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For each of the Ks ranges used in this study, we found that significantly more relocalized duplicates have a Ka/Ks > 1.5 than nonrelocalized duplicates, a result consistent with preferential retention of relocalized duplicates rather than a gradual relocalization over time (supplementary table S3, Supplementary Material online).
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Assuming that preferential retention of relocalized duplicates is due in part to some added benefit and thus subject to positive selection, we examined the data to see whether more relocalized duplicates exhibited evidence of positive selection over nonrelocalized duplicates.
Removing them may have biased the results against retention of relocalized duplicates.
To test the hypothesis that pI changes occur in relocalized duplicates in plants, we estimated the pI difference (ΔpI) between duplicated pairs.
In both types of species, we found evidence to support the idea that relocalized duplicates tend to have higher retention than nonrelocalized duplicates.
As such, PSR would promote retention of those relocalized duplicates and result in significantly lower death rates compared with death rates of nonrelocalized duplicate pairs.
The upper range of relocalized duplicates in individual species were found in rice (Oryza sativa 67,697/1,91,985 = 35.3%), and platypus (Ornithorhynchus anatinus 2,360/4,116 = 57.3%).
In the complete data set, we observed significant retention of relocalized duplicates but when corrected for gene conversion, we no longer saw such retention.
Although we did not quantify our observations, we did note that a number of relocalized duplicates in A. thaliana did appear to belong to large multigene families involved in secondary metabolism.
The hazard ratios can be interpreted as follows: a hazard ratio of 1.58 for V. carteri with 0 < Ks < 0.05 (table 3) mean that nonrelocalized duplicate genes have a 58% higher hazard rate or death rate as compared with relocalized duplicates.
In this particular case, it is possible that 1) gene conversion was biasing the data so that nonrelocalized duplicates appeared to have low Ks or that 2) a number of relocalized duplicates are located in large multigene families in A. thaliana.
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