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Overfractionated: The copy of a duplicate chromosomal region from which more genes were lost.
Underfractionated: The copy of a duplicate chromosomal region from which fewer genes were lost.
Second, one copy of a duplicate gene pair may retain the original function, but the other copy may become lost or silenced [ 3, 13, 14, 23- 26].
This agrees with the observation in yeast that early gene losses were equally likely to remove either copy of a duplicate gene pair (Scannell et al. 2006).
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This would imply that one copy of a duplicated gene has diverged from the roles of the pre-duplication ortholog.
There are four types of functional changes at this level depending upon whether co-option is occurring to one gene or a copy of a duplicated gene, and whether the co-opted gene changes function completely or retains its plesiomorphic (ancestral) role as well (Table 1).
More rapid evolution of one copy of a duplicated gene is a well-documented phenomenon [44], [45] and greater DIA1R divergence, than DIA1 divergence, is therefore expected.
In particular, new insertions into one copy of a duplicated genomic segment will not pose a problem.
Genome analysis suggests that one copy of a duplicated gene could drift and potentially acquire a new function.
We also assumed that the phenomenon of gene duplication is always related to ecological adaptation and that a new copy of a duplicated gene is not essential.
Fifth, a second homolog set was defined as the second reference, which may be the second copy of a duplicated gene, and the sequences from each individual that best aligned to that reference sequence (after excluding those sequences that were chosen for the first homolog set).
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