[Taxacom] Molecular data and synapomorphies

Alan DAvid Forrest aforrest at rjb.csic.es
Tue Dec 2 07:46:15 CST 2008

I agree with your final comments - however the discussion then becomes 
not about the attributes of the data itself but how different people use 
and abuse it. No doubt this has received much discussion over the years 
- and indeed over the past few weeks.
I also agree with your point regarding data storage - for molecular data 
this CAN be straightforward but the multiplicity of available formats 
defeats this possibility (along with the lazyness of researchers and the 
research community to extensively standardize - I guess journals need to 
take the lead on this as they are the currency of successful careers). I 
personally stick to simple text or fasta alignments that can be used 
virtually anywhere else without conversion. I am not sufficiently 
knowledgable about morphological, biogeographical or cytological data to 
comment on how such data is currently stored, but would be happy to 
learn (suggestions welcome).
As for 'more informed interpretation' I mean simply: how can one decide 
if a particular type of data is 'best' or 'correct' without comparison 
to other data? If you are seeking a particular statistic (for example in 
population genetics) then a particular type of marker may be most 
suitable for a very specific question - but in terms of systematics and 
evolution a single marker analysis means that you ignore the possibility 
of more resolution or of uncovering different patterns. I agree that ad 
hoc decisions to use or not use characters is a feature of all data - 
and should be a feature of none.

John Grehan escribió:
>> -----Original Message-----
>> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
>> bounces at mailman.nhm.ku.edu] On Behalf Of Alan DAvid Forrest
>> Finally, while molecular data may be based on a few exemplars, when a
>> list of extensive analyses (cytology, biogeography et al) is given it
>> should be noted that this list is missing for the vast majority of
>> groups studied, and for some (ie cytology) it is very unreliable due
> to
>> the lack of voucher specimens deposited and the low level of detail
>> published.
> I would add emphasis to this in that one of the problems I am finding is
> that if the molecular data is available, it is in formats that require
> some familiarity with, and access to, software that will make the data
> accessible. I have found that even molecular systematists can have
> trouble with accessing other data formats. Also, there is the additional
> problem of the lack of permanency of access (as mentioned before) or
> refusal of authors to provide the data (even when they say in the
> published article that requests for the data can be made to the
> authors). This is voodoo systematics.
>> I would re-iterate that a combined analysis of several data can be
> more
>> informative than either a single type of data, or a priori measuring
> one
>> data against another. 
> Not necessarily. If the several types of data are being analyzed
> phonetically, for example, then it's no better for that.
> In the group we have been working on
>> (Antirrhineae) one can find morphological data to support different
>> hypotheses depending on the characters chosen - including characters
>> that follow the same patterns as the moleclar data. For
> classification,
>> this means different authors will give different classifications based
>> upon personal opinion, preference or even reasoned argument about the
>> evolution of the characters themselves. Better, surely, to use
> alternate
>> data sources for comparison for a more informed interpretation?
> Not necessarily (depending on what one means by a 'more informed
> interpretation'). Ad hoc arguments for or against a particular set of
> data are just as possible in molecular as in morphological evidence, and
> I have seen molecular systematists come up with quite inventive ways of
> dismissing molecular data they do not like.
> John Grehan

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