rising@utzoo.UUCP (Jim Rising) (10/30/87)
Joe, I'd be interested in your reasoning for saying that DNA hybridization is not phenetic. It would seem to me that a commparison of the unweighted overall similarity in the DNA base sequences between two species could be the ultimate phenetic method--depending, I suppose on how it was analysed. Of course, I doubth that this is what DNA hybridization studies actually do, but don't they purport to do so? --Jim Rising -- Name: Jim Rising Mail: Dept. Zoology, Univ. Toronto Toronto, Ontario, Canada M5S 1A1 UUCP: {allegra,ihnp4,linus,decvax}!utzoo!rising
felsenst@uw-entropy.UUCP (11/02/87)
In article <8858@utzoo.UUCP> rising@utzoo.UUCP (Jim Rising) writes: >Joe, > >I'd be interested in your reasoning for saying that DNA hybridization >is not phenetic. It would seem to me that a commparison of the unweighted >overall similarity in the DNA base sequences between two species could be >the ultimate phenetic method--depending, I suppose on how it was analysed. >Of course, I doubth that this is what DNA hybridization studies actually >do, but don't they purport to do so? > >--Jim Rising People calling themselves cladists generally hold that use of the full character data (such as DNA sequences) is "cladistic" and that methods that first reduce the data to a table of species-by-species similarity (or distance) measures are "phenetic", and that the latter loses large amounts of information (many believe: all the useable information) and is invalid. No doubt it loses some information, but certainly NOT all the useable information. Certifiably "cladistic" methods such as parsimony, which ignore all information from supposedly "phylogenetically uninformative" sites also lose some information, but that doesn't cause them to get labelled with this unfortunate useage, and I wouldn't dismiss them out of hand for that reason. My point is simply that "cladistic" and "phenetic" refer to approaches to classification, and that labelling a method intended to infer a phylogeny as "phenetic" wrongly implies that it is irrelevant to the task. The algorithmic similarity to methods of cluster analysis used to create phenetic classifications is irrelevant -- you have to ask how good these data and the analysis methods are for the task at hand. I have done a crude calculation (for publication in a paper in Journal of Molecular Evolution early in 1988) that Sibley and Ahlquist's data have about as much statistical power as 4.4 KB of DNA sequences. That doesn't sound like a qualitative distinction to me, especially since even with much less sequence a "cladist" would call sequence data "cladistic". The (usual) confusion between classification and inferring phylogenies is not helped by this useage. Joe Felsenstein, Dept. of Genetics SK-50, Univ. of Washington, Seattle WA 98195 BITNET: uw-entropy!uw-evolution!joe%uw-beaver.ARPA@UWAVM or uw-entropy!uw-evolution!joe%uw-beaver.ARPA@UWAVM.ACC.WASHINGTON.EDU or uw-entropy!uw-evolution!joe%uw-beaver.ARPA@WISCVM.WISC.EDU ARPANET: uw-entropy!uw-evolution!joe@beaver.cs.washington.edu or uw-evolution!joe%entropy.ms@beaver.cs.washington.edu UUCP: ... uw-beaver!uw-entropy!uw-evolution!joe