This indicates that NaOH pretreatment significantly increased the total methane yield of PPRs, and soil addition in the appropriate proportions effectively improved the total methane yield of both NaOH-pretreated and non-NaOH-pretreated PPRs.
However, unicells and multicells are likely to differ in their effective population sizes and this suggests a simple explanation; that the proportion of effectively neutral mutations changes more in response to differences in the effective population size in the 18S rDNA than in the proteome.
Furthermore, they are likely to have a higher proportion of effectively neutral mutations, which tends to obscure the signature of adaptive evolution.
In the case where positive selection is not operating, the value of ω summed across the entire sequence is equal to the proportion of effectively neutral sites, denoted f[ 5].
The low rate of adaptive evolution and the high proportion of effectively neutral substitution in species with small Ne are expected to combine to make it difficult to detect adaptive molecular evolution in species with small Ne.
There is evidence that the proportion of effectively neutral mutations is negatively correlated to Ne across many species (Popadin et al. 2007; Piganeau and Eyre-Walker 2009), so a positive correlation between α and Ne might be entirely explained by variation in the number of effectively neutral substitutions.
Curiously, species believed to evolve at fairly large population size, such as yeast, still exhibit a fairly large proportion of effectively neutral mutations; as discussed above, at this point it is not clear whether these differences reflect overall demographics or the existence of a class of mutations with very small fitness effects.
To investigate whether the proportion of effectively neutral nonsynonymous mutations was correlated to Ne, we calculated a variant on the ψ statistic suggested by Piganeau and Eyre-Walker (2009): (9) where Pn and Ps are the numbers of nonsynonymous and synonymous polymorphisms, and Ln and Ls are the numbers of nonsynonymous and synonymous sites.
The formula and the criterion allow us to omit windows containing very few SNPs and require the identical homozygous SNPs to be in large proportions while effectively detecting a local reduction of heterozygosity.
Costs were expressed in Australian dollars and the effectiveness outcome by the proportion of grants effectively funded.
