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About 25% of the genes had an average Relative Divergence Factor above 2.
The average Relative Divergence Factor from all genes, over all calculations, is 1.68.
The average Relative Divergence Factor over all genes for each reference set ranged from 1.50 to 1.69 (all significant, p < 0.0001).
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They lead, on average, to a relative divergence of +60% to +105% in favor of the scale model for different points located in the side lit room.
We then determined the ratio of these two averages to determine a "Relative Divergence Factor" for each gene.
For these genes individually, a comparison of average pairwise distances indicates that relative divergence in Welwitschia ranges from amounts about equal to other seed plants to amounts almost three times greater than the average for non-gnetophyte seed plants.
We ran ten independent chains with 4,000,000 generations and subsequently averaged the estimates on the relative divergence times.
Counterintuitively, some amino acids which show divergence or convergence in average relative usage across the chronology actually have ZV values indicative of the opposite trend, as error often varies substantially across the alignment (e.g., U1,L Tyr)−U−1,L Tyr) vs. ZV,L Tyr)).
The Relative Divergence Factor was calculated by dividing the average distance calculated from Welwitschia to each non-gnetophytes by the average distance from comparisons among the 10 non-gnetophytes.
When the Relative Divergence Factor was determined as an average of the five different calculations, only one gene (psaJ) had a divergence rate about equal to the non-gnetophytes (factor of 0.97), whereas 38 genes had Relative Divergence Factors above 1.5 and 14 above 2.
If the Relative Divergence Factor is less than one, then that gene in the Welwitschia plastome shows less divergence than average, if it is one, the gene is equally divergent, and, if greater than one, the Welwitschia gene exhibits above average divergence.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com