We compared degree difference and edge conservation, following waves of duplications of different ages.
These two waves of duplications, in close temporal succession, and of similar quantitative contributions, should be interpreted as differential signatures of two consecutive rounds of genome doubling of 2R-WGD, with similar retention rates (approximately 10%-15 10%-15 is, half of the overall 2R-WGD retention rate).
The second wave of duplication and transposition occurred after the branching of the gorilla lineage at 7 8 MYA and involved the chromosome 15 homologous sequence in the yellow-amplicon.
The second wave of duplication is vertebrate-specific and leads to a diversification inside the subfamilies, with the emergence of the presently known isotypes such as PPAR α, PPAR β, and PPAR γ [ 3, 7].
On the lineage of PODs leading to human, the Smads clearly appear to have gone through a major wave of duplications, fitting well with the 2R hypothesis of two-fold genome duplication at the base of vertebrates [ 47- 50].
Waves of gene duplication events were found to have happened at approximately the time of the emergence of early vertebrates and mammals [ 2].
It has been demonstrated that a large number of NHR members are likely to result from two waves of gene duplication events.
Phylogenetic reconstruction of beta-keratin gene evolution suggests that separate waves of gene duplication within a single genomic location gave rise to scales, claws, and feathers in birds, and independently the scutes of the shell in turtles.
We propose here that other "waves" of genome duplication events could also be linked to periods of extinction such as the Triassic/Jurassic (called Tr J, 200 Mya regarding the pelohexaploidization characterized in eudicots) transition or more recent periods during the Paleogene and Neogene (for the characterized family- or lineage-specific duplications).
These two networks share not only their topological features but also their evolutionary histories, since they both emerged by two waves of gene duplications – at the origin of metazoa, and the origin of vertebrates.
