[Taxacom] Paraphyly (was: Wikispecies as an open alternative...)

Fri Dec 16 15:52:33 CST 2011

John, 
For the example of human-great ape relationships, where the precise phylogenetic relationships seem to be forever debatable, the most sensible thing to do is to keep the phylogenetic uncertainties out of classification, by defining the first suprageneric level broadly enough to avoid paraphyly on any phylogenetic theory. In this case, that would mean putting Homo, Pan, Gorilla, Pongo, and possibly even Hylobates etc. in one big (counting fossil taxa)?family called Hominidae, and not splitting it up into subfamilies or tribes. Scientists can still investigate and debate the phylogenetic details, but the uncertainties should not, in my opinion, be allowed to destabilise the classification ...
Stephen

________________________________
From: John Grehan <jgrehan at sciencebuff.org>
To: taxacom at mailman.nhm.ku.edu 
Sent: Saturday, 17 December 2011 3:41 AM
Subject: Re: [Taxacom] Paraphyly (was: Wikispecies as an open alternative...)

A paraphyletic arrangement (really referring to a paraphyletic group) is
not consistent with either possibility. Only an unresolved tree might
be.

For example, one might have 

Pongo (Gorilla [chimp, human]}

and designate Pongo, gorilla, chimp as a paraphyletic group 'Pongidae'.
In this particular case the paraphyletic group is not consistent with a
human-orangutan clade at all.

I doubt we ever know 'for sure' what is the sister group of any taxon.
What we have is that some are in more dispute than others (and often
enough where there is not dispute there is no more than a single
individual or research group involved).

What I have 'admitted' is that there is no objective recipe for choosing
between contradictory molecular and morphological results. 

As for the 'vast majority' of biologist regarding the morphological
evidence as very weak, who cares? Opinion is opinion. What matters in
science (in my myopic opinion) is the published scientific demonstration
or support for the opinion, and when it comes to the orangutan
characters, these have, for the most part, been ignored by that 'vast
majority'.

My 'refusal' to accept the morphology as being plesiomorphic is based on
specific arguments about the phylogenetic significance of morphological
and molecular characters and these arguments have been published. So I
am entitled to take a particular stance (which could be right or could
be wrong).

John (extremist biogeographer and morphologist and proud of it)

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kenneth Kinman
Sent: Thursday, December 15, 2011 11:33 PM
To: taxacom at mailman.nhm.ku.edu
Subject: [Taxacom] Paraphyly (was: Wikispecies as an open
alternative...)

John,? 
? ? ? Blah, blah, blah,? You think the human-orang clade is real, and
many others think the human-chimp clade is real.? In any case, a
paraphyletic Pongdae (sensu lato and in the traditional sense), IS
ACTUALLY consistent with either possibility.? It recognizes that either
of these possibilities (or even something like a chimp-gorilla clade
being sister to Hominidae).? ? 
? 
? ? ? So whether you recognize it or not, it does solve the problem
(and long has done so) by admitting that we just don't know yet for sure
what clade is the immediate sister group to Hominidae.? And even once we
do know for sure (at least with more certainty from a comprehensive
genome analysis), a paraphyletic Pongidae could still be maintained,
much as a paraphyletic Class Reptilia can be maintained, even though we
have narrowed down the sister clade of Class Aves to being within
coelosaurian dinosaurs (well, except for a very vocal, but tiny minority
that still insists that birds did not evolve from dinosaurs at all).

? ? ? I don't think the orangutan-human clade theory is quite as extreme
as that minority (called "BANDits"; "BAND" theory being that "Birds Are
Not Dinosaur" descendants), but I think the vast majority of biologists
regard your morphological evidence as also very weak and corroborating
molecular evidence as virtually non-existent (and thus not "stable" at
all, and certainly not "very stable" as you put it).? ? 
? ? 
? ? ? Many of the chimp-hominid folks seem blissfully unaware (or
refuse to consider) that their molecular evidence for an exclusive
chimp-hominid clade could be plesiomorphic.? Likewise, you seem to
refuse to seriously consider that your morphological evidence for an
exclusive orangutan-hominid clade could be plesiomorphic.? But whether
you want to recognize it or not, a paraphyletic Pongidae is compatible
with either of those possibilities, or with the third alternative (that
the immediate sister group of Hominidae is a chimp-gorilla clade).

? ? ? ? ? ? ? --------------Ken? 

------------------------------------------------------------
John wrote: 
I don't see how a paraphyletic Pongidae solves anything since I think
the human-orang clade is real so there is no necessity for a
paraphyletic Pongidae. The latter would not be consistent with the
human-orang clade unless the sequence ended with humans and orangutans,
and then in which case there would be no need for a Pongidae for great
apes to exist. Pongidae as proposed by Schwartz would be restricted to
orangutans and their nearest fossil relatives. 
The difference between myself and the chimp-hominid folks is that I am
willing to acknowledge that there are two incompatible phylogenetic
reconstructions and I am happy to see both side by side in
representations of primate phylogeny. According to the chimp-hominid
folk, at least those who have made public declarations, this can never
be allowed. The orangutan must stay in the closet. 
I am interested in the reality of phylogeny. Perhaps the ultimate
reality for some taxa is instability. Perhaps 'ture' phylogeny of life
is inherently ambiguous. Morphologically, however, the human-orangutan
clade seems very stable indeed. 
John 
-----Original Message----- 
From: taxacom-bounces at mailman.nhm.ku.edu 
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kenneth
Kinman Sent: Wednesday, December 14, 2011 10:00 PM 
To: taxacom at mailman.nhm.ku.edu 
Subject: Re: [Taxacom] Wikispecies as an open alternative to Catalogue
ofLife 
Gee John, 
? ? If you are so upset about minority reconstructions being 
excluded, I would think you would actually embrace a traditional,
paraphyletic Family Pongidae (for orangutans, chimps and gorillas).? A
Global Hierarchy using such a taxon is thus consistent with either
chimps or orangutans being sister to Family Hominidae, or even my
minority inclination that it could be a chimp-gorilla clade that is 
sister group to Family Hominidae.? ? ? ? 
? ? ? But instead of embracing such a traditional taxon for the "Global
Hierarchy", you are just as guilty as the chimp-hominid folks in
insisting that "we know best" and want a strict cladification (even
though the strict cladifications are incompatible with one another).? It
seems to me that it is just such cases where paraphyletic taxa are the
most useful and stable, and I am willing to admit that any of the above
groupings could be sister group to Family Hominidae.? Strict cladists
apparently just don't care about stablility in such cases.? They would
rather just continue to fight each other over their incompatible strict 
phylogenies.? ? ? ? ? 
? ? ? ? ? ? ? ---------Ken 
? 

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