Taxacom: Evolution, systematics, and the unnatural history of mitochondrial DNA

[John Grehan]

For anyone interested in issues with molecular systematics, I can provide a
copy of "Evolution, systematics, and the unnatural history of mitochondrial
DNA" (2021). It includes quite an extensive historical overview as well as
description of some of the circular reasoning involved and other problems.

A few excerpts below. Any disagreement, don't argue with me as I have no
molecular expertise, but happy to pass on any such.

Ferris et al. could embrace a recent divergence of humans and apes, which
permitted using mtDNA to sort their relationships.

However, when one invokes explanations to reject alternative theories of
relatedness, one is not generating but defending one’s preferred theory of
relatedness.

869 bp segment of mtDNA generated a number of alternative theories of
relatedness

But of greater theoretical and systematical concern is Ruvolo et al.’s
conflating gene with species trees, even while acknowledging
their difference.

And this could lead to interpreting molecular similarity as synapomorphy,
and difference as primitive retention or no change, even though the reverse
was true

molecular similarity/difference are not synonymous, the question is: How,
without referring to morphology, can one test molecularly-based hypotheses
that supposedly represent relatedness? For while protein and DNA sequences
are real, they do not reflect the developmental history of the
molecule-morphology continuum that produces an organism: that is, the
history of RNA polymerase and transcription factors exploiting nDNA in a
highly-organized hierarchy of signaling pathways, alternative intron
splicing, and gene
regulation

First, Ruvolo states (Ruvolo 1997, p. 249, 250) she is generating gene
trees. Second, she tests only relationships between humans, Pan, and
Gorilla. And third, she rejects any ‘tree’ that does not yield ‘expected’
relationships

All four hypotheses are alike in assuming that the rest of the tree shows
the traditionally accepted primate evolutionary relationships, which are
supported by extensive genetic data: Pongo is the sister to the clade
containing Gorilla, Homo, Pan; the small-bodied hominoids in Hylobates
[gibbons, siamangs] are sister to all other hominoids; all Old World
monkeys…comprise a clade sister to the hominoid clade; and the clade of New
World monkeys is sister to the cercopithecoid plus hominoid clade.


By assuming any phylogeny not conforming to expectation is ‘wrong’, she
rejected 18 trees presenting other patterns of relationship and the
molecular similarities supporting them.

Aside from the circularity of the argument – using assumptions of molecular
processes to divine molecular processes – a historical irony is that, first
Nuttall (Nuttall 1904), and subsequently Zuckerkandl and Pauling
(Zuckerkandl and
Pauling 1962), from their study of hemoglobin-anti-hemoglobin reactivity,
concluded that molecular similarity/dissimilarity reflected evolutionary
propinquity because the pattern of relatedness they achieved mirrored that
based on morphology
(

Consequently, from a philosophical perspective, when molecule- and
morphology-based phylogenies conflict, the latter should serve to test the
former, especially considering the possible disconnect between gene and
species trees.

given the universality of a developmental molecular-morphological continuum
(plants included), it is not the DNA sequence, but the chronology of RNA
polymerase and transcription factor exploitation of these sequences that
should be the source of comparison in phylogenetic  reconstruction.

Yet, Caccone and Powell (Caccone and Powell 1989) did admit: Virtually all
molecular phylogenetic studies… have a major underlying assumption: the
genetic similarity or difference among taxa is an indication of
phylogenetic relatedness.

Details: like Ruvolo, they ‘first eliminate[d] uninformative nucleotide
positions (nonvariable positions and those variable positions that would
have the same number of mutations regardless of the branching order of the
tree)’

Further, shared similarity can be achieved in different ways: (1) change,
or (2) no change. In other words, human–Neanderthal similarities could be
due, as interpreted, to change from a chimpanzee sequence, or they could be
similar because they did not change and the chimpanzee did. Objectively, in
the absence of a broader comparative sample, or information other than
preference, one can’t choose between them.

Reich et al. reject the phylogenetic relevance of morphology – except when
the fossil record serves their needs.

heteroplasmy invalidates characterizing and, thus, ‘barcoding’, a species
with a single mtDNA sequence

Nevertheless, no matter how sophisticated the technology, the results and
their interpretation are no better or more ‘correct’ than their underlying
assumptions.

-- 
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