Although in the primate lineage it would appear that the original episodes of positive selection following duplication were usually followed by negative selection.
Another known cause of changes in protein evolutionary rates is the relaxation of functional constraints acting on duplicate genes following duplication events [ 10].
Classical population genetic theories suggest that duplicated genes have identical sequences immediately following duplication, and then gradually diverge over evolutionary time [ 1].
Ohno's theory hypothesizes that duplicates are mostly silenced by degenerative mutations following duplication due to a redundancy in function.
Consistent with the hypothesis of rapid divergence following duplication, there is clear evidence for neofunctionalisation of the duplicated genes, in both ecdysozoan and deuterostome species.
Indeed, studies on the evolutionary rates of duplicated genes showed that acceleration tends to occur immediately following duplication [ 5, 6].
The correlations between maximum indel lengths and nucleotide substitution rates are generally trivial, perhaps because duplicated genes losing long coding segments are preferentially lost following duplication.
This is particularly interesting given that evolutionary forces, which act in the early stages following duplication, may be crucial in determining the ultimate fate of duplicated genes (Moore and Purugganan 2003).
Because gene duplication often precedes the functional diversification between duplicates, it has been predicted that evolutionary rates should increase following duplication [ 3, 4].
The larger bCRK-I subclade further divides into distinct branches with tandemly duplicated Amborella bCRKs at their roots (Supplementary Figures 5 and 6a, b) suggesting rapid differentiation following duplication in ancestral angiosperms42.
We are studying the consequences of WGD in this clade by tracking patterns of gene loss and retention following duplication and scanning the genome of a recently evolved tetraploid species.
