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Autonomous hAT-HT2 elements are extremely young and in fact their mean divergence from consensus is 0.00%.
The coalescence times were estimated with ρ statistics (mean divergence from inferred ancestral haplotype), and standard errors were calculated following the method of Saillard et al. [ 34].
For HVSI, the age of clusters or expansions was calculated as the mean divergence from inferred ancestral sequence types [ 59, 60] and converted into time by assuming that one transition within np 16090 16365 corresponds to 20,180 years [ 61].
For HVSI, the age of clusters or expansions was calculated as the mean divergence from inferred ancestral sequence types [ 58] and converted into time by assuming that one transition within np 16090 16365 corresponds to 20,180 years [ 59].
For calculation of the time to the most recent ancestor (TMRCA) for specific clades in the phylogeny, ρ statistics (mean divergence from inferred ancestral haplotype) were used with a coding region (nts 577 16023) mutation rate estimate of one transition per 5138 years [ 45].
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Overall, these results did not change when we used the mean divergence of introns from each CNE's nearest down-stream opsin as a null hypothesis, except that O. niloticus and M. zebra also exhibited significant divergence at CNE 4 (divergent TFBS = 2, total TFBS = 2, Pdiv = 100.0%, p = 0.001).
Both clades show low differentiation (maximum haplotype divergence being under 1% in SAF and under 3% in NAF) over a broad geographical range (see Figure 2), but are highly divergent from one another (mean divergence 6.6%), with haplotypes differing by 7% separated by less than 200 km.
Time estimations, based on control region mtDNA, were calculated as the mean divergence ρ [ 39] from inferred ancestral sequence types and converted into time by assuming that one transition within np 16090 16365 corresponds to 20,180 years [ 29].
Of the 49 HGT transcripts from Rafflesia that could be directly compared with Tetrastigma, sequence divergence ranged from 0.05%39.7%% (mean divergence, 22.5%).
On average, the six methods differed only 5.5 (4.6 6.4) % from the mean divergence time for a particular node.
According to the result of molecular clock calibration, the mean divergence time of nodes ranged from 2.70 Ma (node A) to 0.35 Ma (node L) or 1.90 Ma (node A) to 0.25 Ma (node L), assuming, respectively, minimum and maximum rates of synonymous substitution in cpDNA [ 26].
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