Re: MRCA question

From: Perplexed in Peoria (jimmenegay_at_sbcglobal.net)
Date: 02/26/05 

Date: Sat, 26 Feb 2005 14:44:13 -0500 (EST)

"Joe Felsenstein" <joe@removethispart.gs.washington.edu> wrote in message news:cvovj3$2coh$1@darwin.ediacara.org...
> In article <cvmjrl$1jam$1@darwin.ediacara.org>,
> Perplexed in Peoria <jimmenegay@sbcglobal.net> wrote:
> >
> >"Joe Felsenstein" <joe@removethispart.gs.washington.edu> wrote in
> >message news:cvm8eu$1f80$1@darwin.ediacara.org...
> >>
> >> Going back 20 generations (500 years or so), you may have as many as a
> >> million ancestors.
> >> But your genome will have come from maybe about 300 of
> >> them, and the others contributed no genes to you.
> >
> >This estimate (300) seems too low to me, particularly if there is little
> >inbreeding. 1/300 of a genome works out to about 1/6 of a chromosome,
> >and I would have thought that recombination would slice and dice things
> >much more finely than this over 20 generations.
> >
> >Could you sketch a justification for
> >this number or provide a reference?
>
> I can sketch it. Consider a place in one copy of the genome. It comes from
> some ancestor at a remove of T generations (say). Another place far enough
> away from it to have recombination fraction r will come from the same
> ancestor, up the same lineage, if there is no recombination in any of those
> T generations. So the probability of being in the same chunk is (1-r)^T.
> If the recombination is uniformly spread with c recombination fraction
> per base, then 1-r = (1-c)^b when one is b bases away. Putting this
> together, one can see that the length of the chunk on this side of the original
> place then has exponential distribution with mean length 1/(cT) bases.
> On the other side of the marker the length of the chunk is also that.
>
> So if, as in humans, c approximately equal to 10^(-8), at a remove of 20
> generations the average chunk length is about 2 x 10^8 / 20 = 10^7 bases.
> As we have 3.2 x 10^9 bases per haploid set and 23 pairs of chromosomes, a
> chromosome length averages 139 Megabases. This chunk length is 10 Megabases,
> so about 13.9 chunks per chromosome. I think you got 1/6 by taking
> a diploid individual, while I took a haploid. So you were closer as we
> would want to count how many chunks in a whole genome, not just a haploid
> genome.
>
> Of course, the chunks are not of uniform size, and also they coalesce
> with each other, and recombination has "hot spots". Still, this shows the
> basis for this surprisingly small number.

Thx. The surprise for me in this analysis is that c is as small as 10^(-8).
I could have looked it up, I suppose, except that I didn't know the
correct name ("recombination fraction") for this number.

But this changes my whole picture of evolution! Dawkins (in "The Naked Gene",
I think) offers a heuristic definition of a gene as a stretch of DNA long
enough to have some function, but short enough so that it is not broken
up by recombination too soon. Ok, so how soon is TOO soon? It depends on
the time frame you are interested in. And, I think we have just shown that
if the time frame is 20 generations, then the human genome has on the order
of 300 loci! (Well, in a manner of speaking, anyways.)

Edser's "epistatic information" appears to be much more "heritable" (over
the short term) than I had thought. (The portion of "epistatic information"
that lives on a single chromosome, anyways.) Also, linkage equilibrium
is approached much more slowly than I had thought. And selection coefficients
much smaller than I had thought can maintain linkage disequilibrium.

None of this seems to make any difference in the unending Hamilton debate.
Except for the amusing point that if you accept Dawkins' definition of
a gene, and set the number of generations small enough, then the "gene
for altruism" really will be a rare allele - only your close relatives will
have it.

Relevant Pages

  • Re: MRCA question
    ... So it's a genealogical ancestor but probably not a genetic ... >and I would have thought that recombination would slice and dice things ... Consider a place in one copy of the genome. ... So the probability of being in the same chunk is ^T. ...
    (sci.bio.evolution)
  • Re: Part 1 (of 3): What are major aspects of evolutionary theory?
    ... Just don't call it group selection, ... to decide whether it has the exact allelle you want ... >>length of the average human gene, so that recombination between and even ... > between adjacent genes and sometimes within the same gene. ...
    (talk.origins)
  • News: Gene Variants May Help To Distribute The Work Of Evolution Between Men And Women
    ... Gene Variants May Help To Distribute The Work Of Evolution Between Men And ... genome that regulate one of the principle motors of evolution. ... Recombination is largely ...
    (sci.bio.evolution)
  • Re: Junk DNA: A hypothesis
    ... >> with the same probability, regardless of how long they are. ... > I'm assuming that the recombination rate is under genetic control ... > probability is proportional to the density of the genes in the genome. ...
    (sci.bio.evolution)
  • Re: recombination question
    ... In my basic understanding of genetic recombination, ... recombine with crossings at essentially random locations in the DNA ... sometimes a crossing point must occur within a gene. ... if the two chromosomes have different alleles at that point in the DNA ...
    (sci.bio.evolution)