[Taxacom] Molecular data and synapomorphies

Alan DAvid Forrest aforrest at rjb.csic.es
Wed Dec 3 00:56:27 CST 2008

It is nice when this discussion group generates compatibility and 
usefulinformation exchange!

FASTA format, to me, was near universal - therefore it is good to 
discover that this is not the case. I have modified my viewpoint 
accordingly. I find NEXUS over complex and also have to resort to online 
conversion software, some of which is not very good.

Further, from Richard Zander's comments, it is clear that there still 
exists an unproductive split in opinion between molecular systematists 
and their more 'traditional' counterparts. It is reminiscent of 
phenetics vs.cladists, horticulture vs. science depts in botanic 
gardens, barcoding vs. the loss of field systematic expertiseetc etc. 
Perhaps the most enlightened are those who prefer to take a 
multidisiplinary and co-operative approach. As such, it would be nice to 
see funding proposal success based on this. I note the comment about a 
lack of funding for morphological taxonomy - although in the UK (my home 
base) it is also very difficult to obtain funding for molecular 
systematics as well (unless you have a permanent position and access to 
institutional labs).

The lack of standards and their rigorous enforcement seems to be an 
issue that needs addressing in all disciplines.


John Grehan escribió:
>> -----Original Message-----
>> From: Alan DAvid Forrest [mailto:aforrest at rjb.csic.es]
>> I personally stick to simple text or fasta alignments that can be used
>> virtually anywhere else without conversion. 
> As an ignorant non-molecular biologist I had never heard of this format
> until recently. Then I was not able to open some such files, even with
> software that was supposed to do that. I had to have a colleague convert
> to nexus and also direct me to some web programs before I could do
> anything. I came across a website that was designed as a repository for
> molecular data that would make access automatic, but not many were using
> at such.
> One key requirement is access to the alignments as they were aligned by
> the original authors since different alignment programs may give
> different results. In at least one case the data was not in its aligned
> format.
> Another problem I have had is identifying EXACTLY how many sequences
> comprise each gene of each taxon compared. That might be easy for a
> molecular systematist to figure out, but not for me.
> 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).
> At least with morphological data, one would expect accurate descriptions
> and illustrations for each taxon for a particular character, or at the
> very least citations to sources with such information. Unfortunately
> that seems to be wanting in many morphological studies (so a counterpart
> to access to molecular data) - particularly for larger groups. All too
> many systematists just make proclamations about characters and
> concentrate on generating 'lots' of them as if this will somehow snow
> everyone on the lack of actual documentation. I've seen this in the
> human origins field where various studies get acclaim for their many
> characters without any attention to the fact that most don't even have
> comparative illustration of their veracity. Other characters continue to
> be recycled even when they have been shown to be incorrect.
>> 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? 
> Ok. 
> John Grehan

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