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The SDs in (91%, 10/11) BACs were confirmed to be positive duplications by qRT-PCR.
The results are shown in figure 5 B. Indeed, for lineages in the fit set, the early fitness landscape is biased toward positive duplications.
We thus see that the higher likelihood of positive duplications in future fit lineages promotes the expansion pattern, providing the building blocks for their successful future adaptation.
Our choice was driven by the preference of getting some false positive duplications, which are actually transposable elements, instead of losing most real segmental duplications (false negatives).
To test if genome expansion can be explained by a bias toward positive duplications relative to deletions, we constructed mutational landscapes of cells in the line of descent separating duplication and deletion mutants.
These false positive duplications were found in tandem on the same chromosome (n = 90, Additional file 1: Table S2A; for example, Additional file 2: Figure S3B), or on separate chromosomes (n = 59, Additional file 1: Table S3A).
Similar(54)
After the most likely false positive tandem duplications are eliminated in this step, the set of conflict-free duplications are reported to the user.
In terms of F1-score, our method outperforms all the other methods with increasing error rate and data coverage, showing the superiority of our method in identifying the largest set of true positive tandem duplications with the least number of false positives.
Unless some mechanism (e.g., positive selection, duplication, gene conversion) preserves them, TEs may be subject to degeneration once inserted and immobilized, and may become unrecognizable.
It could be possible that positive selection on duplications (based on functional effects) has occurred for these particular gene categories or that these enrichments might instead have been arisen from nonuniform negative selection on gene copy changes.
We obtained a sample from the F30 generation of PERA/EiJ (1982) and found that this sample was positive for the duplication, whereas the modern samples (F99) were negative for the duplication.
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