Human segmental duplications are hotspots for nonallelic homologous recombination leading to genomic disorders, copy-number polymorphisms and gene and transcript innovations. The complex structure and history of these regions have precluded a global evolutionary analysis. Combining a modified A-Bruijn graph algorithm with comparative genome sequence data, we identify the origin of 4,692 ancestral duplication loci and use these to cluster 437 complex duplication blocks into 24 distinct groups. The sequence-divergence data between ancestral-derivative pairs and a comparison with the chimpanzee and macaque genome support a 'punctuated' model of evolution.
Our analysis reveals that human segmental duplications are frequently organized around 'core' duplicons, which are enriched for transcripts and, in some cases, encode primate-specific genes undergoing positive selection
. We hypothesize that the rapid expansion and fixation of some intrachromosomal segmental duplications during great-ape evolution has been due to the selective advantage conferred by these genes and transcripts embedded within these core duplications.
...In the Nature Genetics paper they highlight two big picture findings. First, the researchers suggest that specific regions of the human genome experienced elevated rates of duplication activity at different times in our recent genomic history. This contrasts with most models of genomic duplication which suggest a continuous model for recent duplications. Second, the researchers show that a large fraction of the recent duplication architecture centers around a rather small subset of "core duplicons" -- short segments of DNA that come together to form segmental duplications. These cores are focal points of human gene/transcript innovations.
This is all great. Why should positive selection be all about SNPs? And it makes sense that bouts of positive selection wouldn't be continuous and constant. Consider the expansion of our species out of Africa 100,000-50,000 years B.P., it seems that rapid migration into new ecologies would result in almost immediate pressures toward new adaptations. Related:SNP, SV, CNV...does the substrate matter?
