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

[John Grehan]

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>
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.
>
>
> -------
> 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: Kenneth Kinman [mailto:kinman at hotmail.com]
> Sent: Saturday, February 24, 2018 4:24 PM
> To: Richard Zander; 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
>
>
>
>
>
> ________________________________
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu<mailto:taxacom-bounces@
> mailman.nhm.ku.edu>> on behalf of Richard Zander <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>
> 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>
> 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] 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>
> 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
> 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
> 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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