gene conversion
Thornton KR 2007 The neutral coalescent process for recent gene duplications and copy-number variants. Genetics 177:987-1000.
- E[π|τ = 0] = 2θ Σi = 12N − 2 ai (1 / (i + 1) − 1 / (2N))
- ai = 2(2N + 1) / ((i + 1)(i + 2)(2N − 1))
- it is straightforward to extend Tajima's results to show that the expected number of segregating sites, conditional on τ = 0, is
- E[S|τ = 0] = θ Σi = 22N (1 / (i + 1))
- patterns of polymorphism in copy number variants:
- when the conversion rate increases, such that 4Nc ≥ θ, shared polymorphisms will tend to be observed only as singletons unless the sample frequency of the duplicate is relatively high
- for evaluating hypotheses concerning the evolution of very young gene families, the standard coalescent is not an appropriate null model
- tests of neutrality:
- a reduction in diversity and an excess of rare alleles are expected for recent duplicates, particularly when the rate of ectopic conversion is low
- young duplicate genes are expected to show a reduction in diversity and an excess of rare alleles
- the most obvious effect of a fixation by positive selection is a more pronounced skew in the site-frequency spectrum when selection is very strong
- a second effect is fewer shared polymorphisms between gene duplicates, as the rate of coalescence during the sweep becomes much faster than the rate of conversion
