More on the 'cladistics' of sequences

[Richard Jensen]

Bu Richard, when I loooked under that same bridge last year, the
phylogeny I found was not the same as the one you found yesterday!

You are right, we can uncover the real pattern in nature; the
fundamental questions is, will we recognize it when we see it?

Cheers,

Dick

Richard.Zander at mobot.org wrote:

>
>
> No, if we engage in a "discovery process" we can actually uncover the
> real pattern in nature. It may be incredible to some, but I found the
> true cladogram for the hominids hiding under a bridge just yesterday.
>
> I here share this discovery with fellow taxacomers:
> http://ridgwaydb.mobot.org/resbot/phyl/Cladogram_Wild.jpg
>
> I hope this puts the argument to rest.
>
> ______________________
> Richard H. Zander
> Bryology Group
> Missouri Botanical Garden
> PO Box 299
> St. Louis, MO 63166-0299
> richard.zander at mobot.org <mailto:richard.zander at mobot.org>
> Voice: 314-577-5180
> Fax: 314-577-9595
> Websites
> Bryophyte Volumes of Flora of North America:
> http://ridgwaydb.mobot.org/bfna/bfnamenu.htm
> Res Botanica:
> http://ridgwaydb.mobot.org/resbot/index.htm
> Shipping address for UPS, etc.:
> Missouri Botanical Garden
> 4344 Shaw Blvd.
> St. Louis, MO 63110
>
>
> -----Original Message-----
> From: Richard Jensen [mailto:rjensen at saintmarys.edu]
> Sent: Tuesday, June 08, 2004 8:39 AM
> To: Richard.Zander at MOBOT.ORG
> Cc: TAXACOM at LISTSERV.NHM.KU.EDU
> Subject: Re: More on the 'cladistics' of sequences
>
> Richard,
>
> "Well, not really" what.  Of course morphological data can be used the
> same way
> as molecular data.  My point to John was that morphological data are
> no more
> likely to yield a "correct" phylogeny than are any other type of
> data.  And, as
> we all know, we can never know if we have the "correct" phylogeny or
> not.
> Lamboy's simulations documented that even when the correct phylogeny
> is known,
> maximum parsimony of the kinds of data matrices that most systematists
> generate,
> is not very accurate (his word).
>
> Cheers,
>
> Dick
>
> Richard.Zander at MOBOT.ORG wrote:
>
> > Well, not really. Morphological data can be used in the same way as
> > molecular data to come up with testable, well supported hypotheses.
> Proof is
> > that morphological results generally duplicate molecular results.
> See my:
> > http://www.phyloinformatics.org/pdf/2.pdf paper for how to estimate
> > confidence intervals for morphologically based cladogram internodes.
>
> >
> > Accuracy is of course the big bugaboo but is a problem for molecular
> data,
> > too.
> >
> > -----Original Message-----
> > From: Richard Jensen [mailto:rjensen at SAINTMARYS.EDU]
> > Sent: Tuesday, June 08, 2004 7:23 AM
> > To: TAXACOM at LISTSERV.NHM.KU.EDU
> > Subject: Re: [TAXACOM] More on the 'cladistics' of sequences
> >
> > Morphological data are especially difficult to
> > evaluate and, in fact, are unlikely to provide "accurate"
> phylogenies (see
> > Lamboy, 1994. Systematic Botany 19: 489-505). Yes, Lamboy's analyses
> were
> > based on simulated data, but the data matrices generated were not
> unlike
> > real morphological data matrices.
> >
> > ______________________
> > Richard H. Zander
> > Bryology Group
> > Missouri Botanical Garden
> > PO Box 299
> > St. Louis, MO 63166-0299
> > richard.zander at mobot.org <mailto:richard.zander at mobot.org>
> > Voice: 314-577-5180
> > Fax: 314-577-9595
> > Websites
> > Bryophyte Volumes of Flora of North America:
> > http://ridgwaydb.mobot.org/bfna/bfnamenu.htm
> > Res Botanica:
> > http://ridgwaydb.mobot.org/resbot/index.htm
> > Shipping address for UPS, etc.:
> > Missouri Botanical Garden
> > 4344 Shaw Blvd.
> > St. Louis, MO 63110
>
> --
> Richard J. Jensen              | tel: 574-284-4674
> Department of Biology      | fax: 574-284-4716
> Saint Mary's College         | e-mail: rjensen at saintmarys.edu
> Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen

--
Richard J. Jensen              | tel: 574-284-4674
Department of Biology      | fax: 574-284-4716
Saint Mary's College         | e-mail: rjensen at saintmarys.edu
Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen