selective constraints
Eöry L, Halligan DL & Keightley PD 2010 Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Mol Biol Evol 27:177-192.
- the level of selective constraint operating in hominid noncoding sequences is subject to uncertainties
- constraint has been reported to be nearly absent in first introns of hominids
- first introns appear to be among the most strongly constrained intronic regions in murids
- selective constraint has also been reported to be essentially absent in intergenic regions
- alternative splicing is believed to be prevalent in mammals, potentially operating in more than 60% of human genes
- here we use ... ancestral repeats (ARs), which are TEs inserted into the common ancestor of the species under consideration as a paradigm for neutrality
- ARs are widespread in mammalian genomes
- they comprise 45% of the human genome (Ensembl release 48) and are sufficiently scattered as to serve as local neutral standards
- the distribution of insertion and deletion (indel) events in human and mouse ARs fits a neutral indel model
- whereas the genome as a whole appears to be under indel purifying selection
- our results show that evolutionary rates of ARs in hominids are very close to that observed in pseudogenes, which are usually assumed to evolve free of constraints
