Study: Recent Selection in Many SNPs

[selfAdjoint]

A big new hapmap study has concluded that there has been strong recent selection (indicated by significant decay of linkage disequilibrium) in over 1800 gene-sites.

http://www.pnas.org/cgi/reprint/0509691102v1

Here, we construct a probabilistic model, based on our prior
experimental approach (6, 8), designated the LD decay (LDD) test.
The method relies only on high-heterozygosity SNPs for analysis,
exactly the type of data obtained in the Perlegen and HapMap
efforts (1, 2). This ‘‘first-pass’’ analysis uncovers a surprising number
of alleles with the fingerprint of recent positive selection, in
contrast to other global approaches using less-sensitive methods (1,
2). We outline several predominant biological themes among genes
detected with this strategy and suggest that selection for alleles in
these categories accompanied the major ‘‘out of Africa’’ population
expansion of humankind and/or the radical shift from hunter–
gatherer to agricultural societies (23–26).

 

[pattylou]

Did you see the article about a month ago that specu;ated that human-chimp differences may be more a result of inversions, than actual DNA sequence differences?

This is not directly related to snrps (which I assume are the same as SNP's) but on the other hand if you like the one, you probably dig the other.

http://www.sciencedaily.com/releases/2005/10/051026081736.htm

Flipped Genetic Sequences Illuminate Human Evolution And Disease


By comparing the human genome with that of the chimpanzee, man's closest living relative, researchers have discovered that chunks of similar DNA that have been flipped in orientation and reinserted into chromosomes are hundreds of times more common in primates than previously thought. These large structural changes in the genome, called inversions, may account for much of the evolutionary difference between the two species. They may also shed light on genetic changes that lead to human diseases.

Although humans and chimpanzees diverged from one another genetically about six million years ago, the DNA sequences of the two species are approximately 98 percent identical. Given the 2005 publication of the draft chimpanzee genome sequence, researchers can now readily identify the differences between the human and chimp genomes. These differences lend insight into how primates evolved, including traits specific to humans.

 

[Monique]

A big new hapmap study has concluded that there has been strong recent selection (indicated by significant decay of linkage disequilibrium) in over 1800 gene-sites.
http://www.pnas.org/cgi/reprint/0509691102v1

Interesting study, I like the approach they've taken.

I don't understand your comment though that a significant decay of LD (linkage disequilibrium) would indicate selection. They base their results on the fact that a novel allele would be lost quickly in a population and that old alleles have small LD blocks. A high frequency allele with a large LD block must thus be caused by positive selection (or the other causes they mention: inversion, bottleneck, admixture).

They do mention progressive decay specifically on page 136, where I think they distinguish between linear decay (no selection) and exponential decay (selection) because as they say "the number of possible meiotic recombinations not eliminating the advantageous allele increases as a function of distance from the selected site", which make sense.

For those not familiar with the term linkage disequilibrium: you have equilibrium when you can NOT predict the neighbouring state of a marker, since they are in equilibrium the state is 'random'. You have DISequilibrium when you can predict the state of a marker by knowing the state of its neighbour.

An example when this happens is when the chromosome has a common ancestor: the states of all markers will be the same on the whole chromosome. Since recombination happens (about 40 per meiosis) this linkage disequilibrium decays because markers are exchanged between chromosomes. When there is linkage disequilibrium, marker states are inherited together (no recombination took place).

 

[Monique]

Did you see the article about a month ago that specu;ated that human-chimp differences may be more a result of inversions, than actual DNA sequence differences?

That's interesting..

This is not directly related to snrps (which I assume are the same as SNP's)

The only definition I know for SNRPs are small nuclear ribonuclear proteins, which make up a complex splicing machine that removes introns from RNA, not related to this.