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This implies that demographic structure, such as that studied here, is difficult to detect with a classical measure of deviations from the standard neutral frequency spectrum.
We used patterns of polymorphism within each group to detect instances of selection causing departure from the neutral frequency spectrum.
Because a whole asexual genome forms a single linkage group, such background selection [ 31] is likely to produce a considerable distortion in the neutral frequency spectrum toward an excess of rare variants in all loci including neutral ones [ 30].
The authors attribute this result to lower levels of sequence diversity in neutral genes in sorghum compared with maize and to genome wide departures from neutral frequency distributions indicative of a complex demographic history for cultivated sorghum.
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For each gene, we set the neutral frequencies of non-STOP codons (1/61) and the probability that adjacent codons share the same selection coefficient (P = 0.02).
Additionally, the lower ambient magnetic field will slightly enlarge the upward vertical drift, lifting the plasma irregularity to higher altitude, where the ion-neutral frequency, ν in, is lower.
As can be seen in Eq. (3), the ion-neutral collision frequency and neutral wind also contribute to the growth rate.
For a data set with a given number of polymorphisms, S, we simulate neutral allele frequency distributions by generating multinomial samples that distribute these polymorphisms into 19 frequency bins using the "Multinomial" function in the R statistical package (http://www.r-project.org).org
These formulae are given by Schunk and Nagy (1978) for the electron neutral collision frequency and by Schunk and Walker (1973) for the ion neutral collision frequencies.
They estimated the F-region ion - neutral collision frequency at 260 km altitude using the ambipolar diffusion equation - and also found good agreement with the MSIS model.
The TjD test is influenced not only by selection but also by the population history that can alter neutral allele frequency expectations [43], as in the case of previous population expansion that causes the neutral index for P. falciparum to be negative rather than zero [15], [44].
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