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For none of the three genes was mean divergence within species significantly related to the sample sizes per species, as revealed by regression analysis (cox1: R2 = 0.001, p = 0.465, 16S: R2 = 0.001, p = 0.465, cob: R2 = 0.001, p = 0.338) (Figure S1).
The mean divergence between copies of the two subfamilies was 13.6%, whereas the mean divergence within subfamilies was much smaller (1.3% and 3.1%) (Table 3).
The mean divergence within clade 1 was much lower (0.009) than in clade 2 (0.051) or between them (0.074) [Additional file 9].
The mean divergence within all Vietnamese viral sequences was 0.3%, but there was 3.3 11.3% nucleotide divergence over the N-450 region compared with WHO reference strains (Fig. 1).
Subsequently, we estimated mean divergence within dataset composed of sequences from the four closely related focal species and compared it to estimated divergence at 3rd positions to get an idea about relative mutation rate in both datasets.
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Mean divergences within families and orders were 6.51% (SD = 2.45%) and 10.69% (SD = 2.37%) respectively (Figure S2c).
The Oregoniidae also exhibits very low mean divergences within taxa (S = 0.66%; G = 5.56%; F = 12.96%), here represented by five deep water species from two genera.
This trend was not observed in the distribution of interspecific K2P divergence values across all taxon combinations (Figure 1); however, comparison of mean divergence values within each genus (θ' values) by genus pair did statistically support an overall faster rate of divergence in trnH-psbA relative to rbcL (see Results).
The two subfamilies have a modest mean divergence between copies within each one (4.7 and 6.7%, respectively) compared with the mean divergence between them (24%) (Table 2).
Analyzing the species groups separately, the mean divergence of the Zaprionus sequences was 0.033; it was 0.047 within the melanogaster species subgroup, and 0.073 between the Zaprionus and the melanogaster sequences (Table 2).
We name them as Clade 1, Clade 2 and Clade 3. The mean COI genetic divergence within each clade is tiny (0.11%, 0.11%, 0.49% respectively), while the mean divergence among the clades is large (4.22%-5.28%) enough to suggest different species.
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