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

[Peter Uetz]

Marko is right: it’s only a matter of time until a lot of genome sequences and a lot of AI will allow us to predict phenotypes (and thus morphology) from genome sequences, similar to the prediction of protein structures from sequences (thought to be impossible just 20 years ago).

Until then, we have to collect BOTH genome sequences AND morphology, otherwise AI does not have enough data to figure it out :) Only DNA or only morphology won’t do it.

I disagree with Marko that species delimitation is “arbitrary” — it’s not — it’s just very difficult as you need a lot of genetic (and morphological) data to demonstrate (or refute) gene flow and thus not objectively feasible for the vast majority of species at this point. 



> On Sep 1, 2023, at 2:53 AM, Marko Mutanen via Taxacom <taxacom at lists.ku.edu> wrote:
> 
> 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
> 

————————————————————————————————————
Peter Uetz
Center for Biological Data Science
(formerly Center for the Study of Biological Complexity)
Virginia Commonwealth University
Richmond, VA 23284
USA

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