Of the non-synonymous variants, 10 (38.5%) are predicted to be probably damaging by Polyphen, 13 (50%) are predicted to be deleterious by sorting intolerant from tolerant, and seven (26.9%) are predicted to be damaging by both methods (Supplementary Material, Table S2).
At the time of the Hague convention of 1899 no one had actually tried to use projectiles "the sole object of which is the diffusion of asphyxiating or deleterious gases"—the sort the convention banned.
Characterization of these 29 rare variants revealed 19 that were predicted to deleterious by SIFT (Sorts Intolerant From Tolerant substitutions) [ 24] and 11 predicted to be probably or possibly damaging by PolyPhen2 (Polymorphism Phenotyping 2) [ 25].
To sort potentially deleterious variants from benign polymorphisms, perl scripts were used to filter the SNVs against those of dbSNP135.
The amino acid change seems to have deleterious effects based on Sorting Intolerant from Tolerant (SIFT) analysis with a SIFT score of 0.03.
However, before LD is broken, a strong directional selection could already have led to the rapid purging of deleterious genomic blocks via lineage sorting, just as it can lead to the rapid spread of favorable alleles (Rieseberg et al. 2002; Morjan and Rieseberg 2004) during selective sweeps.
Alternatively, it may be that the sorting procedure itself is deleterious.
Mouse cells, present in xenografts can be separated using lengthy depletion protocols and fluorescent activated cell sorting (FACS) which can have deleterious affects on transcriptional profiles.
Lastly, we will turn to quantitative genetic models of IGEs of the sort being used to reduce the deleterious effects of IGEs in modern animal breeding and relate the parameters of these models to those developed in the evolutionary theory of social behaviors.
Finally, we assessed the deleterious effect of non-synonymous SNPs using SIFT (Sorting Intolerant From Tolerant) program (sift.jcvi.org/).jcvi.org/
Paternal leakage, sorting-out of genome types, selection against deleterious variants as well as oDNA stability and recombination dynamics are now accessible at much finer scale (Boxes 1 and 4) and at all levels: in cells, tissues, individuals, and entire populations.
