One likely explanation is the presence of slightly deleterious segregating mutations caused by reduced effective population size, resulting in inflated non-synonymous SNPs relative to non-synonymous substitutions [ 17, 18].
Despite the promise of becoming social mixing grounds, the District's charter schools are slightly more racially segregated than the city's traditional public schools.
Segregating slightly deleterious amino-acid mutations will bias the estimate of α downwards, because slightly deleterious mutations tend to contribute relatively more to polymorphism than they do to divergence, when compared to neutral mutations [ 2, 32, 33].
We then estimated that 44% of amino acid mutations are strongly deleterious and not found in the sample, and 33% are slightly selected and segregate at low frequency.
For CYTB in the La Jolla and Santa Cruz regions, MK tests suggest an excess of replacement polymorphism, which could be attributable to segregating slightly deleterious mutations.
Such deviations could be the result of adaptive processes, or they may indicate the presence of slightly deleterious mutations segregating in the population [ 31].
The use of single nucleotide polymorphisms (SNPs) with high derived allele frequencies (DAFs) minimized the influence of segregating slightly deleterious mutations and improved the estimation of the number of adaptive sites.
Conventional MDK tests such as those based on the α statistic are usually used to detect only positive selection (but note that a negative α is an indicator of purifying selection or of slightly deleterious mutations segregating in a population).
In general, human sequences showed higher PN/PS ratios than sequences from the other analyzed species, probably due to the presence of many slightly deleterious mutations segregating in the population (Eyre-Walker, 2002).
Slightly deleterious polymorphisms segregate at low frequencies due to weak negative selection and can increase the nonsynonymous-to-synonymous polymorphism ratio to a greater extent than that of divergence.
One likely cause is the presence of segregating, slightly deleterious mutations in humans; for example, those caused by a recent population bottleneck, which will increase the number of Pn polymorphisms relative to the neutral expectation and downwardly bias the estimation of the FI and α value [ 17, 18].
