[Taxacom] Names and naming of dark taxa

Sat Feb 24 16:19:23 CST 2018

So to me this all centers of a general question that would be a problem for
any kind of taxonomy or systematics. And not one for which there is a
universal recipe it would seem.

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On Sat, Feb 24, 2018 at 4:58 PM, Richard Zander <Richard.Zander at mobot.org>
wrote:

> We have two problems. The molecular sequence and taxon level recognition
> problem, which Henrik discusses, sort of. Then there is the cladistic
> problem in which Henrik fairly clearly couches the possible solution to the
> molecular sequence and taxon level recognition problem in terms of a
> cladistic solution. Since cladistics only identifies sister groups, the
> evolutionary process is not modeled.
>
>
>
> What other solution might deal with this? Well, maybe cluster the
> sequences and then match them with known taxa to the extent possible, then
> see if such matching might genuinely model unknown species. Maybe.
>
>
>
> I wish studies were done with expressed traits first, not second. But then
> sequencing is easy, and studying expressed traits is tedious and requires
> difficult ratiocination. One is never wrong mechanically juggling
> sequences, but often developing and testing valid theories about
> evolutionary processes are fraught with snares and trials.
>
>
>
>
>
> -------
>
> Richard H. Zander
>
> Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis – Missouri –
> 63110 – USA
> <https://maps.google.com/?q=4344+Shaw+Blvd.+%E2%80%93+St.+Louis+%E2%80%93+Missouri+%E2%80%93+63110+%E2%80%93+USA&entry=gmail&source=g>
>
> 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:* Saturday, February 24, 2018 2:55 PM
>
> *To:* Richard Zander
> *Cc:* taxacom at mailman.nhm.ku.edu
> *Subject:* Re: [Taxacom] Names and naming of dark taxa
>
>
>
> But how is Henrick's question of taxa only being known from sequence data
> that cannot be linked to any physical specimen or resolved taxonomic name a
> specifically cladistic problem? What other systematics approach would not
> make it a problem?
>
>
>
>
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>
>
> On Sat, Feb 24, 2018 at 3:33 PM, Richard Zander <Richard.Zander at mobot.org>
> wrote:
>
> Well, Henrik wrote: “Furthermore, a name can be correct for some taxon or
> a synonym of another name depending on the specific taxonomy. If it is
> required that taxa be monophyletic, then changes in the taxonomy should be
> expected due to changes in the understanding of evolutionary relationships.
> Even if this stabilises with time as better estimates of evolutionary
> relationships are obtained, there may still be conflicts as to what clades
> are considered as taxa and at what taxonomic level.”
>
>
>
> Note “clades” and “monophyletic”. The problem described by Henrik is
> simply that of using sequences without clear connection to expressed traits
> united as an evolution-based taxon. Using cladistics to try to deal with
> the problem is problematic.
>
>
>
>
>
>
>
> -------
>
> Richard H. Zander
>
> Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis – Missouri –
> 63110 – USA
> <https://maps.google.com/?q=4344+Shaw+Blvd.+%E2%80%93+St.+Louis+%E2%80%93+Missouri+%E2%80%93+63110+%E2%80%93+USA&entry=gmail&source=g>
>
> 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:* Saturday, February 24, 2018 2:20 PM
> *To:* Richard Zander
> *Cc:* taxacom at mailman.nhm.ku.edu
> *Subject:* Re: [Taxacom] Names and naming of dark taxa
>
>
>
> How is the problem described by Henrik created by cladistics?
>
>
>
>
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>
>
> On Sat, Feb 24, 2018 at 3:14 PM, Richard Zander <Richard.Zander at mobot.org>
> wrote:
>
> 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
> <https://maps.google.com/?q=4344+Shaw+Blvd.+%E2%80%93+St.+Louis+%E2%80%93+Missouri+%E2%80%93+63110+%E2%80%93+USA&entry=gmail&source=g>
> 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
> 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/
>
> 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/
>
>
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