A burst of segmental duplications in the genome of the African great ape ancestor:
It is generally accepted that the extent of phenotypic change between human and great apes is dissonant with the rate of molecular change...Between these two groups, proteins are virtually identical...cytogenetically there are few rearrangements that distinguish ape-human chromosomes3, and rates of single-base-pair change...and retrotransposon activity...have slowed particularly within hominid lineages when compared to rodents or monkeys. Studies of gene family evolution indicate that gene loss and gain are enriched within the primate lineage...Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orang-utan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of base pairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single-base-pair mutations, there has been a genomic burst of duplication activity at this period during human evolution.
ScienceDaily has some breathless coverage. But are we, H. sapiens, so special in our evolutionary history?* The title above about human uniqueness seems to be the major framing assumption when this sort of research gets spun....
* Well, Mike Lynch very specific ideas about how we are special.
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The bolded section in the quote above indicates practically nothing particularly new, except perhaps the timing of this particular burst of this particular mutation type in this particular lineage. It is an interesting bit of genomic natural history (if it holds up), but I think the key insights regarding how unique duplications are have been made well before Evan Eichler came onto the scene.
Fisher started thinking about that in 1935:
Fisher,. R. A., 1935. The sheltering. of lethals. Am, Nat. 69:. 446-455.
Susumu Ohno did a lot of thinking about it in his seminal 1970 book, "Evolution by Gene Duplication". Bruce Walsh, Michael Lynch, Allan Force, Andy Clark, and John Conery also put in several important pieces in the mid '80s through 2000.
Not to detract from this paper at all, it is excellent work. But I think this is one of those "I got there first and so can confirm some obvious hypotheses". In fact, from Eichler's own work, you could already claim that given the amount of segmental duplication in humans, a large source of difference between humans and chimps (for example) or humans and lemurs (for another) is due to duplication.
I am interested in reading it more carefully to determine how robust the "burst" of duplication is, and whether it is related to population processes, mutation processes, or adaptive forces. (In other words, Is it a genetic drift thing, change in mutation, or change in adaptive preservation?)
So what is the big deal behind copy number variation? Will it be used in future human genetic variation studies?
Actually there's relatively little "human uniqueness" hype in the SDaily article besides the title. The bolded sentence from the abstract is more misleading, IMO:
"there has been a genomic burst of duplication activity at this period during human evolution." - But "this period during human evolution" actually refers to "the ancestral branch leading to human and African great apes", nothing human-specific...