> At 03:11 PM 8/29/96 +1000, Peter Hughes wrote:
> (snip)
> >Actually I would not worry so much about that because the study was not
> >designed to pick up differences between individuals. It was a study of
> >the ITS region of the mitochondrial genome and although it is the fastest
> >mutating point of the genome, it still is does not represent the greatest
> >level of genetic variation in the animal. There are other regions that
> >can be used to pick individuals apart, I just don't think that this was
> >one of them. The study was about assessing the divergence among the
> >species tested and i think that it did a very good job of that. Only some
> >of the very recent PCR technolgy ie RAPD's and AFLP's may begin to answer
> >some of the questions that you are talking about Peter.
>
> Shameless name-dropper ;-) - seriously, Peter, could you churn out a little
> vegemite and laymanise the above acronyms for us?
Ok for you andrew.
The ITS region of the mitochondrial genome is a region between two very
important genes that are critical for the function of the mitochondrian.
The important genes are very very highly conserved accross distances as
great as bacteria and humans (well at least the major functional bits
are). The bit in between is the exact opposite and changes very
frequently. It is thus used to detect distances that are not all that
great eg the aforesaid differences between the melanotaenid fish in the
study. It is not useful for greater distances because after a while the
changes tend to start to fall on top of each other and so the distance
between the two is an under estimate of the real one, the same is true of
shorter distances because there is not enough variation and so a single
change may be as big as it gets. It also has another problem because it
is only maternally inherited, while this is fine for intra species and
intra population studies it gives no information about variation at the
individual level. What it can give is who is the mother of who and that
is about it.
Ok, the next bit is a bit more tricky. RAPD, is "random amplified
polymorphic DNA". Random stretches of DNA are artificially multiplied and
the bits run out on a gel that separates them according to size. If you
are lucky and have the right combination of primers and cut DNA starting
the reaction, then you will see a piece of DNA that is in one individual
but is not in another. In conventional technology it is called a
"marker" and the apperance of that band in children of that individual
shows that they have that piece of DNA from that parent, its absence
indicates that it came from the other parent.
AFLP is "amplified fragment length polymorphism" (ok I can see
everybodies eyes glaze over at that one, but I was asked). This is
similar to the one above but produces more bands and is a more powerful
technique. The downside is that you may get too much information and
sorting through it becomes a difficult process.
These two techniques can find the small differences that exist between
individuals of the same species and can be used as markers in breeding
experiments that would be able to show how the variation within the
population was changing. The experiment would need fish from about 4-6
generations to test it properly because it is about this generation
number that is needed to make a population almost identical deliberately.
Peter Hughes