Abstract
We recently reported that the human genome is ‘‘splitting” into two gene subgroups characterised by polarised GC content (Tang et al, 2007), and that such evolutionary change may be accelerated by programmed genetic instability (Zhao et al, 2008). Here we extend this work by mapping the presence of two separate high-evolutionary-rate (Ka/Ks) hotspots in the human genome—one characterized by low GC content, high intron length, and low gene expression, and the other by high GC content, high exon number, and high gene expression. This finding suggests that at least two different mechanisms mediate adaptive genetic evolution in higher organisms: (1) intron lengthening and reduced repair in hypermethylated lowly-transcribed genes, and (2) duplication and/or insertion events affecting highly-transcribed genes, creating low-essentiality satellite daughter genes in nearby regions of active chromatin. Since the latter mechanism is expected to be far more efficient than the former in generating variant genes that increase fitnesss, these results also provide a potential explanation for the controversial value of sequence analysis in defining positively selected genes.
Highlights
The genomes of higher species are under negative selection to maintain complexity, yet must remain adaptable in order to defer extinction in changing environments
Geographical isolation and inbreeding accelerate positive selection [9]— for genes related to sexual pheromones, mate choice, fertility or neurodevelopment, many of which have been implicated by sequence (Ka/Ks) analysis [10,11,12]
Prior to this we reported a positive correlation between intron length and 3 gene evolutionary rate, suggesting that this association reflected DNA misrepair due to intron-dependent transcriptional attrition [17]
Summary
The genomes of higher species are under negative selection to maintain complexity, yet must remain adaptable in order to defer extinction in changing environments. Geographical isolation and inbreeding accelerate positive selection [9]— for genes related to sexual pheromones, mate choice, fertility or neurodevelopment, many of which have been implicated by sequence (Ka/Ks) analysis [10,11,12]. Whether such analyses suffice for sensitive and specific detection of positively selected genes, is debated [13, 14]. The results implicate two separate pathways to adaptive evolution, at least one of which seems likely
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