Partial and chimeric duplicates comprise pairs wherein one or both paralog(s) have unique exon(s) to the exclusion of the other copy, respectively.
Duplicate pairs wherein one copy or both copies have unique exonic sequence to the exclusion of the other copy (partial and chimeric duplicates, respectively) may be expected to display higher rates of pseudogenization, given the massive alterations to the ancestral exon-intron structure entailed during such incomplete duplication events.
The frequencies of complete, partial, and chimeric gene duplicates within our data set were 83, 13, and 4%%, respectively.
As such, partial and chimeric duplicates may be worthy candidate genes for investigations into the genetic basis of human-specific traits.
The median duplication span in the human genome far exceeds that in C. elegans and yeast and likely contributes to the high prevalence of complete duplicates relative to structurally heterogeneous duplicates (partial and chimeric).
In addition, human duplicates have, on average, much larger duplication spans which are more likely to capture entire ORFs leading to complete duplicates compared to higher proportions of structurally heterogeneous duplicates (partial and chimeric duplications) in Drosophila and C. elegans.
This method also serves to effectively exclude nonhomologous sites present in one paralog to the exclusion of the other (such as those found in partial and chimeric duplicate pairs).
To our knowledge, this study is the first to delineate the relative fractions of complete, partial, and chimeric paralogs within an unbiased population of gene duplicates in the human genome.
Contrary to expectations, there was no significant difference in the frequency of pseudogene containing duplicate pairs among the three structural categories of duplicates (complete, partial and chimeric), nor were pseudogene-containing duplicate pairs more likely to display asymmetric rates of sequence evolution relative to pairs comprising both putatively functional paralogs.
For gene duplicate pairs displaying structural heterogeneity in their coding regions (partial and chimeric structure discussed in the subsequent section), all measures of sequence divergence (synonymous divergence K S and degree of sequence asymmetry/symmetry via Tajima's relative rate test) were calculated using only the homologous regions between the focal C. elegans paralogs.
