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Rate asymmetry between paralogs has also been demonstrated for more ancient duplicates in eight yeast species following a whole-genome duplication event in their common ancestor [ 33].
More ancient duplicates could be tracked based on gene collinearity on SCBs within and between species.
As such, one would expect the more recent gymnosperm-specific duplicates to be physically less spread across the genome than more ancient duplicates predating the GA split.
Nevertheless, under a more broad age category, such as before the split of land animals and fishes versus the more ancient duplicates, the difference is statistically significant (P < 0.01).
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These more ancient duplicated blocks must be identified and removed from genomic comparisons aimed at identifying duplicates from the more recent tetraploidy shared by all grasses.
Based on such a phylogenetic approach together with gene mapping, one could also ask if the spread of gene families over the gymnosperm genome is more likely for ancient duplicates predating the GA split than for more recent duplicates postdating this split.
First thought for why ancient duplicates are more conserved is puzzling, because it is generally believed that duplicated genes may have experienced a relaxed evolution due to the functional redundancy.
Since developmental genes are more essential than other genes, it is reasonable to suspect that the positive P E - t correlation might be simply because of the trend that ancient duplicates have more developmental genes.
As one may expect, with a higher identity criterion, only those recently duplicated genes were identified as duplicated paralogs, while with a lower identity criterion, those more ancient of the paralogs were included as duplicated genes.
Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays.
We found that ancient duplicates tend to be more conserved, and the ancient duplicate gene tends to be more essential than an average single-copy gene.
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