Taxacom: On describing new taxa without using phylogenetics: some suggestions

[Lücking, Robert]

Dear Kirk,

phylogenetics is not a philosophical exercise, but evidence-based science. Once you identify phenotypic homoplasies based on molecular trees, they often make sense. Homoplasy is not ad hoc, on the contrary. Traditional classifications are based on ad hoc "homology" and homoplasy is shown a posteriori by testing such classifications. There is a simple exercise that shows DNA sequence data are substantially less homoplasious than phenotype data. Take any such dataset and subsample it randomly, then construct the most parsimonous or most likely tree/classification. The trees based on subsampled phenotype data are usually more conflictive than those based on sequence data. This is well-known as the classical conundrum of traditional taxonomy: each worker considers a different character more important.

Going back to the humans vs. orang-utan vs. chimp problem: what about when one uses behaviour as classification criterion? If you compare behaviour vs. morphology/anatomy, then you obtain a conflict, as each set of characters results in a different classification. There is no objective way to sort this out, other than using an unrelated set of characters, DNA sequence data. These tell us that behaviour is a better predictor of relationships in this case than morphology/anatomy.

When it comes to DNA data, one has to understand what we are looking at. Unless we do phylogenomics, we are not usually looking at DNA that codes for phenotype (which anyway is also influenced by epigenetics etc.). The classical markers all code for universal cell functions, such as ribosomes, DNA polymerases etc. This is why we can compare across a broad range of organisms but this also makes sure that we avoid potential causal correlations when looking at supposedly independent sets of characters. For instance, the mitochondrial genome exclusively codes for basic functions in the primary metabolism and has nothing to do with a specific phenotype. It therefore reflects true (maternal) relationships with higher confidence than any set of phenotype characters could.

I often see people questioning the power of molecular data only partially. For instance, in a given tree, 90% of the topology may agree with one's viewpoints, and 10% may disagree. It makes little sense in such a case to question the underlying data only in part. Rather, it suggests that one's viewpoints on these 10% may be wrong. Which does not mean phenotype data are useless, on the contrary: one just has to interpret them differently.

Regards
Robert






Von: Kirk Fitzhugh <kfitzhugh at nhm.org>
Gesendet: Mittwoch, 8. Oktober 2025 21:18
An: Marko Mutanen <Marko.Mutanen at oulu.fi>
Cc: Lücking, Robert <R.Luecking at bo.berlin>; John Grehan <calabar.john at gmail.com>; Kuoi Zhang <zhang.guo-yi at outlook.com>; taxacom at lists.ku.edu
Betreff: Re: Taxacom: On describing new taxa without using phylogenetics: some suggestions

Marko Mutanen,

Given that our intent with phylogenetic inferences is to causally account for observed homologous characters, and this occurs via the non-deductive form of reasoning known as abduction, there are no logical arguments supporting the view that sequence data has some priority over other classes of characters. Homoplasy is an ad hoc hypothesis that is the product of inferring hypotheses, so it can't be used as an excuse to exclude morphological characters (indeed, one can just as easily argue that sequence data are just as prone to lead to hypotheses of homoplasy). The only rational approach to abductively inferring phylogenetic hypotheses is to abide by the requirement of total evidence (sensu Carnap 1950) and consider all relevant observed characters.

Kirk Fitzhugh

On Wed, Oct 8, 2025 at 12:02 PM Marko Mutanen via Taxacom <taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>> wrote:
Dear Robert, all, I agree with you. Morphological evolution is indeed fascinating, but it should be studied in the context of DNA-based phylogenies rather than by continuing to infer evolutionary relationships solely from morphology, which is

Dear Robert, all,



I agree with you. Morphological evolution is indeed fascinating, but it should be studied in the context of DNA-based phylogenies rather than by continuing to infer evolutionary relationships solely from morphology, which is highly prone to homoplasy. Of course, when dealing with fossils, we must still rely on morphological data, but this inevitably introduces substantial uncertainty into the taxonomy of extinct taxa - likely persisting indefinitely.



Sincerely,



Marko M.