[Taxacom] Surprise from a whole-genome study - more pepper inthe soup

Thu Oct 28 15:14:11 CDT 2010

it is worth noting here that this issue highlights the difference between 
taxonomy and systematics. The origin of gene sequences is irrelevant to taxonomy 
(genes or even evolution need not even exist, all that is needed are individuals 
that fall into diagnosable kinds) ...

________________________________
From: John Grehan <jgrehan at sciencebuff.org>
To: taxacom at mailman.nhm.ku.edu
Sent: Fri, 29 October, 2010 1:43:16 AM
Subject: Re: [Taxacom] Surprise from a whole-genome study - more pepper inthe 
soup

My thanks to all those who commented on this subject. I get the impression that 
if a 'gene' does not fit and it matches in some way to the genome (all or in 
part I am not sure) of some other organism such as a virus then that is the 
attributed origin. Whether this matching is exact (i.e. one to one 
correspondence of each base pair) or approximate (in which case how 
approximate?)I do not yet have any idea. Hopefully if I get time I will try to 
read more on this. If genes are supposed to diverge constantly as most molecular 
theorists and systematists appear to believe, then how would any externally 
originated sequence ever be matched with its origin since the two would now be 
different?

I've received the comment that basically this is a situation of incongruence 
that may be comparable to that of biogeography where incongruence is usually 
attributed to dispersal. In this case it is the "strange" sequences that are 
regarded as anomalous and therefore an external agency is invoked because no 
other option is regarded as tenable - I presume.

John Grehan

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu 
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Vitor Fernandes O. de 
Miranda
Sent: Thursday, October 28, 2010 6:34 AM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Surprise from a whole-genome study - more pepper inthe 
soup

Hi John,

I remember a paper that authors, after producing some few sequences to
several taxa, applied basically the similarity to figure out HGT. But do not
remember have noticed any explicit method to corroborate or even verify its
likelihood. If someone knows one, I would really appreciate having it!

I guess that each case is a case. In my opinion, as safer the method as more
sampled was the genome. Comparative analyses of whole genomes are safer than
applying the HGT hypothesis only with few sequences on hands. After some
rounds (replicates) when producing a genome, if one found some "strange"
sequences in all or most replicates, it's unlikely to thank simply by
contamination. But of course each case is a case.

Attached is a very curious paper. It's postulated a fifth principle to the
Modern Synthesis including the HGT idea :-)

Best,
Vitor.

_______________________________
Prof.Dr. Vítor Fernandes Oliveira de Miranda
Universidade Estadual Paulista - UNESP
Campus Jaboticabal
Departamento de Biologia Aplicada à Agropecuária
Faculdade de Ciências Agrárias e Veterinárias - FCAV
Via de Acesso Prof. Paulo Donato Castellane s/n
CEP 14884-900    Jaboticabal - SP
Fone: +55 (16) 3209-2620  Ramal 213
email: vmiranda at fcav.unesp.br  Skype: vmirandum

-----Mensagem original-----
De: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] Em nome de John Grehan
Enviada em: terça-feira, 26 de outubro de 2010 17:12
Para: taxacom at mailman.nhm.ku.edu
Assunto: Re: [Taxacom] Surprise from a whole-genome study

I guess it's the specifics of these that need to be explained to me.
Maybe there is a paper out there that presents the evidence for how such
sequences are recognized as viral derivatives rather than convergences.
I would be interested. John

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Sergio Vargas
Sent: Tuesday, October 26, 2010 3:04 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Surprise from a whole-genome study

Hi,

>I admit to being very ignorant of the research basis for recognizing
lateral gene transfer. Out of curiosity, what is the evidence that a
genetic sequences is derived from another organism rather than
representing a convergent development?

gene structure I think, syntheny, different evolutionary rates (not sure
about this one), different codon-usage or nucleotide frequencies, etc.

sergio

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