[Taxacom] Extinction, diversity, and conservation

Mon Apr 9 20:19:09 CDT 2018

Hi All,

      Reflecting on my response this morning concerning how extinction prunes most multifurcations from the tree of life (especially further back in time, at higher taxonomic levels), I found an interesting paper related to this subject and how it might be relevant to conservation efforts.  It was published in 2015, "Losing history: how extinctions prune features from the tree of life".

      It says: "Phylogenetic diversity (PD), the summed branch lengths that connect species on the tree-of-life, might provide a valuable metric for conservation prioritization because it has been argued to capture feature diversity."  Anyone have any opinions about this as a valuable metric concerning conservation priorities?  A weblink to the article is given below.

                      -----------------Ken

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290420/

________________________________
From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Kenneth Kinman <kinman at hotmail.com>
Sent: Monday, April 9, 2018 9:37 AM
To: Richard Zander; Stephen Thorpe
Cc: taxacom
Subject: Re: [Taxacom] A Cladist is a systematist who seeks a natural classification

Hi Richard,

       Although that is indeed a problem at species level, I don't think multifurcations are as much of a problem at higher taxonomic levels.  That is because extinction wipes out almost all evidence of relevant multifurcations (there is no record of the species involved, just the descendants of one of the species).

      This usually results in simpler bifurcating trees being a close approximation of the relationships between higher taxa (such Families and Orders, etc.).  Is there any evidence of any true multifurcations at family or higher level?  But to be clear, I am defending careful cladistic analysis (not cladistic classification) of such taxa.

                  ---------------Ken

________________________________
From: Richard Zander <Richard.Zander at mobot.org>
Sent: Monday, April 9, 2018 9:03 AM
To: Stephen Thorpe
Cc: taxacom; Kenneth Kinman; Elena Kupriyanova
Subject: RE: [Taxacom] A Cladist is a systematist who seeks a natural classification

Perhaps one should examine what a cladistic hypothesis really is. I think such is an attempt to wrench evolutionary relationships between species into a dichotomous tree with relationships between unknown shared ancestors.

Consider the scenario of one species generating four descendant species.

First off, cladists cannot conceive or countenance such an idea. What happens is that a cladogram based on morphological data commonly shows either a multification from an unknown shared ancestor of all taxa, or an entirely or partially "resolved" tree of dichotomous relationships. These trees are hypotheses of what?

Molecular analysis can give you dichotomous trees of these taxa, all species derived from a postulated four additional unknown shared ancestors, because the species are probably generated from one progenitor species at different times. This means what? What is the hypothesis?

Cladistic analysis has abandoned evolutionary theory and is stuck in a structuralist hole. This sort of hierarchical cluster analysis is 30-year old technology. As millennials say, "It's so yesterday."

-------
Richard H. Zander
Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis – Missouri – 63110 – USA
richard.zander at mobot.org
Web sites: http://www.mobot.org/plantscience/bfna/bfnamenu.htm and http://www.mobot.org/plantscience/resbot/
bfnamenu - Missouri Botanical Garden<http://www.mobot.org/plantscience/bfna/bfnamenu.htm>
www.mobot.org
B ryophyte F lora of N orth A merica. W EB S ITE . MENU • The Treatments: Descriptions, Keys, and Illustrations • Participants, Guides for Authors, and References • Research Results Published Elsewhere

bfnamenu - Missouri Botanical Garden<http://www.mobot.org/plantscience/bfna/bfnamenu.htm>
www.mobot.org<http://www.mobot.org>
B ryophyte F lora of N orth A merica. W EB S ITE . MENU • The Treatments: Descriptions, Keys, and Illustrations • Participants, Guides for Authors, and References • Research Results Published Elsewhere

-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Stephen Thorpe
Sent: Saturday, April 07, 2018 10:27 PM
To: taxacom; Kenneth Kinman; Elena Kupriyanova
Subject: Re: [Taxacom] A Cladist is a systematist who seeks a natural classification

Elena,
That really isn't the point. The point is that too many phylogenetists go on to say something along the lines of "the results of the phylogenetic analysis indicate that X is paraphyletic wrt Y, so we hereby synonymise X=Y". This makes little sense if the results of the phylogenetic analysis are merely a hypothesis.
Stephen

--------------------------------------------
On Sun, 8/4/18, Elena Kupriyanova <Elena.Kupriyanova at austmus.gov.au> wrote:

 Subject: RE: [Taxacom] A Cladist is a systematist who seeks     a       natural classification
 To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>, "taxacom" <taxacom at mailman.nhm.ku.edu>, "Kenneth Kinman" <kinman at hotmail.com>
 Received: Sunday, 8 April, 2018, 12:57 PM

 Therefore, what advantage does
 cladistics/phylogenetic analysis have over any other method  for generating hypothesis, such as "taxonomic intuition"?

 Sorry, I would really love to know what  these other methods for generating hypotheses, other than  cladistics/phylogenetic analysis  and  "taxonomic  intuition" are

 Dr. Elena Kupriyanova
 Senior Research Scientist
 Marine Invertebrates

 Associate Editor,
 Records of the Australian Museum

 Australian Museum Research Institute
 1 William Street Sydney NSW 2010
 Australia
 t 61 2 9320 6340   m
 61402735679   f 61 2 9320 6059
 Visit: http://www.australianmuseum.net.au
 Like: http://www.facebook.com/australianmuseum
 Follow: http://www.twitter.com/austmus
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 Inspiring the exploration of nature and  cultures

 -----Original Message-----
 From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
 On Behalf Of Stephen Thorpe
 Sent: Sunday, 8 April 2018 7:04 AM
 To: taxacom <taxacom at mailman.nhm.ku.edu>;  Stephen Thorpe <stephen_thorpe at yahoo.co.nz>;  Kenneth Kinman <kinman at hotmail.com>
 Subject: Re: [Taxacom] A Cladist is a
 systematist who seeks a natural classification

 Ken said: "there is no problem with
 cladistic analysis as an hypothesis generator"

 Actually, I think that there is a
 problem. A method for generating hypotheses does just that,  i.e. generates hypotheses, and nothing more. Now, it doesn't  actually matter where a hypothesis comes from (i.e. it  doesn't matter how it is generated). The (only) value of any  hypothesis lies in subsequent testing. Therefore, what  advantage does cladistics/phylogenetic analysis have over  any other method for generating hypothesis, such as  "taxonomic intuition"?

 Stephen

 --------------------------------------------
 On Sun, 8/4/18, Kenneth Kinman <kinman at hotmail.com>
 wrote:

  Subject: Re: [Taxacom] A Cladist is a
 systematist who seeks anaturalclassification
  To: "taxacom" <taxacom at mailman.nhm.ku.edu>,  "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
  Received: Sunday, 8 April, 2018, 1:23
 AM

  Hi all,
         There is
  no problem with cladistic analysis as
 an hypothesis  generator.  The problem is that  phylogenetic systematists  only formally recognize taxa  which are clades.  By  branding paraphyletic taxa  as unnatural
   and refusing to recognize any of
 them, they often fail to  put in the added work of  incorporating divergence  information into their  classifications when it would make  them more stable  and usable (as advocated by Mayr, Ashlock,  Cavalier-Smith, and other evolutionary
   systematists).

        This is
  especially true of higher taxa
 (families to kingdoms).  It  is therefore no  surprise that it is at the level of  Kingdoms, Phyla,  and Classes that the debate between  evolutionary  systematists and phylogenetic
   systematists is most
 heated.  Phylogenetic systematists  have too often  generated instability at those levels, and  thus  severely affecting usability.

         That is
  why Ernst Mayr called them
 cladifications (not  classifications).  At the  level of species and genera,  cladifications often turn  out to be good classifications,  but the same is too  often not true at higher
   taxonomic levels.  The
 worst case is the Three Domain  cladification which was  (and continues to be) horribly  simplistic.  It is  people like Cavalier-Smith who is  putting in the hard  work of attempting to construct more  natural, stable,  and usable classifications.

   --------------Ken

  From: Taxacom
  <taxacom-bounces at mailman.nhm.ku.edu>
 on behalf of  Stephen Thorpe <stephen_thorpe at yahoo.co.nz>

  Sent: Saturday, April 7, 2018 1:01 AM

  To: taxacom; John Grehan

  Subject: Re: [Taxacom] A Cladist is a
 systematist who  seeks a natural classification

  The issue
  that I still haven't been able to get
 a clear answer to  is whether cladistics is just a way  of generating hypotheses  for future testing (which, as  we all know, is ongoing and  never conclusive), or  whether it somehow generates
   something which can be more or
 less thought of as a  "fact", i.e. something which is  at least more  likely to be "true" than not. My own  suspicion is  the former, i.e. just a hypothesis  generator, based on  various assumptions (such a s
 parsimony) and given values
   of certain variables
 (weightings, etc.) which may  themselves be quite  subjective.

  Stephen

 --------------------------------------------

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