[Taxacom] RES: Re: about alternative splicing

[Vitor F. O. Miranda]

Dear Igor and colleagues,

In phylogenomic approaches, NGS-DNA (not cDNA from RNA) has been the more common data.
As each base is usually codified as a single (and "independent") character, one can choose using only coding regions, or all the sequences that could be aligned between the taxa. 
Since you could infer a possible homology, indeed.

Best regards,
Vitor

_______________________________
Vitor Fernandes Oliveira de Miranda, Prof.Dr.  
São Paulo State University (Unesp)
School of Agricultural and Veterinarian Sciences, Jaboticabal
Laboratory of Plant Systematics – DBAA/LSV
Via de Acesso Prof. Paulo Donato Castellane s/n
CEP 14884-900     Jaboticabal – SP – Brazil
Phone: +55 (16) 3209-7205
email: vmiranda at fcav.unesp.br   Skype: vmirandum
http://www.fcav.unesp.br/vmiranda 


-----Mensagem original-----
De: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] Em nome de David Campbell
Enviada em: segunda-feira, 23 de outubro de 2017 18:19
Cc: taxacom
Assunto: ***SPAM*** Re: [Taxacom] about alternative splicing

I think cDNA has been the most common "genomic" approach in mollusks, so there is some possibility for alternative splicing, paralogs amplified under different condition (e.g., age reproductive cycle, or stress), and similar issues to be of concern.

On Mon, Oct 23, 2017 at 3:47 PM, Peter Uetz <peter at uetz.us> wrote:

>
> Most people use genomic DNA for phylogenomics studies (not RNA or 
> cDNA) so I suspect splicing is irrelevant in most cases.
>
>
> > --------------------------------------------------------------------
> > --
> >
> > Message: 1
> > Date: Mon, 23 Oct 2017 08:00:40 +0300
> > From: igor pavlinov <ipvl2008 at mail.ru>
> > To: TAXACOM <taxacom at mailman.nhm.ku.edu>
> > Subject: [Taxacom] about alternative splicing
> >
> >
> >
> > Dear all,
> > does anybody know if there are any discussions of possible impact of 
> > the
> effect of alternative splicing onto the character concept among 
> phylogenomics practitioners?
> > As far as I know, they routinely consider each site in DNA seqeunce 
> > as a
> separate character to be used in taxonomic investigations.
> > Do they or not?
> > Thanks to all who may wish to respond.
> > Igor
> >
> >
> > - - -
> > Igor Ya. Pavlinov, DrS
> > Zoological Museum of Lomonosov Moscow State University ul. Bol'shaya 
> > Nikitskaya 6
> > 125009 Moscow
> > Russia
> > http://zmmu.msu.ru/personal/pavlinov/pavlinov_eng1.htm
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--
Dr. David Campbell
Assistant Professor, Geology
Department of Natural Sciences
Box 7270
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