Taxacom: building such a bridge (between DNA sequence and name)

Tue Sep 5 09:40:51 CDT 2023

Dear Richard,

I agree with you in many points. Paraphyletic (or ancestral as you call them) species have been demonstrated to exist using molecular evidence. Evolution and speciation could not work any other way. We also often forget that we are only able to resolve classifications because we ignore all extinct individuals. And, as you well noted, cladistic practice demands that individuals are always placed as terminals, whereas in reality individuals are to be placed all along an evolutionary tree, so cladistic phylogenetics is always a distortion of reality when it is translated 1:1 into classifications.

However, I think you are mixing two different things: one is to work out taxon concepts, for which you need a large amount of data, and the other is nomenclature. To fix nomenclature, you always need a single type. Ideally, the type should be representative of a taxon, although often it is not. But as long as the type can be shown to belong to the taxon bearing the corresponding name, it serves its purpose. Therefore, the idea of a sequence (or genome) as type works equally well as having a single specimen as type. It is not to reflect the entire taxon but it is to fix a name to the clade that includes the sequence. There is nothing laughable about it, it is exactly the same principle that applies for any other type. Of course, when you have a specimen, the specimen should be the type, not the sequence, as the sequence by default is associated to the specimen and there is no need to have the sequence itself as type.

Robert

-----Ursprüngliche Nachricht-----
Von: Taxacom <taxacom-bounces at lists.ku.edu> Im Auftrag von Richard Zander via Taxacom
Gesendet: Dienstag, 5. September 2023 15:50
An: Jared Bernard <bernardj at hawaii.edu>; Adam Cotton <thaibaggie at gmail.com>
Cc: taxacom at lists.ku.edu
Betreff: Re: Taxacom: building such a bridge (between DNA sequence and name)

Many think molecular sequences track evolution. Well, they track generation of new species but also track microevolution, if any, of the surviving ancestral species. Such survive over millions of years. This continuation of the genotype of the descendant within the population of the ancestor means that ancestral species may generate several genotypically different descendant species over millions of years, with extant populations of the same set of different genotypes in the ancestral species then popping up in different parts of the molecular cladogram. This is the source of cryptic molecular species, genera and families. Where the different populations of the ancestral species occur in a cladogram depends on extinction of some but not all populations of different genotypes of the ancestral species. 

So when you map morphology to a molecular cladogram, presto, you get multiple origins of major traits. (The only person to have mapped molecular connections to a morphological dendrogram is myself, with disconcerting results.) What sustains this is the continued belief contrary to fact that ancestral species no longer exist. "Proof" is that cladograms have all species being terminal, ergo .... Proof is also that scientific theory consists of made-up stories and narratives that are simply memes sustained by a paternalistic cabal that ignores accepted mathematical demonstration that nothing is certain (Heisenberg), everything is relative (Einstein,) and evolution is random and neutral (Kimura). So pattern cladism is culturally relevant. Genomics and Markov chain analyses are culturally relevant, proof being the abundant funding, many students, and big salaries of Giant Intellects of Phylogenetics. 

I have found that about half of all species I have studied critically are morphologically ancestral to other species. Given the bad resolution of molecular systematics (bad sampling, bad logic, bad postmodern biases), I encourage a positive reexamination of Mayr's "adaptationist program" as a better method of making systematics relevant to the biodiversity crisis.

Note: Ancestral species may have surviving populations with the molecular sequences of each of several descendant species or none. Given extinction, adequate sampling is impossible. The whole idea of assigning a molecular sequence to one name as part of nomenclature is nugatory and laughable.

-------
Richard H. Zander
Missouri Botanical Garden - 4344 Shaw Blvd. - St. Louis - Missouri - 63110 - USA richard.zander at mobot.org Ofc: +1 314 577-0276 Web sites: https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mobot.org%2Fplantscience%2Fbfna%2Fbfnamenu.htm&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cac09f50409fc48bb591408dbae1e2034%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638295216644403741%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=86vIDiDGQzPgTWI1oDRgXsk5%2F1FK%2BtvNL%2BPYseoSj2s%3D&reserved=0 and https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mobot.org%2Fplantscience%2Fresbot%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cac09f50409fc48bb591408dbae1e2034%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638295216644403741%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ba08aNMifA901yBu6EuQTZ%2FpiWOpuTGoGpt2gqpHn5w%3D&reserved=0 

-----Original Message-----
From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Jared Bernard via Taxacom
Sent: Monday, September 04, 2023 5:21 PM
To: Adam Cotton <thaibaggie at gmail.com>
Cc: taxacom at lists.ku.edu
Subject: Re: Taxacom: building such a bridge (between DNA sequence and name) - was Minimalist revision of Mesochorus

Just a quick side note on Adam's comment. Everything he said is correct about fossilization and DNA... however, Mary Schweitzer has pioneered a way of extracting protein from dinosaur fossils, including blood vessels. So, just one step removed from DNA. Just food for thought.

Read more here:
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.smithsonianmag.com%2Fscience-nature%2Fdinosaur-shocker-115306469%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cac09f50409fc48bb591408dbae1e2034%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638295216644403741%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=hG9brSAoL7fCDtbvmGUWKjqVwUx0xNfx%2BC7pBklElEU%3D&reserved=0

And here:
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pone.0020381&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cac09f50409fc48bb591408dbae1e2034%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638295216644403741%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vBpnUvUH6eGoC5k3rGJAOeBGznUhlsrZywiQ9XpwaQ0%3D&reserved=0
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Nurturing nuance while assailing ambiguity and admiring alliteration for about 36 years, 1987-2023.