Evolutionary genomics and the reach of selection

Abstract

Unexpected findings in evolutionary genomics both question the role of selection in genome evolution and clarify how genomes work.

Figure 1

The protist Paramecium has short introns in which some contain stop codons. Introns in multiples of threes are more likely to contain a stop codon as a fail-safe measure for correct splicing. (a) The failure in removal of an intron that is not a multiple of three will cause a frameshift and this will most likely introduce an out of place stop codon in the resulting mRNA. This transcript can then be degraded by nonsense mediated decay (NMD). (b) When an intron that is a multiple of three long is not removed, it will not cause a frameshift and therefore the mis-spliced transcript will not be degraded. (c) This can be overcome by having stop codons in introns of multiple of three. Therefore when the intron is not removed, NMD can act on the incorrectly placed stop codon and remove the transcript.

Figure 2

Influence of genomic co-localization on gene coexpression as a function of similarity in transcriptional control. Transcriptional control similarity (TCS) is a measure of the similarity in the suite of transcription factors that regulate a pair of genes. A score of zero means no similarity, a score of one means the very same transcription factors regulate the two genes. Mean levels of coexpression of neighboring genes are shown as black circles and of non-neighbors as white squares; error bars represent standard error of the mean. Note that neighboring genes with no transcription factor control similarity (TCS = 0) have, on average, the same level of coexpression as two unlinked genes with TCS = 1. Adapted from [9].