Taxacom: replacing un-sequenceable types (was Re: Minimalist revision of Mesochorus)

[Nick Grishin]

Doug, thanks much for your thoughts. Yes, you are absolutely right, and 
that's why, as the Code users, we look up to you guys to phrase it all in 
a palatable way into the C5. Yes, if a specimen cannot be the name-bearer, 
it should not be the name-bearer. Impediment is created by having the 
types that do not convery the meaning of the names they bear. Please think 
more about it. Luckily, it rarely happen in real life.


A few points:

First, about "This is an unrealistic estimate." I failed to mention that 
the estimate was for the actual lab work for 1 person, provided that 
[usually leg] samples are already in the lab. The estimate is accurate and 
it was to show that the technology of genomic sequencing (not "barcoding", 
not gene amplification, no parts but the whole thing) we have today is not 
limiting progress.

1)
The current version of the Code (C4) is great, it is very much workable, 
it is hard to spot problem with its major principles and logic.

2)
If anything could use improvement, it would rather be too frequent 
reference to "plenary powers." One of the problems is that these powers 
may not be fast enough to keep up with the racheting pace of the world. 
Art.23.9. or Art.70.3. are great examples of what will be good to 
see, and 75.5. or 65.2. would be something that may be improved. Give the 
power to the people by providing sensible rules.

3)
Whether we like it or not, the work-flow of a Code-compliant taxonomist is 
moving towards the following pipeline:

1. genome-sequence your specimens of interest;
2. genome-sequence primary types involved in this group;
3. find the best neotypes for the names with lost or unidentifiable or 
unsequenceable types and sequence them;
4. analyze the data, assign types to more recent specimens (=assign 
names), delineate species, carry out phylogenetic and population analysis;
5. come back to morphology and correlate morphology with genomics, find 
morphological characters and fieldmarks to recongize as many species as 
you can by phenotype.

This pipeline is equivalent to the following traditional workflow of a 
Lepidopterist:

1. dissect your specimens of interest;
2. inspect genitalia preps/dissect primary types involved in this group;
3. find the best neotypes for the names with lost types and dissect them;
4. analyze the data, delineate species (i.e. those where you think you see 
differences in genitalia);
5. come back to wing patterns and other characters and correlate them with 
genitalia, find expernal characters and fieldmarks to recognize as many 
species as you can by facies.

I.e., largely replace the word "dissect" in the old workflow with the word 
"sequence" in the new, not much else differs.

Therefore, the best service ICZN can provide to promote the tradition of 
Code-compliance is to faciliate integration of type specimens into the 
workflow.

4)
You can praise Sharkey et al., or attack them, but I view this more as a 
cry for help in bridging the old and the new. Out of desperation, their 
solution simply cuts off the old, being unable to address it with the 
pipeline proposed above. Well, help them (and others), please. And 
everything is already in C4, but in a milder form, e.g., 72F.3.

5)
Collections benefit tremendously from specimen sequencing (beyond what 
many may imagine), because the contribution of the collection jumps across 
disciplines (e.g., expands from websites with pictures to websites with 
sequences, like GenBank, SRA, etc.) thus expanding their influence over a 
much larger group of people (to include now all people in the biomedical 
domain who use GenBank), and thus gains potential to attract other sources 
of funding. DNA extracted from the type and type parts used for the 
extraction are still the type stored separately and preserve the type in 
case something happens to the rest of the specimen. Type DNA sequences 
diminish the need to actually handle the type, thus adding to the safety 
of the specimen. There are only benefits to all this, no downsides. The 
real problem is still the same -- funding (or the lack of it).

6)
To be honest, I'm not quite following the suggestion to establish a 
parallel "DNA-type" system. It basically boils down to "DNA-type" (well, 
not the DNA, but the entire specimen, including its DNA) serving the role 
of the neotype, and setting aside the real type. The way to do it, is to 
genome-sequence (not "barcode") the real type, and if it is 
"unsequenceable" (that implies unidentifiable, not fit to serve as the 
name-bearer for taxa that are currenly eligible for the neotype 
designation), set it aside, and replace it with the real neotype. From our 
experience, there aren't that many "unsequenceable" types. The ones we had 
were from a private collection (too wet conditions? too much Vapona?) -- 
an argument to deposit your holotypes in institutional collections, and 
better those, which already hold many type specimens and know how to care 
for them. But maybe even these several (out of throusands) failed types 
would work when muscle tissue is used instead of a leg. Need to try.

7)
Enough already ... n



On Thu, 31 Aug 2023, Douglas Yanega via Taxacom wrote:

> On 8/30/23 9:28 PM, Nick Grishin via Taxacom wrote:
>>  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). 
>
> This is an unrealistic estimate. The "all other extant primary types" are 
> probably scattered in over a dozen different museums in different countries, 
> and you would be lucky if you would be able to get this step done within a 
> year, and all that travel will be fairly expensive. Also, see my comment 
> below.
>
>>
>>  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 sure you realized when you proposed this just what a proverbial 
> bombshell this would be.
>
> Think carefully about this:
>
> Imagine you are the curator of a major collection, and one of the *most 
> valuable* parts of your collection is the set of a few hundred type specimens 
> from the private collection of a famous taxonomist from the early 1800s, 
> maybe SEVERAL famous taxonomists. These types are fragile, many in poor 
> condition, and irreplaceable. People come from all over the world to examine 
> these types, and you have also invested a large amount of money in taking 
> images of them, and putting these images online. They are kept in special 
> cabinets in a separate room from the main collection.
>
> Someone then writes to you asking whether all of those types are available 
> for molecular sequencing, and you write a response saying "None of these 
> specimens is available for such purposes".
>
> A few months later, the person who contacted you publishes a paper in which 
> they quote your response, and they summarily declare that *every single type 
> specimen in your collection is henceforth no longer a type specimen*.
>
> That part of your collection has just gone from being incredibly valuable and 
> irreplaceable, to effectively worthless. The money you spent on taking images 
> of your specimens has been for nothing. The special cabinets and room now 
> contain nothing of any value to anyone, and will never be visited again.
>
> Implementing such a provision in the Code might not bother many taxonomists, 
> but I doubt that a single museum curator in the world would consider this 
> acceptable. You might argue that the purpose of type specimens is not to 
> benefit the collections in which they reside, and that's true enough - that's 
> admittedly not the PURPOSE of types. But, in reality, *they do have that 
> effect*. Types confer prestige. This effect influences not only the number of 
> visitors a museum gets, but the amount of external support - a very tangible 
> benefit can accrue by virtue of being a type repository. You won't generally 
> get an NSF grant to take photos of random specimens in your collection, but 
> you CAN get grants to take photos of types.
>
> Speaking now as a museum curator:
>
> You're talking about a policy that "sounds good on paper", but would do a LOT 
> of collateral damage to most of the world's most prestigious collections. It 
> would be analogous to holding a flame thrower in front of a cabinet of 
> specimens and saying "Either you let me sequence these, or I'll incinerate 
> them". No curator would enjoy being compelled to make such a choice, and you 
> could expect some *serious* resistance.
>
> Peace,
>
>