When I wrote >> One could argue that your characters are not defined using a >> phylogenetic criterion; that is, when performing a phylogenetic >> analysis (either by ML or Parsimony), you have to assume that your >> dataset is made of homology hypotheses. That is, one could argue that >> your data are based on similarity relationships rather than on >> hypotheses of historical transformations. >> Having this in mind, it is questionable whether, using these data, any >> method could produce an acceptable estimate of the phylogeny of your >> group of interest.
Joe Felsenstein responded- > If one simply measures the same character in different species, > is that not good enough? I would say "yes", always that the character of interest could be traced back to a trait present in the oldest common ancestor of these species, and assuming that this ancestral trait evolved into the structures that were measured in the ancient species. Otherwise we would be comparing apples (fruits) with potatoes (roots), much as if we homologate a fly fly with a bat fly: they could be SIMILAR in a given context, but certainly they are not the same thing. > My curiousity is because I suspect that > if Stephane had coded his characters 0/1 before trying to analyze > them, they would then be accepted as "made of homology hypotheses". I'm not against Elsa and Stephan's strategy. As a matter of fact, I do accept, and consider very promising, their approach. I only say that there is a potential problem in determinig character states based _solely_ on similarity. That is why I have harangued for adhering to the philosophical principles that guide our methods: Phylogeny estimates should be based in homology hypotheses, not in similarity. This is true for "cladists" and "probabilists" as well (and please note that I'm quite eclectic regarding these two schools). In summary: If Elsa and Stephan would have assigned 0 to "fly absence" and 1 to "fly presence" and then they have recorded this "character" for flies and bats, I would have taken the same position (and I also would have criticized the use of "absent" as a character state, but this is a different problem...). L > J.F. > ---- > Joe Felsenstein j...@gs.washington.edu > Department of Genome Sciences and Department of Biology, > University of Washington, Box 355065, Seattle, WA 98195-5065 USA > -- Leandro R. Jones, Ph.D. http://www.efpu.org.ar "... To use a computer implies abandoning all techniques developed before to the advent of automated calculation, I say techniques, not sciences..." (J. P. Benzecri) _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
