In discussing these results, first, I will discuss the potential deeper level relationships among these duplicates within and between species and then, second, I will look at the interesting patterns of gene conversion in two pairs of more closely related duplicates.
For the CYP5005 family, the best "nonphylogenetic-free" model suggested that more closely related duplicate genes are no more likely than more distantly related genes to share similar expression patterns.
The wHSP90.3 gene located in the long arm of wheat homeologous group 5 is more closely related to the recently duplicated rice genes rHSP90.3 and rHSP90.4, which are both located in the colinear rice chromosome 9 and differ from each other only by a single amino-acid (Additional file 1: Table S1; Additional file 1: Figure S1C [ 46]).
This suggests that rabbit CYP1A2 is rather of the 1A1-type than of the 1A2-type and it could explain why rabbit CYP1A2 duplicate is found more closely aggregated with the two CYP1A1 clusters than with human CYP1A2 duplicate).
Codon usage analysis clearly showed that the duplicated genes cluster more closely to the plasmid genes than to the genome background [see Additional file 3], which suggests that the genes originated from the plasmids.
This provided us with greater temporal resolution in mammals than in Drosophila, and allowed us to more closely examine the functional diversification of mammalian duplicates over evolutionary time.
However, the two well-conserved GATA456 duplicates from both Capitella and Lottia (Na, Nb) group more closely within each species then across species, suggesting these could be recent lineage-specific duplicates.
Therefore, duplicated copies within individuals were more closely related to each other than either was to copies from other individuals.
We then examined more closely the resistance-associated markers in the six strictly duplicated regions on the E, J, R, T U and W blocks.
