It is well-known that duplicate genes face three possible fates: pseudogenization, subfunctionalization and neofunctionalization. Pseudogenization is considered as the most common fate of duplicate genes [ 8- 10], but more evidence support the models of subfunctionalization or neofunctionalization, as the mechanisms for the preservation of duplicate genes under adaptive selection [ 6, 15, 48, 49].
During this process, the expression domain shifting is the most common character of duplicate genes.
However, the most common fate of duplicate pairs is that one of the copies becomes a pseudogene by the fixation of deleterious mutations, and will finally be lost in the genome.
Although it has been suggested that gene duplication occurs at a high rate of 0.01/gene/million years, the most common fate of duplicated genes is silencing and loss [ 62].
Many models have been proposed that pseudogenization could be the most common fate of duplicated genes [ 8- 10].
Although the nonfunctionalization model is thought to be the most common fate of duplicates, previous research supports the subfunctionalization model in the preservation of complex genes after duplication [ 52].
Estimates of the rate of gene duplication in vertebrates vary from 1 gene per 100 to 1 gene per 1,000 per million years (Lynch and Conery 2000, 2003; Cotton and Page 2005), and the most common fate for a duplicate gene is the loss of its function (nonfunctionalization, pseudogenization [ Mighell et al. 2000; Presgraves 2005]).
Complete duplicates represent the most common structural category even when gene duplicates of varying evolutionary age were analyzed (cohorts K S = 0, 0 < K S ≤ 0.025, and 0.025 < K S ≤ 0.1).
The most common fate of a duplicated copy, however, is nonfunctionalization (pseudogenization), raising the question of how and why both copies of some duplicates manage to persist as functional entities.
Although the most common fate of gene duplicates may be immediate pseudogenization upon arrival, the extraordinary high rates of spontaneous gene duplication likely have a substantial influence on the trajectory of evolution by enabling the origin of discernible numbers of gene substrates for neofunctionalization [ 8].
