At least three hypotheses could explain the parallel accumulation of nested gene structures in different taxa. First, a nested structure might confer a selective advantage because of a functional or co-regulatory relationship between its members [16
]. Second, according to the transcriptional collision model, members of a nested gene structure could interfere with each other’s transcription [21
], resulting in alternative expression of these genes in different tissues or during different times in development. Finally, acquisition of a nested gene structure could be a neutral process [8
], driven by the presence of numerous long introns that provide niches for insertion of genes. Each of these hypotheses leads to a distinct prediction about the relationship between the expression of internal and external genes in a nested pair. The functional co-regulation hypothesis predicts a positive correlation between levels of their expression in similar tissues, the transcriptional collision hypothesis predicts a negative correlation and the neutral hypothesis predicts no correlation.
To discriminate between these three hypotheses, we analyzed gene expression data from human and D. melanogaster
genomes (see Supplementary Material
). We compared correlations of gene expression in 109 and 752 nested gene pairs in humans and D. melanogaster
, respectively, to 1000 random sets of 109 and 752 adjacent gene pairs from corresponding genomes. There was no significant difference in mean correlation coefficients of gene expression levels between nested and adjacent genes in either human (0.33 ± 0.03 for nested and 0.33 ± 0.0008 for adjacent pairs) or D. melanogaster
(0.041 ± 0.014 for nested and 0.030 ± 0.00046 for adjacent gene pairs), which is consistent with the neutral hypothesis. The observation that external genes have substantially more and longer introns than average in the respective species (Ref. [7
] and Supplementary Material
) is also compatible with the neutral hypothesis. Furthermore, examination of the available functional information for nested gene pairs (Table S1
) did not reveal any obvious connections [7
]. Fixation of originally neutral or even slightly deleterious sequence segments, such as introns and transposable elements, through genetic drift acting in relatively small populations is a common phenomenon in eukaryotic evolution that might be partially responsible for the evolution of complex phenotypes [8
]. The increase in organizational complexity of intron-rich genomes via emergence of nested gene structures seems to be another facet of this process.