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
>>chromosome.
>>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. 128.95.12.41)
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA



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