducted previously (Lyrholm et al. 1996; Whitehead 1998), these tests were limited to only a fraction of the mitogenome.
The distribution of normalized substitution rates (r) provides a test of whether substitution rates are uniform throughout a genome.
Our method of estimating ti/ tv for subsamples of the data is convenient for this purpose, and provides a simple internal test of the substitution process.
A likelihood ratio test of nucleotide substitution rate constancy across lineages indicated that our data rejected a constant molecular clock model (P = 4.06 × 10−20).
Characteristics of the applied test data sets including the results of the test for substitution saturation in loop and stem partitions.
To test the degree of substitution saturation we used the test of Xia et al. [ 52], as implemented in the software package DAMBE [ 53].
Eight multiparous Holstein cows, 4 of them fitted with rumen cannulas, were used to test the effects of substitution of steam-flaked corn (SFC) for equal amounts of finely ground corn (FGC) in diets on feed intake and digestion, blood metabolites, and lactation performance in early lactation dairy cows.
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