[Taxacom] naming of dark taxa (botanical or zoological?)

Sun Feb 25 11:01:20 CST 2018

I don’t know. On the other hand, John, what is the rationale that cladists have for leaving out ancestors of a group? A clade has neither end, nor beginning. It is just one node generating another node. There is no taxon concept.

My own taxon concept is that of a central generative taxon (core species) radiating descendant, mostly specialized taxa. Groups of specialized descendant species around a more generalized progenitor species is a fine, empirical genus concept. It probably could be extended to families, orders, and so on. Unfortunately cladistic trees cannot model such because optimal trees avoid multifurcations as less parsimonious. Cladists cannot “see” natural groups of radiating taxa.

For much, much more, buy my books on Amazon! Inexpensive, illuminating, at times amusing, always zetetic.

Richard

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Richard H. Zander
Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis – Missouri – 63110 – USA
richard.zander at mobot.org<mailto:richard.zander at mobot.org>
Web sites: http://www.mobot.org/plantscience/bfna/bfnamenu.htm and http://www.mobot.org/plantscience/resbot/

From: John Grehan [mailto:calabar.john at gmail.com]
Sent: Sunday, February 25, 2018 10:40 AM
To: Richard Zander
Cc: Kenneth Kinman; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] naming of dark taxa (botanical or zoological?)

What was Cavalier-Smith's rationale for leaving out some descendants of a group as a way to "understanding stepwise phylogenetic change"?

John Grehan

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On Sun, Feb 25, 2018 at 11:26 AM, Richard Zander <Richard.Zander at mobot.org<mailto:Richard.Zander at mobot.org>> wrote:
Very interesting, Ken. Cavalier-Smith names paraphyletic taxa and writes that this helps in understanding stepwise phylogentic change. Good.

I think much splitting and lumping could be replaced by understanding. This should be done in the context of evolutionary theory, not dichotomous cladograms and strict phylogenetic monophyly, which model no evolutionary processes.

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Richard H. Zander
Missouri Botanical Garden - 4344 Shaw Blvd. - St. Louis - Missouri - 63110 - USA
richard.zander at mobot.org<mailto:richard.zander at mobot.org><mailto:richard.zander at mobot.org<mailto:richard.zander at mobot.org>>
Web sites: http://www.mobot.org/plantscience/bfna/bfnamenu.htm and http://www.mobot.org/plantscience/resbot/

From: Kenneth Kinman [mailto:kinman at hotmail.com<mailto:kinman at hotmail.com>]
Sent: Saturday, February 24, 2018 4:24 PM
To: Richard Zander; taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu>
Subject: naming of dark taxa (botanical or zoological?)

Hi Richard,

       I like your question about the difference between dark mutations and dark taxa.  But whether the "cellar" is cladistic or not, there seems to be the risk of prematurely opening the floodgates of splitting of these taxa at lower taxonomic levels.  I wouldn't be in too much hurry to speed things up too much (numbers into formal names).  It could create a destabilizing mess.   And that is just a lower taxonomic levels.

        At the higher taxonomic levels, there is even the problem of which Code of Nomenclature should govern most of these taxa.  Mycologists have formalized the name Cryptomycota (or Rozellomycota), so I guess the presumption is that ordinal and familial taxa would have botanical names.

       However, Cavalier-Smith. 2013, has formally classified them as Class Rozellidea within Phylum Choanozoa, so I assume family taxa would then have zoological names.  See Table 7 for his classification here:

https://www.sciencedirect.com/science/article/pii/S0932473912000508#tbl0035

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From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu<mailto:taxacom-bounces at mailman.nhm.ku.edu><mailto:taxacom-bounces at mailman.nhm.ku.edu<mailto:taxacom-bounces at mailman.nhm.ku.edu>>> on behalf of Richard Zander <Richard.Zander at mobot.org<mailto:Richard.Zander at mobot.org><mailto:Richard.Zander at mobot.org<mailto:Richard.Zander at mobot.org>>>
Sent: Saturday, February 24, 2018 2:14 PM
To: taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu><mailto:taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu>>
Subject: Re: [Taxacom] Names and naming of dark taxa

Dark taxa? How does one determine the difference between dark mutations and dark taxa? There is no innate taxon criterion in cladistics. Cluster analysis to determine how different sequences group? Is a group of similar sequences a taxon? Does a group of similar sequences imply an evolutionary process involved, maybe some evolutionary trajectory through time?

A dark taxon in a cladistic cellar at molecular night is hard to envision.

-------
Richard H. Zander
Missouri Botanical Garden - 4344 Shaw Blvd. - St. Louis - Missouri - 63110 - USA
richard.zander at mobot.org<mailto:richard.zander at mobot.org><mailto:richard.zander at mobot.org<mailto:richard.zander at mobot.org>>
Web sites: http://www.mobot.org/plantscience/bfna/bfnamenu.htm and http://www.mobot.org/plantscience/resbot/

-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu<mailto:taxacom-bounces at mailman.nhm.ku.edu>] On Behalf Of Henrik Nilsson
Sent: Saturday, February 24, 2018 11:43 AM
To: taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu><mailto:taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu>>
Subject: [Taxacom] Names and naming of dark taxa

Here's a recent commentary on names and naming of dark taxa:

https://mycokeys.pensoft.net/article/24376/
New light on names and naming of dark taxa<https://mycokeys.pensoft.net/article/24376/>
mycokeys.pensoft.net<http://mycokeys.pensoft.net>
A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as "dark taxa" or "dark matter fungi". As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted.

Abstract:
A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as "dark taxa" or "dark matter fungi". As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted.

Best wishes,

Henrik Nilsson
University of Gothenburg

--

http://www2.dpes.gu.se/staff/hennil/
where did technology slow today? - Göteborgs universitet<http://www2.dpes.gu.se/staff/hennil/>
www2.dpes.gu.se<http://www2.dpes.gu.se>
Name: R. Henrik Nilsson Position: Associate professor (docent) Address: University of Gothenburg, Department of Biological and Environmental Sciences, Box 461, 405 30 ...

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