AFLP reliable for study of evolution?

[Lai-Lai Teo]

David Baum wrote:
>1) As with restriction fragment analysis (that doesn't take the trouble to
>map the sites), there is likely to be non-independence between bands.  Thus
>a band of length 300bp could be homologous to a band at 400bp without you
>knowing it.  This length difference erroneously gets scored as two
>presence-absence characters and is, hence, overweighted.  Still, if the
>number of variable characters is high (and it can be much higher with AFLPs
>than with RFLPs) then the occassional non-independent sites might get
>swamped.

I write:
I agree that sometimes fragments of different length might be homologous,
and get scored as two characters.
I understand that some AFLP marker are dominant, whereas others are
co-dominant.  The easiest way is to score the presence-absence of the band
(presuming all the markers are dominant), but I remember I read somewhere
that some markers are codominant.  I don't really understand the author
determine whether an AFLP marker is dominant or codominant.  If it does
exist, I wonder if the two codominant markers are inherited from the same
ancestor (with later insertion of deletion of one to several nucleotides)?
If so, does it mean that co-dominant markers is better in describing the
ancestry of the plant of interest?


David Baum wrote:
>2) If, you are working close to the species level then you have a problem
>interpreting the resultant tree.  Supposing you had sequenced a particular
>gene or had done RFLP analysis on a given part of the genome.  In that case
>the tree obtained would be an estimate of the phylogeny of that part of the
>genome.  So even if this part of the genome has a different tree to other
>parts of the genome (due to reticulation as occur via interbreeding within
>populations, lineage sorting, and hybridization) then at least it has a
>tree like history.  In the case of AFLPs (or RAPD), which are scattered
>through the genome, there may be no underlying divergent tree to be
>estimated.  In that case a standard "phylogenetic" analysis is really a
>glorified "phenetic" analysis and I, for one, am unsure what the resultant
>tree (phenogram) really means.  There may be ways to look at data (post
>hoc) and see if it is representative of a real underlying tree.  But to my
>knowledge these analyses have not yet been developed.
>
>I have been a skeptic about using AFLP data for phylogenetics but, provided
>one is confident that the underlying genomic relationships are divergent
>not reticulate, maybe it has potential.

I write:
I use AFLP to determine the parentage of wild hybrids.  I haven't came
across any publication that use AFLP for this purpose (maybe there are some
of them which are beyond my accession), and thus am not very sure whether it
is suitable for this purpose.  I assume that the AFLP marker of both parents
will be inherited additively in the hybrid, as does RAPD marker which is
commonly used to study hybridization.  I prefer AFLP over RAPD because of
it's high repeatability.

Regards,
Lai-Lai



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