GOAD.DAVISON@BIONET-20.BIO.NET (Dan Davison) (02/16/89)
This is the first of two postings on recent articles discussing phylogenetic analysis of molecular data. First, there is a review by Joe Felsenstein in the Annual Review of Genetics, vol. 22:251-265 (1988), "Phylogenies from Molecular Sequences: Inference and Reliability". It is *very* well written, and very readable. Some of the more contentious areas of molecular phylogeny are discussed, at least at the level of making the reader aware of the issues. For someone such as myself that needs to come up to speed on the subject the article is wonderful Also not to be missed is Nei's 1987 Molecular Evolutionary Genetics (Columbia University Press, NYC). For those that have been puzzled, confused, and lost by Jim Lake's "operator invariants", there are a few helpful words; also helpful is the article by Cavender and Felsenstein in J. Classification 4:57-71 (1987) (good luck finding that one!). It's not easy going but is at least more understandable than the papers I've seen by Lake. My impression when Lake's paper (Molecular Biology and Evolution, 4:167-191 (1987)) came out was that it could be a very powerful technique for those that understood it. The subsequent paper (J. Mol. Evol. 26:59-73 (1987)--I may have the temporal sequence reversed) didn't help me much. The important part of the technique is that it is avoids most (perhaps all, I'm not sure) of the effects of differential rates of nucleotide substitution in different lineages. (This problem is discussed more in the following posting). An important and curious article in the January issue of Molecular Biology and Evolution (6(1):15-32 (1989)) by R. C Lewontin extends the well-known Jukes-Cantor formulation for "Inferring the number of evolutionary events from DNA coding sequence differences". Worth reading if you do such work or might do such work. What is still not clear to me is how DNA sequences whose protein products contain extensive indels (the cytochromes come to mind) are handled with this method. Personally, I've always used the positions in common but I've been dissatified by having to ignore the "inconvenient" areas. dan davison theoretical biology and biophysics t-10 ms k710 los alamos national laboratory los alamos, nm 87545 USA dd@lanl.gov (internet) dd%lanl.gov@CUNYVM (bitnet) ...cmcl2!lanl!dd (uucp, maybe) -------