Next, we investigated each gene in this dataset by looking at which ORFs that were considered likely to be evolved under positive selection, i.e. a directional selection driven by change in phenotype [ 65].
For a population under directional selection, deleterious alleles with large substitution effects would be expected to be at low frequencies.
For MEME, sites were posited to be under directional selection at selected branches if they: i) showed non-synonymous to sysnonymous substitution rate β+ >1; ii) were significant at α = 0.05 level; and iii) also showed an Empirical Bayes Factor >20.
Both wood quality and drought tolerance groups produced a posterior distribution of the mean selection coefficient across loci well centered around zero, indicating that both groups, as a whole, were neither evolving rapidly under directional selection nor under strong selective constraint.
Using Malawi cichlid hybrids, they showed that lower jaw shape, a trait under strong directional selection [ 22], did not exhibit TS while the shape of the neurocranium, a trait not under directional selection, did.
falciparum and P. reichenowi; P. vivax and P. knowlesi; P. yoelii and P. berghei) were compared for a set of 43 candidate ligand genes considered likely to be under positive directional selection and a set of 102 control genes for which there was no selective hypothesis.
In order to create horses with a characteristic uniform appearance and function, some breeds have especially been under strong directional selection to a special breeding goal while other populations still underlie a greater natural selection and have kept their original properties to survive under harsh environment [ 2, 4].
For example, in a Drosophila selection experiment C layton and R obertson (1957) reported increased bristle number variance, which is consistent with the idea that genotypes associated with higher environmental variance have a greater chance of being selected under directional selection (H ill and Z hang 2004).
On the other hand, if a variant is under strong directional selection, changes in allele frequency will be consistent in direction and may become large over several generations.
In contrast, the QTL sign test, which uses QTL effect directions, may be used to evaluate whether a trait evolved under consistent directional selection [ 3], because directional selection will limit the fixation of antagonistic QTL (QTL with effects that are in the opposite direction to parental differences for those traits).
