Taxacom: On species diagnoses and DNA-based descriptions in taxonomic practice

Fri Aug 25 21:54:27 CDT 2023

In discussing your first question, we could say that has already happened.
When even the more modern views of species was determined DNA technology
was far off so that is something that is just a part of science. Science
evolves and we have to take on board and adapt to new technology as they
become available. No doubt better methods will come in the future. Even
among DNA this is true. 30 years ago it was fine to sequence a couple of
mtDNA genes, these days that is not good enough. whole mitagenomics and
large combinations of nuDNA genes being a requirement of a good DNA
analysis. Eventually I would guess that a whole nuGenome will be a
requirement of a good analysis.

I do not think in general those finding cryptic species are describing
every new specimen as a species, there is more to it than that as the
boundaries of those taxa are also needed to be understood. Granted there
are differences of opinion on how much is enough and certainly there have
been taxa elevated to species that are honestly more closely related to
their sisters than some humans are to each other. I have even seen that
justified with the statement that humans are different and do not obey
these rules of relatedness. A statement I disagree with, we are just
another species.

One other issue here is that what works for one group does not entirely
work for all groups, the basic principles do but the details get messed up
particularly for example comparing taxa with sexual and asexual
reproduction for example.

With your second question you say a species is a lineage segment, Ok but
what is the nearest relative of each segment, it is actually the preceding
one. This would in all likelihood be a fossil. Our current species, the
terminal ends of their lineages have directly evolved from their ancestors.
The fossil record is not and never will be complete. Not all organisms
fossilise well, some live in environments where fossilisation is likely
impossible or at least very unlikely, for example unless an animal or plant
dies in a depositional environment it is not going to be fossilised. This
also requires the comparison of living and fossil taxa in the same dataset.
Thus ruling out DNA analysis as an option. DNA under very good situations
only survives a few thousand years at best, the handful of older ones were
extraordinary finds and very rare, usually frozen animals. Remember fossils
are not the extinct animal they are a stone cast of it. There is no DNA.
Therefore we have to use the group of near lineages, if you want to use DNA
they will all be from living taxa and hence not generally on the same
lineage. However the DNA analysis if using good practice should include all
the lineages available that are relevant to the taxon in question.

There is also a proof situation here, yeah I mean a mathematical proof. The
way phylogenetics works is to separate taxa into lineages based on
assumptions that the closer two taxa are the more they will have in common.
Across enough characters it will generally separate the lineages. A new
species is generally a lineage that does not align with a currently
described one. An algorithm is used to do this with statistical support on
the results. In the absence of having every living and fossil taxon of a
lineage that's the best we can do. Now yes a criticism of DNA analysis is
they find too many cryptic species, what I ask them is this a phylogeny or
a pedigree. Used carelessly DNA can find lineages that are not species
level, for the same reason Ancestry.com can tell you where your family tree
originated. Careless use of DNA splits taxa into localised distributions,
migration routes, river systems etc, instead of species. How different the
new taxa is an important factor. One reason I always favor the inclusion of
morphology as well as DNA is that with morphology you can see the selection
pressure on a character, you cannot in DNA and it's assumed to be
pseudo-random.

Hope that begins to answer you.

Cheers Scott

On Fri, Aug 25, 2023 at 10:16 PM Thomas McCabe via Taxacom <
taxacom at lists.ku.edu> wrote:

> Hello. I am a physician biologist with an interest in biological taxonomy
> and the discussions at Taxacom. May I add a comment and questions about the
> journal article referenced by Thomas Pape ("Tightening the requirements for
> species diagnoses would help integrate DNA-based descriptions in taxonomic
> practice", *PLoS* Biol 21(8): e3002251)? The authors of this paper go
> beyond nomenclature to advocate for taxonomic species diagnoses that are
> both contrastive and state-specific. The authors also attend to the
> interesting possibility and problems of defining species solely with
> genome-wide DNA sequences.
>
> Regarding defining species, I request thoughts on two questions, the first
> skeptical, the second leading.
>
> First, a question about using a genome-wide DNA sequence as sole diagnosis
> for a taxonomic species. Suppose technology advances so that a description
> of the complete sequence of all the nucleic acid macromolecules making up
> the genetic complement of each potential specimen supposedly representing a
> newly-discovered taxonomic species is attainable. Then, if each living
> being has a unique genetic complement (at least one single nucleotide
> polymorphism or indel making one of its DNA sequences unique among those of
> other living beings), what will prevent a seeker of cryptic species from
> using every specimen as a type for a separate taxonomic species?
>
> Second, and related to the first question, if each natural species is a
> lineage-segment, why is each taxonomic species diagnosis drawn from one or
> more unrelated specimens instead of from a directly observed
> lineage-segment of specimens? That is, cannot biological taxonomy be an
> experimental, as well as a descriptive, science?
>
> Respectfully,
>
> Thomas McCabe, M.D., M.P.H.
>
> Independent Scholar
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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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