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Phylogenetic trees from DNA including microsatellites

Tom Thatcher ttha at uhura.cc.rochester.edu
Wed Jun 14 07:48:28 EST 1995

In <3rkl2i$l0g at mserv1.dl.ac.uk> Frank Wright <frank at sass.sari.ac.uk> writes:

>Hi Joe,
>       I'm helping someone analyse rRNA ITS data from several
>plant species.  It contains short stretches that look like
>microsatellites (e.g. GC---- in one species, GCGC-- and GCGCGCG
>in others; "-" denotes gaps).  

>My feeling is to exclude thses stretches from the phylogenetic
>tree analysis as they probably are microsatellites and thus
>do not evolve by simple nucleotide substitution.  The trouble 
>is that there is not a lot a variation left in the dataset if 
>these are excluded.

I would exclude any sequence on which there is no evolutionary pressure,
or for which there is no function.  DNA sequences that encode proteins
or functional RNAs, or are promoters or enhancers, have function.
Since introns have no function, they are free to evolve quite rapidly
and drastically, and not neccessarily the same in different species.

Before analyzing intron sequences I would want references to back up
their relevance.

Just my opinion, of course.

Tom Thatcher                          | You can give a PC to a Homo habilis,
University of Rochester Cancer Center | and he'll use it, but he'll use it
ttha at uhura.cc.rochester.edu           | to crack nuts.

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