[Taxacom] New systematics book

[Richard Zander]

Expected comment, Mike. I got a review of a paper once that said "we
solved all these problems back in the 1980's." Really? The 1980's were
when regular taxonomists gave up and stuck their heads in the sand. The
cladists took over with their version of Big Science. 

It has taken this long to work out that parsimony and other optimality
analyses only work with accuracy with pseudoextinction (dying ancestor,
two new species). The correct optimality for branching analysis is that
which makes the shortest (most likely, most credible) tree given
identified surviving ancestors and their daughter taxa based on other
information. This is merely, MERELY less precise, correctly less precise
and therefore with more uncertainty about evolutionary relationships. 

It has taken this long to work out that molecular "lineages" are
molecular strains, and ancestral taxa in stasis generate lots of
molecular strains before and after generation of one or more daughter
species. The DNA continues to mutate in isolation while expressed traits
remain in stasis for millions of years. Molecular phylogenetics gives
precise sister group analyses of extant strains, not taxa. Evidence?
Molecular paraphyly. What about extinct or unsampled strains? They could
have diverged molecularly long before or after any extant strain. Oh,
oh.

My stance is that the alternative to cladism must be addressed now, even
if you see it as 1980's stuff that you and your cladist fellows "solved"
way back in the day.


____________________________
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA  
Web sites: http://www.mobot.org/plantscience/resbot/ and
http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site:
http://www.mobot.org/plantscience/resbot/21EvSy.htm
UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA


-----Original Message-----
From: Michael A. Ivie [mailto:mivie at montana.edu] 
Sent: Thursday, September 05, 2013 5:34 PM
To: Richard Zander
Cc: Ken Kinman; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] New systematics book



Wow, it this had not just come in on a communication system not invented
then, I would  think I was reading something from 1976!  Is this a
1980's theme party?

Mike

> This is really hard to get across, Ken, because phylogenetic jargon 
> has taken a life of its own.
>
>
>
> In evolutionary systematics, classes Reptilia and Aves are 
> evolutionarily monophyletic even if Reptilia is paraphyletic in 
> phylogenetics. In evolutionary systematics, the sister groups of 
> phylogenetics are replaced by transformations of one taxon to another.
> Pseudoextinction is apparently rare, and peripatric (= parapatric) 
> speciation is the rule. Morphological stasis of ancestral taxa is 
> expected as usual condition. At higher ranks, many large groups have 
> other evolutionarily quite different groups embedded in them if viewed

> as sister groups.
>
>
>
> Sure, Reptilia that includes birds is holophyletic. That is a 
> phylogenetic term and that is all. It helps with phylogenetic 
> classification, but says little about macroevolutionary transformatory

> relationships, only sister-group relationships.
>
>
>
> How does traditional class Reptilia include birds, class Aves?
>
>
>
> ____________________________
> Richard H. Zander
> Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA 
> Web sites: http://www.mobot.org/plantscience/resbot/
> <http://www.mobot.org/plantscience/resbot/>  and 
> http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> <http://www.mobot.org/plantscience/bfna/bfnamenu.htm>
> Modern Evolutionary Systematics Web site:
> http://www.mobot.org/plantscience/resbot/21EvSy.htm
> <http://www.mobot.org/plantscience/resbot/21EvSy.htm>
> UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA
>
> ________________________________
>
> From: Ken Kinman [mailto:kinman at hotmail.com]
> Sent: Thursday, September 05, 2013 5:00 PM
> To: Richard Zander; taxacom at mailman.nhm.ku.edu
> Subject: RE: [Taxacom] New systematics book
>
>
>
> Hi Richard,
>
>      You say:
>
> If we exclude extinct groups that force lumping, then whenever 
> Reptilia is used to include birds, it is evolutionarily paraphyletic.
>
>
>
> My response:
>
>       That doesn't sound right to me.  Wouldn't a taxon Reptilia that 
> includes birds actually be holophyletic?  On the other hand, the 
> traditional Class Reptilia does exclude birds and is paraphyletic 
> (whether or not one includes extinct taxa).
>
>
>                         -----------------Ken
>
>
>
>
> ________________________________
>
> Subject: RE: [Taxacom] New systematics book
> Date: Thu, 5 Sep 2013 12:54:34 -0500
> From: Richard.Zander at mobot.org
> To: kinman at hotmail.com; taxacom at mailman.nhm.ku.edu
>
> Ken:
>
>
>
> There are two ways phylogenetics deals with paraphyly. 1. By 
> splitting, which divides a good taxon "on principle." 2. By lumping, 
> which combines two good taxa "on principle."  Strict phylogenetic 
> monophyly is the principle.
>
>
>
> If Reptilia combines two good taxa "on principle" then you have 
> evolutionary paraphyly. But Reptilia is problematic as far as an 
> example is concerned since it can include clear-cut extinct forms. I'm

> not sure of the taxonomically metaphysical aspects of combining dinos
and birds.
> If we have NOW a diagnosable gap between reptiles s.str. and birds 
> s.str. does that mean we have separate taxa?  If there were ever 
> intermediates between two present-day species must they be combined 
> into one species? Since there could be intermediates between all 
> species, maybe we should lump all species together? I wonder what its 
> name would be? Solves a LOT of problems.
>
>
>
> If we exclude extinct groups that force lumping, then whenever 
> Reptilia is used to include birds, it is evolutionarily paraphyletic.
>
>
>
> Richard
>
> ____________________________
> Richard H. Zander
> Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA 
> Web sites: http://www.mobot.org/plantscience/resbot/
> <http://www.mobot.org/plantscience/resbot/>  and 
> http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> <http://www.mobot.org/plantscience/bfna/bfnamenu.htm>
> Modern Evolutionary Systematics Web site:
> http://www.mobot.org/plantscience/resbot/21EvSy.htm
> <http://www.mobot.org/plantscience/resbot/21EvSy.htm>
> UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA
>
> ________________________________
>
> From: Ken Kinman [mailto:kinman at hotmail.com]
> Sent: Thursday, September 05, 2013 12:08 PM
> To: Richard Zander; taxacom at mailman.nhm.ku.edu
> Subject: RE: [Taxacom] New systematics book
>
>
>
> Hi Richard,
>
>            Thanks, but I was hoping for an explanation using an actual

> example of a paraphyletic taxon, such as Class Reptilia 
> (paraphyletically excluding birds). I'm not entirely sure if you 
> consider Reptilia as evolutionary paraphyletic or phylogenetically 
> paraphyletic.
>
>          ----------Ken
>
>
> ________________________________
>
> Subject: RE: [Taxacom] New systematics book
> Date: Thu, 5 Sep 2013 07:54:48 -0500
> From: Richard.Zander at mobot.org
> To: kinman at hotmail.com; taxacom at mailman.nhm.ku.edu
>
> Well, sure, Ken. Whenever an evolutionarily monophyletic group is 
> split to render it phylogenetically monophyletic in two parts, you end

> up with two nonmonophyletic taxa (evolutionarily) that are actually
the same.
> Phylogenetic paraphyly is when you have two taxa that are the same 
> that phylogeneticists treat as different. "Para" implies faulty, 
> wrong, amiss, or merely similar to the true form. The literature is 
> now replete with evolutionarily nonmonophyletic but phylogenetically 
> monophyletic taxa.
>
>
>
> Richard