We believe that it was important, as it is done here, to demonstrate on the same dataset that evolution of duplicated genes is shaped by the interplay of two opposing effects, the initial increase in substitution rate after gene duplication, and generally lower evolutionary rate of duplicates compared to singletons.
In addition, human duplicates have, on average, much larger duplication spans which are more likely to capture entire ORFs leading to complete duplicates compared to higher proportions of structurally heterogeneous duplicates (partial and chimeric duplications) in Drosophila and C. elegans.
It seems that there are two countervailing forces at work on the sequence evolution of duplicate genes: i) acceleration of substitution between paralogs caused by relaxation of purifying selection after duplication, and ii) relative reduction of substitution rate for genes with duplicates compared to singletons, which is predicated upon the stronger functional constraints affecting the former.
The chromosomes were divided into 10 Mb bins and the number of duplicates compared to the number of genes per bin.
A Rab5a Pp2d1 gene cassette on the other side of the Sult1c synteny breakpoint has been duplicated compared to the orthologous genes on human chromosome 3.
As our results indicate, there is a different evolutionary constraint on those no AS duplicates compared to duplicates with AS, the function of those two different groups of genes are interesting and in need of further exploration.
Plasma DNA also shows a higher number of PCR duplicates compared to cellular (3 % vs. 0.5 %), which is expected, given the extra PCR cycles in the library protocol when using a low starting volume of DNA.
Analysis of such triplets reveals an accelerated evolution, or relaxation of constraint, in the peptides of the X. laevis duplicates compared to their orthologs in X. tropicalis and other vertebrates.
Therefore, despite the lack of SWS1 duplicates compared to the SWS2 or RH2 opsins, the SWS1 region is still poorly assembled in the existing annotations of several teleost genomes, potentially complicating direct comparisons of synteny in this region.
