We find that many historically fast-evolving genes in D. miranda and D. pseudoobscura continue to be evolving adaptively on a more recent timescale and are thus detectable in tests of selection using both patterns of polymorphism and LD.
In contrast, polymorphism-based approaches can only detect selection on a much more recent timescale (i.e., within the population coalescent time, most estimators only have reasonable power to detect selection as recent as 0.1 4 Ne generations ago; Przeworski 2002).
Dates are in line with a recent geological timescale [ 45, 46] (see additional file 4).
16 This probably reflects the recent timescale of that review and the fact that it was not restricted to trials in residential and nursing homes.
This suggests that not only are these genes evolving rapidly on the very recent timescale detectable using polymorphism data but also the deeper timescale back to the D. miranda D.
The lack of bias in the chromosomal distribution of cytonuclear genes may therefore reflect the recent timescale of sex chromosome evolution rather than the absence of biased gene movement.
In order to additionally estimate positive selection that acted along the more recent timescale after the primate interspecies split we searched for single nucleotide polymorphisms (SNPs) in the human gene sequences.
An increase of the observed rates towards the tips in a phylogeny (Fig. 4) is assumed to be a result of transient polymorphisms present in the more recent timescales of a phylogeny [33].
In multiple instances, several unique control region haplotypes are collapsed into a single ND2 haplotype, suggesting a slower substitution rate for ND2 over recent timescales and reduced capacity to record information on recent population splitting events in the genetic code.
Stochastic processes, such as mutational variance and gene-sorting, can play a relatively large role in the generation and structuring of genetic diversity, making inferences based on networks or trees of a single locus inadvisable, especially for recent timescales [ 29].
At recent timescales, temporal clusters of diversification caused by biogeographical events can leave a signature in the genetic variation within and among the affected lineages.
