MHC for Badger Paternity

John Ladasky ladasky at leland.Stanford.EDU
Tue Aug 6 00:24:19 EST 1996

In article <biozapj-0408961513080001 at>,
Anabela Pinto Jensen <biozapj at> wrote:
>Dear all
>I'm looking for somebody that can give me some ideas about methods in
>MHC determination. 
>I am a behavioural ecologist and don't have a clue about immunology or 
>mol. biology. My goal is to identify who is fathering the litters of a
>clan of wild badgers. I'm considering to take blood samples of this
>population and identify each individual. Next year I will do the same to
>their litters and try to identify  who is fathering them. 
>Is it possible to do in practice?
>Is there any labs working on this technique ? I would like to spend some
>time learning the technique.
>Please reply to me,to my personal address, since I don't usually check
>these lists.

Greetings, Anabela,

	My group, under the direction of Dr. Peter Parham, studies MHC 
class I genes in humans, chimpanzees, owl monkeys (my personal project),
and even fish.  My advice to you is that you should not use MHC typing 
to identify parentage, unless you also really want to know something about 
badger MHC molecules.  

	I have not seen any literature describing MHC molecules in ursine
species.  If some sequences were known, you might be able to design a PCR
(polymerase chain reaction) method to get you the badger MHC sequences.
This is the *only* method I would recommend to someone who does not want
to spend a lot of time learning molecular biology.  The best alternative
I can think of, making cDNA and genomic libraries from a few representative
animals, screening for clones by hybridization, identifying loci, and then
designing a PCR from the information you obtain, would probably take you
a few years!  You would generate two or three interesting papers along the
way, but you would have completely distracted yourself.

	Look up references for a technique called RAPD -- it stands for 
random amplification of polymorphic DNA.  This is also a PCR technique.
It identifies DNA sequence differences between individual animals.  You
don't necessarily care where those differences are in the genome, only
that they do differ.  In order to explain all the bands you see on the
electrophoresis gels, you will also need to do the RAPD on the mothers.
I have never tried this technique, but others I know attest to its 

	No matter which approach you choose, you need to worry about the
possibility of genetic overlap.  What is the social structure of badgers?
(You should know better than I!)  If the populations are relatively small
and inbred, then two males in an area may likely be brothers.  If you ex-
amine just the MHC, you have at best an 83% chance of telling their
offspring apart, *despite* the high diversity of the MHC.

	Most loci are a lot less diverse.  If there are only two alleles
at a given polymorphic locus (this is the most common condition), you 
have a mere 13% chance of telling the offspring of two brothers apart,
even if you know the mother's genotype!  These odds get even worse if 
the two alleles are not represented at equal frequency in your population
(for example, allele A is present at a 90% gene frequency, and allele B
is present at 10%).  So you need to examine as many independently-segre-
gating *and polymorphic* loci as possible (which generally implies that 
they are on different chromosomes).  The RAPD is the best way to get you
those multiple loci, without forcing you to deal with all of the ugly

	Send me email if you have any more questions.  Good luck!

Unique ID : Ladasky, John Joseph Jr.
Title     : BA Biochemistry, U.C. Berkeley, 1989  (Ph.D. perhaps 1998???)
Location  : Stanford University, Dept. of Structural Biology, Fairchild D-105
Keywords  : immunology, music, running, Green

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