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In particular, dS will serve as a neutral divergence marker among vertebrates while dN will provide a rough indicator of sequence alignment quality across larger phylogenetic distances.
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The cost-effective, rapid and reliable way of obtaining nuclear sequences through transcriptome sequencing also provided insights on gene divergence and marker development in big sagebrush.
The second is the rate of change of ln(Rf(t)) with time, that is, τe sets the time of divergence of marker frequency and αe the rate of divergence.
Mitochondrial genes are useful markers in reconstructing population histories and comparing patterns of divergence in markers experiencing high levels of selection, such as the MHC [ 14].
As a result of this evolutionarily recent divergence, microsatellite markers can be used in the development of comparative genetic maps among the salmonidae.
However, the correlation of marker divergence with trait divergence is not strong enough to be predictive.
This suggests that marker divergence is indicative of adaptive divergence, but the same paragraph warns that the reverse is not true – that low marker divergence should not be taken as evidence of exchangeability, as adaptive divergence can take place in the face of high gene flow.
Yet the textbook observes on the previous page that marker divergence is a good predictor of adaptive divergence (a claim that has been debated at length elsewhere – e.g. Reed and Frankham 2001; Merila and Crnokrak 2001; McKay and Latta 2002).
This divergence between nearby markers and even markers in moderate linkage allows for models incorporating H|H to converge when models utilizing other positive selection measures do not.
In particular, divergent selection is often inferred when the among-population proportion of genetically based trait variance (QST) exceeds the among-population proportion of neutral marker divergence (FST).
FST in QTLs can only exceed the neutral marker divergence in the first 10 generations when the difference in optima is very large (i.e., 50-fold), the quantitative trait is coded by five loci, and the variance for allele effects is small (0.1).
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