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Our alternative hypotheses of selection begin with a working null hypothesis that assumes no historical selective differences among Nsp variants, with current patterns of genetic variation at Nsp solely reflecting demographic effects such as population structure or historical population expansion (H0-demography).
Our study highlights the difficulty to evaluate the probability of the alternative hypotheses of selection for LP in Europe because a correlation between LP frequency and latitude is expected under all of them and also because they are not mutually exclusive.
Three sets of models, commonly applied to test hypotheses of selection, were used.
In AGAP005195, we also tested for alternative hypotheses of selection (H1 and H2) in A. merus and A. melas.
Two sets of site models are commonly used to test hypotheses of selection, and have been used here: M1a vs. M2a and M7 vs. M8.
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The alternative hypothesis of selection on standing variation predicts that the selected allele was segregating at appreciable frequencies in the population on multiple backgrounds at the time of the selective event.
Thus we reject the hypothesis of selection for optimized hydrolytic activity on wheat.
In summary, we have provided observations supporting the hypothesis of selection against transcriptional interference, although rigorous testing will require more knowledge of retroelement activity.
The hypothesis of selection on anticodon wobble versatility [17], which was implicitly proposed before [27], [28] and may be more appropriate for vertebrate mitochondrial genomes because each codon family is translated by a single tRNA species, states that the anticodon should maximize its wobble versatility in paring with synonymous codons.
Because U in general is more versatile than C in wobble pairing with both A and G [29], [30], the hypothesis of selection on anticodon versatility also predicts an UAU anticodon to maximize its paring versatility with the AUA and AUG codons.
It would be informative to see the results of other testing of the hypothesis of selection acting on this locus.
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