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

Tue Sep 5 11:56:06 CDT 2023

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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-- 
Scott Thomson

Centro de Estudos dos Quelônios da Amazônia - CEQUA
Petrópolis, Manaus
State of Amazonas, 69055-010
Brasil

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