One more comment on all of this. From the standpoint of "comparative methods," some similar things have occurred. In particular, the early attempts to take evolutionary relationships into account when performing statistical analyses that compared, say, brain size, were always taxonomic, in that Class, Order, Family, etc. might be taken into account. This was done without much thought given to whether the classification used was or was not very well tied to evolutionary (phylogenetic) relationships for the particular group under study.
As my colleagues and I have written, the first "fully phylogenetic" comparative method was Felsenstein's (1985) independent contrasts. By "fully phylogenetic," I mean that it could use any specified topology (branching order) and set of branch lengths, along with an assumed Brownian-motion like model of trait evolution. This was a huge advance, for several reasons. For example, at least under older taxonomic schemes, named groups at a given level (e.g., different families of birds) were never likely to be very comparable in terms of age -- and hence expected amount of phenotypic variance among species. Anyway, it took a long time, and perhaps some "unnecessary shouting," to convince practitioners that *phylogenetic* comparative methods are fundamentally different from those that are only based on taxonomy, which can never convey as much information as a detailed (and accurate!) phylogenetic tree. Cheers, Ted Theodore Garland, Jr., Ph.D. Professor Department of Biology University of California Riverside, CA 92521 Phone: (951) 827-3524 = Ted's office (with answering machine) Phone: (951) 827-5724 = Ted's lab Phone: (951) 827-5903 = Dept. office Home Phone: (951) 328-0820 FAX: (951) 827-4286 = Dept. office Email: tgarl...@ucr.edu http://biology.ucr.edu/people/faculty/Garland.html List of all publications with PDF files: http://biology.ucr.edu/people/faculty/Garland/GarlandPublications.html Garland, T., Jr., and M. R. Rose, eds. 2009. Experimental evolution: concepts, methods, and applications of selection experiments. University of California Press, Berkeley, California. http://www.ucpress.edu/books/pages/10604.php Associate Director Network for Experimental Research on Evolution http://nere.bio.uci.edu/ (A University of California Multicampus Research Project) ---- Original message ---- Date: Tue, 29 Sep 2009 11:30:23 -0700 From: Wayne Maddison <wmadd...@interchange.ubc.ca> Subject: Re: [R-sig-phylo] is maximum likeyhood a phylogenetic approach? To: r-sig-phylo@r-project.org >If you want some real fun, sign on to the Taxacom mailing list and >post an opinion about whether a particular method is "cladistic" or >not. > >But the heated exchange that might result is already anachronistic. >There's an expression in English, "It's all over but the shouting." >The shouting will go on for some time, but it's over. Whether or not >you agree with it, the matter's settled: the community now very much >considers that an organism's identity arises from its genetic >history, and that classification should as directly as possible >reflect that genetic history. Classification is about words, and it >helps very much to have the words we use reflect the concepts that we >think matter. > >Yes, the questions of evolutionary history and classifications can be >separated, but I wouldn't say that a confusion between them hampered >the progress of evolutionary biology. A battle *within* evolutionary >biology between older and newer paradigms as to what emphasis >mattered (adaptive zones versus genetic history) was fought with >classification as the prize to be won. The fact that most adherents >to the new paradigm weren't concerned about classification, and many >of the traditionalists were, made it seem to the younger generations >as if progress was being hindered by a focus on classification. Of >course, since the battle was won long before the shouting stopped, >it's understandable why the younger generations felt burdened by the >unnecessary shouting. > >Wayne > > >At 10:43 AM -0700 29.9.2009, Joe Felsenstein wrote: >>When I wrote: >> >>> >As what classifications should be, or whether methods should be >>> >considered as making phylogenetic or phenetic classifications, I have my >>> >own position, that no one else seems to back (in public, anyway). I >>> >think that we should not think of these trees as classifications, and not >>> >call them phylogenetic classifications or phenetic classifications, but >>> >consider them as estimates of the phylogeny. The issue of how to classify >>> >is less important anyway. >> >>Emmanuel Paradis responded - >> >>> I have the strong feeling that most users of R and its [phylo]genetics >>> packages are interested in the study of evolutionary processes, not in >>> classification (I rarely see questions about classification or >>> systematics here). So maybe most of us silently back Joe's position. >>> >>> About the issue of how to classify, I think it is very important. The >>> point here is, in my view, that the confusion between classification and >>> evolution greatly hampered the progress of evolutionary biology, but the >>> situation has improved in recent years. >> >>I can't speak for most users of R, but I do suspect that Emmanuel is >>right in that there is agreement with this position among many younger >>evolutionary biologists. But it is a sufficiently intimidating atmosphere >>for them that they do not usually say that out loud. I have stuck my neck >>out, mostly for the fun of it. The reactions among many systematists have >>been strong -- they are really outraged, and figure that this is just >>some arbitrary opinion of mine, which they are (barely) willing to tolerate. >>I suppose the matter will become one of open discussion some day. >> >>Anyway, back to R. >> >>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 >> >>_______________________________________________ >>R-sig-phylo mailing list >>R-sig-phylo@r-project.org >>https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > >-- >-------------------------------------------------------- >Wayne Maddison > Professor and Canada Research Chair > Depts. of Zoology and Botany and > Biodiversity Research Centre > & Director > Beaty Biodiversity Museum > 6270 University Boulevard > University of British Columbia > Vancouver, BC V6T 1Z4 Canada > >email: wmadd...@interchange.ubc.ca FAX: +1 604 822-2416 > >Mesquite: http://mesquiteproject.org >MacClade: http://macclade.org >Salticidae: http://salticidae.org >Tree of Life: http://tolweb.org >Beaty Biodiversity Museum: http://beatymuseum.ubc.ca >Home page: http://salticidae.org/wpm/home.html > >_______________________________________________ >R-sig-phylo mailing list >R-sig-phylo@r-project.org >https://stat.ethz.ch/mailman/listinfo/r-sig-phylo _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
