Message 2000-09-0009: RE: Nathan Wilson's question

Fri, 29 Sep 2000 10:42:21 +0100

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Date: Fri, 29 Sep 2000 10:42:21 +0100
From: Michel Laurin <>
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=
>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=
>When the definition was originally formulated it was believed that species =
>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=

	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=


	Michel Laurin
	Equipe 'Formations squelettiques'
	CNRS - UMR 8570
	Case 7077
	Universit=E9 Paris 7 - Denis Diderot
	2, place Jussieu
	75251 Paris cedex 05
	Tel. (33) 1 44 27 36 92
	Fax. (33) 1 44 27 56 53


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