Taxacom: [iczn-list] Minimalist revision of Mesochorus

[Stephen Thorpe]

 Nick, 
There is one major drawback of splitting a species into cryptic species that cannot be fixed by designation of a neotype. Suppose that Aus bus is described 200 years ago and frequently mentioned in the literature, not only the taxonomic literature, but also widely in ecological, applied and biogeographical literature. If it is then split into cryptic species, that renders all of that literature from the last 200 years pretty much useless, because you don't know which of the cryptic species any of the information applies to. Designating a neotype doesn't help. Worse is that people reading all that historical literature need to know the details of the recent split and it will be very difficult to stop historical published data on Aus bus from continuing to be linked to the species now known as Aus bus.
Stephen
    On Thursday, 31 August 2023 at 04:53:28 pm NZST, Nick Grishin <grishin at chop.swmed.edu> wrote:  
 
 The point of pioneering works is to stur up the minds so that some 
progress can be made. As such, I consider Sharkey et al. papers 
pioneering. They made the point.

The nomenclature part of the aspect is clear: yes, A is a word, or that's 
how it will be eventually. Arguing about words is fun but may not solve 
real problems.

To me, the real questions are:

#1. how would you minimally modify the Sharkey approach to call it 
acceptable?

#2. what would be the estimated time invested in carrying out #1?

#3. what would be the estimated cost of it?


>From where I stand, the real question about the works by Sharkey et al., 
is whether already extracted DNA of the holotypes or their body parts are 
available for additional sequencing. If they are, then Sharkey's works are 
useful. If not, then value of these works sinks by quite a bit, and they 
might create an obstacle for further studies of the group rather than 
promote them. The COI barcode is a tiny randomly selected segment of a 
sequence from mitochondria (which are, after all, bacteria living in 
insect cells) and it doesn't represent the actual insect in {10%-30% ? 
insert your number here} cases.

If these taxonomic groups are worth some serious study, then whole genome 
shotgun of all Sharkey holotypes is the first step (can be done in 1 week 
in my lab). Then, whole genome shotgun of all other extant primary types 
associated with the group and neotype designations (with genomic 
sequencing) for those that could not be found is next (another week). 
These two steps will establish synonymies and estimate reliability of 
barcodes for species delination in these insects within a couple of months 
(give some weeks for laziness, mishaps, additional specimen sequencing, 
and data analysis), opening the floodgates for future research. Sounds 
easy and doable. All the technology is here. The problem? The price-tag! 
Not $10, unfortunately.


> in the event that a DNA sample cannot be extracted from a name-bearing 
> type specimen (for whatever reason), should the Code provide a mechanism 
> for ...

By all means -- YES! (did I say yes? YES!!!)

Actually, the mechanism is already there, it is Art.75.5. But if you guys 
can brainstorm it a bit more and make it better, it would be a wonderful 
service to the comminuty.

Even more generally, there are too many Articles that rely on the "plenary 
power." Thinking about how to give more power to the people by sensible 
rules without any "plenaries" should be better.

Specifically, in the future world, any primary type without whole genome 
shotgun is "unidentifiable" (except fossils, species that do not qualify 
for neotype designations when their types are lost, etc.).

Collections with primary type holdings across the world have been 
incredibly generous and supportive, beyond expectations, of genomic 
sequencing projects in my lab. That's how we were able to sequence >5000 
primary types from 1770-ies on. Not just the barcodes, but all bits of 
genomic DNA extracted from these name-bearing specimens. This is not to 
brag, but to say that such work is on-going, and I think is highly 
successful and promising. It is not because morphology is "bad", it is 
because morphology is not always sufficient, and because we learn so much 
more with genomic DNA and morphology together (e.g. how one encodes the 
other).

But indeed, if "for whatever reason" type sequencing is not possible, 
provided that all the necessary steps were taken to obtain whole genome 
shotgun, should be grounds for the neotype designation without the 
"plenaries." Similar to the neotype designations in case of lost 
specimens. No DNA from the type = this specimen is "lost" as the type 
specimen. Such type specimens are (or will be) mostly useless as name 
bearers for taxa that qualify for neotype designations under the current 
Code.

More specifically, as an example, a letter from some collection authority 
stating that DNA sequencing of the type specimen is not possible could be 
published in a paper and that permanently deprives this specimen from its 
name-bearing status (i.e. it is considered "lost" for nomenclature and 
remains a historical specimen without name-bearning value).

I'm not smart enough to figure out the wording, provisions, and groups of 
organisms these new genomic-friendly rules could apply to, but for most 
dry-preserved insects such rules will do wonders for overcoming the 
"impediment."

Yes, too long, but thanks for the great discussion, n

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