Lower-than-expected linkage disequilibrium

Andrew Gyles syzygium at alphalink.com.au
Fri Sep 7 20:48:00 EST 2001


"Dan Garrigan" <garrigan at asu.edu> wrote in message
news:9n9d0f$jr$1 at mercury.hgmp.mrc.ac.uk...
> On 3 Sep 2001, Andrew Gyles wrote:
>
<snip>

> If intra-genic conversion occurs in an individual that is heterozygous
within
> the conversion tract, you can think of it more as a form of mutation,
whereby
> a new haplotype is created during that round of meiosis.  The donor
haplotype
> can still be reproduced intact, so its not exactly like you're thinking
> about.  There may be some slight effect that you allude to, but certainly
it
> would be nothing compared to the effects of genetic drift and
crossing-over.
>
> Dan
>
> P.S. What did you think of the idea presented in that paper?  Gene
conversion
> can definitely create the heterogenous pattern of L.D. that those authors
> found, but...how widespread and frequent is it? What else could cause that
> pattern of L.D. or is it just random noise?
>
> *********************************************************
> * Dan Garrigan Phone: (480)965-4556    *
> * Dept. of Biology Fax: (480)965-2519      *
> * Arizona State University Email: garrigan at asu.edu *
> * Tempe, AZ 85287-1501 *
> * Internet: http://www.public.asu.edu/~garrigan/ *
> *********************************************************


Thank you for your comments. I am not a specialist in geneticist, so my
opinion carries little weight. The findings reported in the paper I referred
to certainly present a puzzle, and gene conversion seems able to solve it by
letting distant loci remain linked but seeming to 'swap' loci that are close
together. But it is not a complete 'swap', it is a conversion of just one
strand, as you remarked.

Wiehe, Mountain, Parham and Slatkin's paper (Genet Res 2000 Feb;75(1):61-73)
"Distinguishing recombination and intragenic gene conversion by linkage
disequilibrium patterns", concluded: "We find that conversion may have
played a dominant role in shaping haplotype patterns over short stretches of
DNA, whereas reciprocal recombination may have played a greater role over
longer stretches of DNA. However, in order to draw firm conclusions more
independent data are necessary". This is similar to your opinion, I think.
Maybe the pattern is just random noise.

My interest was in finding a mechanism that might have reduced sequence
variation in humans compared with apes. I thought that biased gene
conversion might have achieved this. However, one geneticist has told me
that the evidence for low sequence variation in humans is very weak; if that
is the case it does not have to be explained! But Steve Jones, geneticist at
University College, London, says that there is less sequence variation
between two human groups at each other's antipodes on the planet than there
is between two groups of chimpanzees living 20 miles apart in Africa, so I
don't know what to accept.

Regards,

Andrew Gyles




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