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

[Marko Mutanen]

Nick,

Nice to meet you! I am a person who finds that taxonomy being based entirely on DNA would be the best way to do it. As you wrote, basing it on full genomes would be the best option. However, in real life, at least for the time being, this approach is not a very feasible one. This being said, I deeply appreciate your works on butterfly genomes and hope being able to do something similar - to the same incredible scale!

I don't think I am the only one sharing this opinion. The recent proposals of DNA taxonomy based on standard nuclear markers might suggest that we are more. With this, I don't mean that the integrative approaches would be wrong. I am doing it a lot myself. But I doubt it is the best way, especially in the future as genomics tools become increasingly available to taxonomists.

Why do I think that that only-DNA would be the best approach? In short, because species delimitation is largely bound to be arbitrary. For example, probably most species' distribution is patchy, with isolated populations being differentiated to the various degrees. With my colleagues, I have written about this allopatry problem in species delimitation in several articles. Because speciation is a gradual process, delimitation of diverging populations is inherently arbitrary. As so, the best would be to base it all on quantifiable data, i.e. DNA. That would serve the stability the best as enabling standardization. Also, finally all taxonomically relevant data is encoded in DNA, as you also stated. Be it ecological, morphological or whatever. Even when we do not know yet where this information is hidden in the genome, it is still there.

I am also convinced, given the unprecedented progress of genomics technologies, that not far in the future recovering entire genomes of organisms is both straightforward and cheap. Once we can retrieve huge amounts of information (and all that matters) in such an easy way, why shouldn't we take a full benefit of it?

With this, I of course do not mean that we should stop working on morphology. I love morphology and spend a lot of my time on mounting insects. I only mean that delimitation of species would be best done if based on DNA alone.

Best,

Marko Mutanen


-----Original Message-----
From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Nick Grishin via Taxacom
Sent: perjantai 1. syyskuuta 2023 7.47
To: taxacom at lists.ku.edu
Subject: Re: Taxacom: replacing un-sequenceable types (was Re: Minimalist revision of Mesochorus)

> Doug, I agree with your reasoning here, except for one major problem! 
> If you promote DNA-only based taxonomy,

I have not met a person who promotes "DNA-only taxonomy." Does such concept even exist? If there are such people here, please speak up.

Personally, I promote Code-compliant integrative taxonomy that is guided by genomic DNA sequencing (not barcoding) of primary type specimens. Why so? Because morphology has been studied for centuries, and the genomic approach most efficiently reveals what has been missed before. Genomic sequencing first (with morphology-guided specimen selection), morphology second, to explain and rationalize sequencing results.

Genomic sequence = the blueprint of the entire organism, including its adult morphology, and also eggs, larvae, food, behavior, habitat and mating preferences. Just more information than in a pinned adult.


> then those old, unsequenceable types lose any utility that they may 
> once have had anyway, regardless of whether or not they formally lose 
> type status! Nobody will have any reason to examine them. They will 
> effectively become types of nomina dubia.

A note: "old" and "unsequenceable" are uncorrelated properties. Nearly all "old" types sequence great. And there was an insect specimen collected in
2020 that we couldn't sequence. Maybe it got COVID and the virus destroyed all of its DNA?

But if "unsequenceable" types for difficult groups (=those that are eligible for the neotype designation) are kept as types, these names indeed are nomina dubia. They would either be ignored, or the groups with them will not be addressed by revisions, and nobody will work on them for years until someone solves the problem somehow.

I think it may be an opportunity for the ICZN to weigh in here and help the community, n


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