Re: Making sense of HLA (I)

In sci.archaeology message news:Xns983FCD6AFB659lisandbredbandnet@
66.150.105.47 by Lisbeth Andersson <lisand@xxxxxxxxxxxx> . . . :

prd <X_header@xxxxxxxxxxx> wrote in news:JDXMg.98377$5i3.51962
@bgtnsc04-news.ops.worldnet.att.net:

I've finally gotten around to reading this thread. You can save
yourself a lot of questions by recommending a website or a book that
explains this stuff to a non-expert.


If you go to
http://tech.groups.yahoo.com/group/DNAanthro/

The picture on the front shows the genetic distance between A and B
45.28-44.9 = 0.38% per generation.


Maybe it does. It is not immediately obvious to a non-expert. How do
you get that? What does the cM unit measure?

A morgan is a length of recombination.
Basically one expects a recombination event every
generation of length Morgan. So that a centimorgan (cM)
is the length of chromosome in which one expects
one recombination event every 100 generations.



Before we had any idea of what DNA was made up
of, people working on drosophila, peas, etc
had determined the 'linkage map' of the chromosome

Did you know the word "linkage group" is the old
name for a chromosome? In C. elegans they are still
called linkage groups.

Two genes that are called unlinked when they show
no less than 1 morgan in distance, the best example
of non-linkage would be any mtDNA gene and the Y chromosome.
Any degree of linkage means that two genes are on
the same chromosome, but lack of linkage does not. For
example the distal end of chromosome 1p shows no
genetic linkage to 1q, but they are one the same cromosome
most chromosomes are about 2 to 3 Morgans in genetic length
the numbers are derived by adding successive small sections of linkage
together since no individual measure of linkage is greater than 1.

Genetic length of chromosome from short to long arm.

0.....1...... 2....3
XXXXXXXXXX XXXXXXX
XX
XXXXXXXXXX XXXXXXX

If one were to take a chromosome of the above
Maternal and Paternal derived for say a reproductive female

P Q Chromosome side (arm)

MMMMMMMMMM MMMMMMM
MM Chromsome N (from mother)
MMMMMMMMMM MMMMMMM
X X Xs mark points of recombination(can be anywhere in
pppppppppp ppppppp each arm)
pp
pppppppppp ppppppp Chromsome N (from father)

to form an egg

AND

MMMMMMMMMM MMMMMMM
MM Chromsome N (from mother)
pppppMMMMM MMMMppp

MMMMMppppp ppppMMM
pp Chromsome N (from father)
pppppppppp ppppppp

The egg however gets one of these chromosomes
from

pppppMMMMMMMMMMMppp Chromatid N (from Egg)

So that in each generation an offspring gets a copy
a chromosome that is different from its parents chromosomes.
Many scientist believe that this ability to recombine
genes in a programmed manner has allowed eurocaryotes
to develope and supercede most procaryotes in complexity.

I am going to mark of the chromosome.

ABCDEFGHIJKLMNOPQRS

MMMMMMMMMM MMMMMMM
MM Chromsome N (from mother)
MMMMMMMMMM MMMMMMM
X X Xs mark points of recombination(can be anywhere in
pppppppppp ppppppp each arm)
pp
pppppppppp ppppppp Chromsome N (from father)

Suppose I have a gene which is an allele at locus D allele 1 (A1)
Now suppose I have a gene which is an allele at locus F allele 3 (I3)

Suppose you have a gene say (A8) and suppose you have
another (I2)

Now suppose you are in a population with mostly A8:I2
Now suppose your population and my population A1:I3

Over time, dependent on the genetic distance recombination
will occur

Let us suppose the D is on the end of Chromosome N
and F is at the middle. Now let us suppose when populations
mix the breeding was random and the number of females
and males of each group are 50:50

Homologous pairs.

A8:I2 x A8:I2 pairs will be 25% and will not result in
any recombinants (recombination will occur but will not be
productive)

Their progeny will be A8:I2/A8:I2 same as the parents.

A1:I3 x A1:I3 will have the same result - No 'effective' recombination.

Their progeny will be A1:I3/A1:I3 same as the parents.

But 50% of the pairs will be
A1:I3 x A8:I2


Heterlogous Pairs

Their progeny will be A1:I3/A8:I2 same as the parents.

and when the progeny of this couple generate sperm and eggs
they will be

A1:I2 or A8:I3

Therefore after generation 2 of we call F2 we shall see
Progeny with A1:I2 type or A8:I3 and the population
of that generation will be

25% A1:I3
25% A1:I2
25% A8:I3
25% A8:I2

IF A and I are closer together say 10 cM apart we expect

45% A1:I3
45% A8:I2
5% A1:I2
5% A1:I3

If A and I are closer still, say 1 cM we can expect
per generation

49.5% A1:I3
49.5% A8:I2
0.5% A1:I2
0.5% A1:I3

If we role this process out over 10 generations we would

~45% A1:I3
~45% A8:I2
~ 5% A1:I2
~ 5% A1:I3

The assumption that recombination is a means of measuring
since time of mixing depends on
1. The genetic distance, measurable in real time
2. The relative frequencies of haplotypes on mixing
3. The randomness of mating.

The big problem is that mating is never random. And while
two alleles may be 'effectively' neutral geographic
and isolative barriers, drift, etc alter the 'effective'
longterm rate of recombination from ideal to observed.

.

Relevant Pages

  • Re: Part 1 (of 3): What are major aspects of evolutionary theory?
    ... sure whether there was recent gene flow between them or the same SNP ... But any single haplotype block has *many* different states, ... a set of genes at different loci on the same chromosome that except ... many linkage groups as there are homologous pairs of chromosomes. ...
    (talk.origins)
  • Re: Size of Y Chromosome
    ... If Chromosome don't get partner to recombine than there is tendency ... If gene deletion by natural selection if it is correct why there is ... chances that the organism with the mutated B gene surviving 99 ... eventually gene B will mutate. ...
    (sci.bio.evolution)
  • Re: Part 1 (of 3): What are major aspects of evolutionary theory?
    ... to more than 100 million per chromosome. ... >> many linkage groups as there are homologous pairs of chromosomes. ... something portrayed as just a linkage map, with two genes indicated at ... codon and ends with a nonsense codon. ...
    (talk.origins)
  • Re: chromosome repair leading to expression of recessive genes?
    ... > I was reading this article talking about the future of the Y chromosome ... Every time a cell ... > when a gene on a chromosome is damaged, ... There are different reasons why one allele is dominant over another ...
    (sci.bio.evolution)
  • Re: Part 1 (of 3): What are major aspects of evolutionary theory?
    ... haplotype blocks offer a really powerful way to ... > one Y chromosome, and then these blocks are split from each other as ... > many linkage groups as there are homologous pairs of chromosomes. ... That was a terrible definition of "linkage group". ...
    (talk.origins)
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