Re: common ancestry

From: Paul Nelson (
Date: Tue Aug 01 2000 - 03:45:20 EDT

  • Next message: David Campbell: "Re: common ancestry"

    David Campbell wrote:

    > Paul's comments have confused a couple of factors.
    > First, the argument that various groups may be
    > polyphyletic does not refute more distant common
    > ancestry; rather, it means that the traditional
    > group includes taxa with separate origins within
    > a larger clade.

    Thanks for the clarification, David. It is only the
    polyphyly of the living state itself (e.g., as argued
    for by Webster and Goodwin 1982, Schwabe 1994,
    or Gordon 1999) that necessarily excludes more
    distant common ancestry.

    David continues, in commenting on my post:

    >> Philippe et al. also draw attention to 'artifacts'
    >> that lead to such 'topological errors' as the portrayal
    >> of Drosophila and Aedes [both insects] as a sister
    >> group of nematodes, which they attribute to the rapid
    >> evolution of both groups...(1996:46)
    >> But today, in the year 2000, the grouping of flies with
    >> worms isn't an artefact (i.e., error) at all. Drosophila
    >> and C. elegans are now thought to be cousins within the
    >> Ecdysozoa. Both animals molt, although by classical
    >> morphological criteria they have precious little else
    >> in common.
    > This misunderstands the problem of the first paper.
    > In that analysis, nematodes and flies are sister taxa,
    > not nematodes and arthropods. In other words, the first
    > analysis came out putting flies and nematodes not just
    > at the same family reunion but as siblings, something that
    > even most molecular biologists realize is highly improbable.

    Actually, Philippe et al. (1994) took Drosophila and Aedes
    as representatives of Insecta, a class within the Arthropoda.
    Thus in their 1994 18S rRNA phylogeny, they give Insecta and
    Nematoda as sister taxa, and argue that this is artifactual,
    because of long-branch attraction (see David's explanation
    of what long-branch attraction is, below).

    But now the clade Ecdysozoa [the molting animals] places
    nematodes and flies together. Thus in 1994 what was an
    artifact is now thought to be well-supported. As Aguinaldo
    et al. (1997:492), the original authors of the Ecdysozoa
    clade, write:

         Given the tremendous interest in the nematode
         Caenorhabditis elegans and the arthropod Drosophila
         melanogaster as model systems, the hypothesis that
         both are closely related has important implications
         for developmental and genomic studies.

    About long-branch attraction. David writes:

    > The quoted discussion [in Paul's post] explains the problem,
    > though in jargon. The basic problem is that DNA has five
    > options-A, G, T, C, or a deletion. Thus, two random strands
    > will have some similarity by chance. Rapidly evolving
    > sequences (which can be detected by various statistical
    > tests) are somewhat randomized. If the number of random
    > similarities outweigh the number of inherited similarities,
    > then the analysis can be misled. This situation is known
    > as long-branch attraction or the Felsenstein zone.

    Any gene sequence, considered by itself, is not phylogenetically
    misleading. DNA and proteins have the patterns they exhibit for
    many reasons, only one of which may be descent with modification
    from a common ancestor. Phylogenetic "errors" and "artifacts"
    thus emerge against the background of a prior evolutionary
    or systematic hypothesis.

    "Long-branch attraction," therefore, arises as a problem only
    after one has assumed some hypothesis of common descent,
    i.e., before the molecular data are analyzed.

    In other words, the "rapid evolution" of a DNA sequence, giving
    rise to a "misleading" similarity, isn't directly observed, but
    emerges as a complex inference only in the context of a given
    phylogeny. Indeed, one typically discovers which genes are
    "rapidly evolving" only comparatively, i.e., against the
    backdrop of some phylogenetic hypothesis.

    I mention this not to hassle David ;-) but to remind folks
    how exceedingly tricky phylogenetic inference is. Is the
    rapid evolution of a DNA sequence a reliable observation?
    Depends on what one is assuming.

    > An additional factor is that molecular biologists are
    > notorious for not knowing anything about organisms or
    > paleontology and sometimes present their latest results
    > as the final word, without considering problems such
    > as long-branch attraction.

    Yup. Thank goodness organisms and fossils didn't go away
    because DNA was discovered.

    Paul Nelson
    Senior Fellow
    The Discovery Institute

    Aguinaldo, A.A. et al., 1997. Evidence for a clade of
       nematodes, arthropods and other mouling animals.
       _Nature_ 387 (29 May):489-493.

    Gordon, M. 1999. The Concept of Monophyly: A
       Speculative Essay. _Biology and Philosophy_

    Philippe, H. et al., 1994. Can the Cambrian Explosion be
       inferred through molecular phylogeny? In Michael
       Akam et al., eds., _The Evolution of Developmental
       Mechanisms_ (Cambridge: The Company of Biologists Ltd.),
       pp. 15-25.

    Schwabe, C. 1994. Theoretical limitations of molecular
       phylogenetics and the evolution of relaxins. _Comp.
       Biochem. Physiol._ 107B:167-177.

    Webster, G. and Goodwin, B. 1982. The origin of
       species: a structuralist approach. _Jl Social Biol
       Struct._ 5:15-47.

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