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Giribet et al., [29, fig. 10], using a relaxed clock analysis for multiple genes and multiple fossil calibration points, estimated a divergence value for the common ancestor of Erebomaster plus Theromaster at over 100 Ma.
In ATon-II, 83 elements have sequences identical to the consensus sequence and 166 copies have a divergence value ≤ 1%.
Ninety-five percent of all SNPs were contained within a divergence value of 44% or less, suggesting that the overall level of nucleotide divergence is low.
For example, a SNP that was fixed for a different allele in each ecotype would have a divergence value = 1.0; a SNP where the major-allele was fixed in shore and had a frequency of 60% in stream would have a divergence value = 0.40.
A divergence value (based on the index implemented in Juekens et al. [ 40]) was calculated for each SNP, defined as the absolute value of the difference in the frequency of the major allele among ecotypes.
The highest divergences within species were found in populations of A. tincella, particularly between the population from the Quitupan River Balsas Basinn), which had a divergence value of = 0.014-0.018 ± 0.004 with respect to the remaining A. tincella populations.
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A threshold of 2.0% intra-specific sequence divergence was employed to screen for overlooked species following the recommendation that a sequence divergence value set at 10X the average within species variation (0.21 in this study- see later) is likely to be effective in this regard [15].
A further advantage of the Euclidean distance method is that it is more flexible, in that it is possible to either combine data from all tissues into a single divergence value or to consider each tissue separately.
In the high functioning community a, all the dominant species are specialists (i.e. with extreme combinations of traits), which contributes to a high functional divergence value.
Conversely, the low functioning community b has a lower functional divergence value with some dominant species being generalists (i.e. close to the center of the functional space occupied by the community) that are functionally redundant (Figure 3b).
Three loci, ITS1, trnH-psbA, and rpoB2, had a mean sequence divergence value greater than two percent while the remaining loci ranged between 0.2% and 1.55% (Tables 1, 2, Figure 2).
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