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For example a polymorphism underlying a robustness QTL could be under balancing selection, or could be currently undergoing a selective sweep; different alleles could have been fixed in different (normally isolated) populations that were each advantageous to their own environments; or the robustness QTL observed in laboratory settings might not be expressed as such in the wild.
Similarly, SNPs were demonstrated to be under balancing selection, and the frequency of SNPs as a signature of selection was used to identify new vaccine targets in known antigens [27] or in the entire Plasmodium falciparum genome [3].
A gene that was previously shown to be under balancing selection in other populations (ama1, PF11_0344) was incorporated as a positive control, and a merozoite stage-specific gene encoding an internally expressed protein (etramp10.2, PF10_0323) was included as a negative control as well as one of the genes that had neither an extreme MK skew nor HKA index in the analysis above (rama).
We targeted exon 2, which codes for the peptide-binding region of the class II B molecule and has been shown to be under balancing selection [ 4].
In addition, FDIST detected the upstream gene SNP variants rs4643699 and rs1488467 to be under balancing selection (Table 1, Fig. 2).
Major Histocompatibility Complex (MHC) genes are central to vertebrate immune response and are believed to be under balancing selection by pathogens.
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Results indicate that polymorphism in TRAP is under strong selection for amino acid sequence diversity and that allele frequencies are under balancing selection within the Gambian P. falciparum population.
The HKA and TjD indices with the respective types of data sets are promising for large-scale analyses to detect the important minority of all parasite genes that are under balancing selection.
Our results support the findings that PrP gene is under balancing selection as determined using molecular evolution techniques comparing the ratios of synonymous (amino acid non-changing) and nonsynonymous polymorphisms [30].
For instance, among the 250 SNPs with the lowest PPP-values, from 92.8% to 98.4% (with model 1) and 100% (with model 2) were subjected to positive selection, while among the 250 SNPs with the highest PPP-values from 29.3% to 45.6% (with model 1) and from 27.3% to 42.6% (with model 2) were under balancing selection.
Whether or not SRF1 is under balancing selection remains to be seen.
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