Jean-Francois Martin wrote:
>> In butterfly mtDNA, the composition bias is extreme toward A-T (80 to 90%
> depending on gene and codon position).
> It seems also unlikely that every kind of substitution has equal probability
> to occur.
> Furthermore a selection against substitutions providing G and C, which has
> been demonstrated in Dloop of mammalians (A-T rich), is not correctly
> represented by ML models. At least for what I know about Maximum Likelihood
> and PAUP* options, it is impossible to use a non reversible model. Even if
> it was possible, what kind of weighting sheme could fit to the actual (not
> the observed) substitution pattern?
>
Jean-Francois,
There has been a wonderful advance recently in work towards
non-homogenous ML models, led by your own compatriots in Lyon.
Nicolas Galtier and Manolo Gouy have developed a model and accompanying
program for using a non-homogenous ML model in order to infer
phylogenies. It is possible, using this method to allow for variation in
base composition across lineages in the tree.
It has been a little while since I read the paper, so I'm a bit rusty on
the specifics and I don't have the paper to hand, however, you can see
the reference at:
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9656487&form=6&db=m&Dopt=b
They then went on to use the method in:
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9880254&form=6&db=m&Dopt=b
You can pick up the program at:
ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/nhml/
Hope this helps,
James
--
Dr. James O. McInerney,
Dept. Biology, Dept. Zoology,
Natl. Univ. Ireland, The Natural History Museum,
Maynooth, and Cromwell road,
Co. Kildare, Ireland London SW7 5BD, UK.
Phone +353 1 708 3860 +44 171 938 9163
Fax +353 1 708 3845 +44 171 938 9158
email james.o.mcinerney at may.iej.mcinerney at nhm.ac.uk
