Paraphytlly is real.

B.J.Tindall bti at DSMZ.DE
Wed Jan 16 15:54:56 CST 2002

Richard Zander wrote:
>Both inference and probabilistic demonstration of phylogeny are used in
phylogenetic estimation. With molecular data sets, a non-parametric test
like bootstrapping will give a probability that a particular arrangement of
the three lineages terminating any internal branch is due to chance; and a
bootstrap value of 95% or greater is pretty good evidence of a phylogenetic
signal in a gene tree. You need at least three agreeing gene trees (an no
contradiction), however, to get a 95% chance or greater that the gene trees
reflect species evolution (given a pre-selected 95% confidence level).
Okay, but this assumes that the data set conforms to the assumption laid
down in bootstrapping before I do the test. One of the problems is
independence in the data set - do adjacent bases in a gene sequence evolve
independant of each other?
Perhaps you could answer a simple question - you have three gene trees
which agree and then you have a set of 3 other genes which agree with
eachother but disagree with the first set - so which one is correct?
Given the rate at which microbial genomes are being sequenced the first
indications suggest it may not be that easy to find 3 genes which agree in
detail. Perhaps we have to live with that fact?

>Morphological data sets, however, because of the paucity of characters,
seldom actually demonstrate probabilistic inequalities of support for the
three different arrangements of lineages terminating an internal branch,
but instead good support must be based on inference; even with no support
for contrary arrangements of the three lineages terminating an internal
branch, you simply can have 100% confidence in the inference of a
phylogenetic relationship based on evolution (fossils, microevolution)
demonstrated elsewhere.
>So we have confidence in inference of well-supported morphological
relationships, and confidence in high bootstrap values for molecular
results. In the first we have no actual demonstrated signals, and in the
second few demonstrated signals at a decent confidence level.
>Given that demonstrated reliability is low for the published results of
the past 30 years of phylogenetic analysis, arguing about how to treat
paraphylly in nomenclature is a bit premature, I think. Although there are
“uncontested” groups, most relationships that now warrant discussion need
more research first. We need more genuine phyly before we can profitably
discuss paraphyly.
>Richard H. Zander
>Emeritus Curator of Botany
>Clinton Herbarium
>FNA Editorial Center at Buffalo
>The Buffalo Museum of Science
>1020 Humboldt Pkwy
>Buffalo, NY 14211 USA
>email: rhzander at NEW EMAIL ADDRESS! (Note “h” infix)
>voice: 716-896-5200 x 351 FAX: 716-897-6723
>BFNA home: http://www.buffalomuseuofscience/BFNA/BFNAmenu.htm
>FNA home:
>----- Original Message -----
>From: “Ken Kinman” <kinman at HOTMAIL.COM>
>Sent: Tuesday, January 15, 2002 4:04 PM
>Subject: Re: Paraphyly is real (+ “strict cladist” defined)
>> We can only approximate the
>> reality through inference, so conventions will always be necessary.

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