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

Tue Sep 5 14:13:36 CDT 2023

Jared Bernard wrote, in part:
" What is necessary is to appreciate when the differences have accumulated to the point of the taxa being on separate evolutionary paths."
Molecular differences? What does really determine when a population has entered upon a separate evolutionary paht? Isolation? Adaptations to some different environment? Some arbitrary percentage? 

Or have I snipped something out of context?

-------
Richard H. Zander
Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis – Missouri – 63110 – USA
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-----Original Message-----
From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Scott Thomson via Taxacom
Sent: Tuesday, September 05, 2023 11:56 AM
To: Jared Bernard <bernardj at hawaii.edu>
Cc: taxacom at lists.ku.edu
Subject: Re: Taxacom: replacing un-sequenceable types (was Re: Minimalist revision of Mesochorus)

A large part of my contribution to this has been to ensure that we did not head in a direction that would exclude the validity of fossil and ichnotaxa. In saying that I do agree with Richard that for recent species we should be recording the sequences of all possible types. Of course this is also the majority of species in most groups, though in turtles the fossil taxa outnumber the living taxa 3:1 but turtles have a very long history and are very hard so preserve well. Try keeping turtle specimens in a museum; turtles break the drums, not drums damage the turtles.

So in saying that I want to discuss some issues with DNA, as I have said I work on both living and fossil taxa and combine them into single datasets, my phylogenies include living and fossil taxa. One issue that occurs in DNA though is more problematic in mitagenomics, is introgression. The species Chelodina expansa has no mtDNA of its own, it has its own nuDNA but its mtDNA has been overwritten by other species. It has the mtDNA of Chelodina longicollis, Chelodina canni depending on where it is from. Both species are from different subgenera and are not close relatives of Chelodina expansa. So depending on the locality of the specimen a mtDNA only phylogeny places this species as conspecific with taxa from a different subgenus. In fact turtles in general can hybridise, including across genera even sub families. So if we are going to rely on DNA evidence it must include nuDNA separately assessed from mtDNA so as to assess the level of introgression.

Another problem alluded to previously is the level of detail the DNA gets.
I have seen some phylogenies which I have said that's not a phylogeny its a pedigree. Yes I am being tongue in cheek there I am making the point that the cutoffs being proposed are too closely related. Not all members of a species have identical DNA; there is and should be variation. What is necessary is to appreciate when the differences have accumulated to the point of the taxa being on separate evolutionary paths. Whether two taxa can hybridise is irrelevant, sorry but hybridisation is like all characters divisible into apomorphic and plesiomorphic states, inability to hybridise is apomorphic and testable against a species hypothesis, ability to hybridise is plesiomorphic and has no relevance to a phylogenetic hypothesis.

So yes I agree to the concept of DNA sequences of all types where possible, I think replacing types that cannot be sequenced should be a per need issue only, we cannot set a neotype for curatorial reasons it must be to solve a nomenclatural issue, being unable to sequence a type and suggesting a neotype should be the same only if there is a clear nomenclatural issue at stake.

Cheers Scott

On Tue, Sep 5, 2023 at 1:37 PM Jared Bernard via Taxacom < taxacom at lists.ku.edu> wrote:

> Not only is biogeographical info not in DNA per se, but there are 
> other obvious risks of relying entirely on DNA. Clearly there is now a 
> sentiment that you can simply blast a barcode against a genetic 
> repository to identify something. Arguments about barcoding aside (and 
> there are plenty), a lot of stuff on genetic repositories is 
> misidentified (e.g., Meiklejohn et al. 2019, doi: 10.1371/ journal.pone.0217084; Fort et al. 2021, doi:
> 10.1111/1755-0998.13453; Cheng et al. 2023, doi:
> 10.3389/fevo.2023.1149839). So, someone who may not be an expert in 
> distinguishing species taxonomically has identified their species, and 
> now that name is forever associated with that genetic material. So 
> when the next user blasts their species' DNA, it comes back with an ID 
> (or rather, highest similarity), and that user probably doesn't 
> question it. (Same problem with the new AI tools.)
>
> The task of the underappreciated field of taxonomy must therefore be 
> to distinguish species morphologically so that any following work, 
> like evolutionary relationships or ecology, won't be misapplied to the 
> wrong species. I always wonder, given the above emerging data on 
> misidentified material on genetic repositories, how many papers on 
> ecology, conservation biology, or evolution have misidentified the 
> study subjects. This is the problem with the widening disconnect 
> between people studying biodiversity and people who can identify the basic units of biodiversity.
>
> And of course, this is aside from the fact that only an infinitesimal 
> amount of the world's biodiversity has any sequence in a repository, 
> incorrect or not (Kvist 2013, doi: 10.1016/j.ympev.2013.05.012).
>
> If I'm restating an earlier comment, I apologize.
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