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Date: Fri, 29 Sep 2000 10:42:21 +0100
From: Michel Laurin <laurin@ccr.jussieu.fr>
To: PhyloCode@ouvaxa.cats.ohiou.edu
Subject: RE: Nathan Wilson's question
> I actually see the issue that Nathan Wilson brought up as potentially >being problematic, since a species that may eventually be shown to belong t= o >multiple nonnested clades may be used in phylogenetic definitions (as a >specifier) _prior_ to the knowledge that the species actually belonged to >more than one nonnested clade. =20 > For example, let's say Clade Z is defined as the least inclusive clade >containing species 3 and species 4. Species 3 is then shown to have >originated through the hybridization between species in Clade A and Clade B= =2E >When the definition was originally formulated it was believed that species = 3 >was a member of only Clade A (not B) and the circumscription of Clade Z was >exclusive of Clade B. Doesn't the circumscription of Clade Z have to >include all nonnested clades to which each specifier (see Art. 11.1) is a >member (i.e., the circumscription of Clade Z will have to be expanded to >include Clade B to accommodate specifier Species 3 being a member of the >nonnested Clades A and B)? > Thus (expanding this logic to LGT cases), wouldn't it be hard to apply >phylogenetic nomenclature (without running the risk of having a lot of >circumscriptional changes) to the prokaryotes where so much new information >on lateral (horizontal) gene transfer is being and remains to be discovered= ? > >Gerry Moore >Research Taxonomist >Brooklyn Botanic Garden >27 Sep. 2000 =20 Hi all, I agree with Gerry's comments. This problem is potentially serious, and we= should incorporate a provision in the code to deal with this issue. What= do you think of the following suggestion? In the case in which a species= used as a specifier is later found out to be a hybrid, we could decide that= the reviewer should amend the definition by choosing another, closely= related species of the clade to which the problematic (hybrid) specifier= was believed to belong (before it was found to be a hybrid). This way, the= contents of the clade would not be altered. Of course, the reviewer would= have to be reasonably sure that the new specifier is not also a hybrid... Otherwise, the other obvious solution that I see, and what Gerry pointed= out, is that the definition would now be more inclusive because it would= include both clades from which the hybrid species is derived. Either way,= we should incorporate whatever we consider to be the best solution into the= code. In the case of lateral transfer, I believe that generally, the information= transferred in such a way is a tiny proportion of the genome in each event.= Even though when we take all the events that may have happened in the= history of a bacterial clade, much of the genome may have a "foreign"= source, I believe that it is unlikely to all come from the same source. = Thus, I don't think that horizontal transfer needs a separate provision in= the code, other than a statement that it does not constitute hybridization.= However, before we incorporate this into the code, we should discuss this= issue with scientists involved in gene transfer research to verify my= guesses about the relative amount of genome transfer and the taxonomic= diversity of the sources. If I were wrong about either issues, we might= very well need to incorporate a statement in the code about horizontal tran= sfer. Michel ********************************** Michel Laurin Equipe 'Formations squelettiques' CNRS - UMR 8570 Case 7077 Universit=E9 Paris 7 - Denis Diderot 2, place Jussieu 75251 Paris cedex 05 France Tel. (33) 1 44 27 36 92 Fax. (33) 1 44 27 56 53 **********************************