DNA sequencing + Latin descriptions

Fernando Rivadavia Lopes (ferndriv@usp.br)
Fri, 6 Oct 1995 19:11:02 -0500 (CDT)

I was out for a few days and afterwards too busy to give a long
answer to all the messages sent on DNA sequencing and Latin descriptions.
First of all, I'm not sure if it is finally clear or not, but I
was preaching against Latin DESCRIPTIONS and not the use of Latin/Greek
for NOMENCLATURE!! I see no problem at all with the use of Latin/Greek
for nomenclature. The problem is having to read or write a description
of a new species in a language which fewer and fewer people know
anything about. I prefer to see the short descriptions of the type
"...affinis sed...." followed by a full description in English, Spanish,
or whatever, but believe it would be even better if we could TOTALLY
eliminate the use of Latin for the DESCRIPTIONS (and NOT for the
nomenclature).
It becomes an even more substantial arguement now that
Gordon and others have told us that Latin descriptions have been
abolished in many other taxonomic groups, like protozoans, fungi, insects,
and fish.

As to the remark on Drosera being closer to Nepenthes, I meant that
they were close not only when comparing with other CPs, but other plants
in general too. And don't take the 'close' so literally Jan. OK, there
may be a 2 or 3 genera which go somewhere inbetween Drosera and Neps, but
that still means they're relatively close, at least on that chart
presented in that article.
Most of us do not know enough about plant systematics at high
taxonomic ranks nor the relationships inferred from all the microscopic
morphologic details (like polen and wood anatomy) to be able to compare the
characteristics between dozens and dozens of plant families and agree
that Neps are really not that far from Drosera. I'm not saying they
should or should not be in the same order, I'm just saying that for the
CPers who grow these plants and are used to observing mainly the external
macroscopic morphologic characteristics, these 2 genera do not appear to
be closely related.

> I am a big proponent of morphological analyses, but to dismiss the
> power of molecular phylogenetic techniques out of hand is like, well, like
> dismissing lightbulbs since candles work so well.

Well said Chris!

> >The phenotype *must* be considered in the first line, other data can
> >be used for confirmation, never as the basis of a phylogeny.

Jan, I agree that phenotype must be considered in the 1st line.
The problem is deciding *which* phenotypic characteristics are most
important and which are misleading. I think DNA sequencing is an
excellent tool to show this. We can not look at molecular systematics as
something opposed to traditional methods, but as something to HELP. I
just believe that between a single DNA sequence and a single phenotypic
characteristic, the former is much more reliable. But I also agree that
"monotheistic" classification based on a single DNA sequence probably won't
live up to compete against one based on *numerous* phenotypic
characteristics. But if we had a tree based on numerous DNA sequences
and one based on numerous phenotypic characteristics, I would surely bet
on the former.

> Actually the phenotype, or how things look, may be what selection
> is acting on, but that has precious little to do with the reconstructing
> the historical fact of how lineages diverged, that is, the pattern of
> evolution. Neutral markers make the best indicators of this pattern. In
> other words, to reconstruct phylogeny, it is best to use characters that
> change as a function of time without being influenced by selection.
> Molecular data work particularly well in this regard.
> There are of course several caveats to this. First, one can never
> tell if a gene or sequence is free from the influences of selection.

Chris, even if it's not free from selection, wouldn't selection be
acting equally on a specific gene common to many organisms or at least
acting equally on each intron and exon? Wouldn't introns be the perfect
neutral markers since they don't code for proteins? And what about the
fact that the hundreds or thousands of copies of genes like the ssu-rDNA
sometimes present are maintained extremely uniform among each other in
the genome? Would it make these genes better or worse markers?

> >I thought Fernando was emphasizing the relationships with regard to
> >CP and meant that Drosera closer to Nepenthes than other CP. Did I
> >get that right? Jan, are you saying that is wrong?
>
> It *may* be sort of wrong: if _Triphyophyllum_ took (please note that I am
> not stating this to be so without doubt) an intermediate position between
> the two families, the statement "Drosera closer to Nepenthes than other CP"
> will obviously become oversimplified (which is "wrong" sensu stricto).

Again Jan, don't be so literal! This species was NOT on that chart
and thruth is nobody knows anything about it! Nobody's ever grown the
darn plant and few have ever even seen photos. Even if it does belong
somewhere between Drosera and Neps, that still doesn't change the point
that these 2 genera are relatively close. Please, I'm making relative
comparisons between the plants on that chart!

> > I'm not sure but
> >it seems you guys aren't "on the same wavelength" so to speak.
>
> This is a wrong impression. In fact, I think we are pretty much on the same
> wavelength, but I think I should emphasize some points which need
> clarification. These points are the reasons for most errors and
> misconceptions in contemporary systematic literature (and I really dislike
> to read nonsense).

Hey Jan, take it easy, we all misunderstand each other once in a
while over these expresionless screens. Take the example of the people
who understood I was against Latin nomenclatures (when it was really
Latin descriptions).

> >Yeah, it isn't hard to reach that conclusion without the DNA testing
> >but wouldn't this lend support to the validity of this type of comparison?
>
> I would formulate it the other way round: this type of comparison lends
> support to the conclusions from comparative morphology. All other
> implications are at least dangerous.

I would say it another way: wouldn't both support each other?!?

> > Sequencing of one gene gives you the divergence pattern
> >of that gene which isn't necessarily the same as that for the organisms
> >involved. (...)
>
> This is also my opinion.

And mine too, but doesn't it sound more likely that phylogeny
based on the divergence of several genes would be better than phylogeny
based on morphological characteristics which are just there to be
observed and you don't really know which originated which nor how many
times it could've happened over the course of evolution? Don't you
agree that genes show and record these pathways better?

'Till the next round,

Fernando Rivadavia
Sao Paulo, Brazil