Drimia, Drimiospsis, Ledebouria

Nhu Nguyen xerantheum@gmail.com
Tue, 05 Oct 2010 20:51:17 PDT
Recently evolved, indeed. The GenBank excercise shouldn't be a hard one and
I would love to do it but I'm short on time these days. If anyone is
interested in doing that it would be fun but those free alignment programs
are only the first step. You have to manually align everything afterward
because of all the mistakes that the alignment program makes. You can add
the morphology data but you have to code for the taxa without morphology as
missing data. The quick trees generated from GenBank use a simple algorithm
and can only give you a quick and dirty look at your data and nothing more.
A real phylogenetic tree can take days or even weeks to generate using a
decently good computer.

In Botany and many other groups of "big" organisms, morphology prevails but
in the microbial world (which makes up most of life on Earth), researchers
have for decades moved beyond morphology or phenetic characters. Instead
phylogenetic inference has lead the way. This is a necessity because there's
nothing to see in microbes (at least the bacterial ones)!

Taxonomy is supposed to provide the end users like members of the public
(=members of this forum) and other researchers with good usable names. As
time goes on and we gather new evidence, new hypotheses are formed. A
family, a genus, and sometimes even a species are just hypotheses.
Hypotheses are either accepted or rejected based on the available evidence.
These decisions (naming of taxa) should not be based on scientific hard
evidence and as Aaron said, "not for the sake of nomenclatural

Well, that had been a day of stimulating discussion.

Berkeley, CA

On Tue, Oct 5, 2010 at 7:59 PM, aaron floden <aaron_floden@yahoo.com> wrote:

> ...Lebatha et al. suggest. Their speciation is probably relatively recent
> for most species.
> If you want, check Genebank for the taxa used by both authors and include
> them all, but the morphology of Lebatha et al will have to be excluded. Then
> align them in a free program and run them through another free program.
> Share the results. You could even get one sequence, BLAST it in Genebank and
> see what tree comes back. It would at least give a basic idea of
> relationships.
>  Manning et al. in a very recent paper (2009) backtrack on a previous
> lumping (the same 2004 Ledebouria lumping) of everything in the
> Ornithogaloideae into Ornithogalum and now recognize Albuca, Dipcadi,
> Pseudogaltonia based on 4 gene regions. They acknowledge that other genera
> should/could be recognized but are not for the sake of nomenclatural
> confusion/clarity.....
>  Aaron

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