Taxacom: [iczn-list] Minimalist revision of Mesochorus
Stephen Thorpe
stephen_thorpe at yahoo.co.nz
Thu Aug 31 00:36:06 CDT 2023
Not quite sure what your point is. By "cryptic species", I mean species only distinguishable by DNA. Sure, in some groups, species are externally morphologically indistinguishable, but have morphologically distinct genitalia. But genitalic differences have been taken into account for a very long time, so there is unlikely to be 200 years worth of published data on a species that includes morphologically different forms of the genitalia.
Sure we study nature, but the results of the study are in the literature. It helps if the data is associated with the correct name!
Stephen
On Thursday, 31 August 2023 at 05:21:11 pm NZST, Nick Grishin <grishin at chop.swmed.edu> wrote:
Stephen,
Replace "cryptic specis" in your message with "species morphologically
distinct in genitalia." Nothing changes for me. What about you?
What do we study? Nature or literature? I prefer to think that I study
nature with the help of literature, not the other way around, n
On Thu, 31 Aug 2023, Stephen Thorpe wrote:
> 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
>
> _______________________________________________
> iczn-list mailing list
> iczn-list at afriherp.org
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flist.afriherp.org%2Fmailman%2Flistinfo%2Ficzn-list&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cca5fb379b12c4886a69708dba9e42e02%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638290569732744617%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Lj9JETHaTODyXdhe3pcdp9QadVCxzfR7sXFPmZY8lYc%3D&reserved=0
>_______________________________________________
iczn-list mailing list
iczn-list at afriherp.org
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flist.afriherp.org%2Fmailman%2Flistinfo%2Ficzn-list&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cca5fb379b12c4886a69708dba9e42e02%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638290569732901326%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7HHeOj0P12M8yDq1yQu9llsfheWYt9fw%2FZNRe6RQA3Q%3D&reserved=0
More information about the Taxacom
mailing list