Restriction Enzyme Phylogenies

Joe Felsenstein joe at evolution.genetics.washington.edu
Thu Feb 15 01:52:00 EST 1996

In article <DMqyMw.61p at zoo.toronto.edu>,
Mark Siddall <mes at zoo.toronto.edu> wrote:
>In article <4fpfsm$q3f at newsbf02.news.aol.com> daro at aol.com (Daro) writes:
>>It seems most phylogenies inferred from RE data assay the entire
>>However, my research involves a more limited assay...I use an
>>oligonucleotide probe for a specific gene instead of labeling all the
>>fragments.  Can I still calculate genetic distance (for example, Nei and
>>Li's method) from this data or would this distance reflect the specific
>>gene's (i.e. probed gene) distances?
>In my all-too-typical nay-saying fashion, perhaps you should contemplate
>whether or not these data are reasonable for phylogenetic inference.
>I should bother you that radically different melting curves
>could have identical T50 values for starters.

Mark is raising problems with delta-T50 measures used in DNA hybridization
studies.  That seems quite irrelevant to Daro's question, which was whether
restriction-fragments-based distances normally used oon whole genomes
can be applied to local regions.  As far I can see they can be, and T50
measures are not part of the discussion.

Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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