April 30, 2005 | David F. Coppedge

Is a Darwinian Tree Visible in the Genes?

Current Biology1 has an article on the status of searching for Darwin’s “tree of life” via comparative genomics.  The expected simple picture has become complex and difficult to decipher:

The traditional view of animal evolution is one of gradually increasing complexity.  The earliest-branching flatworms lack the body cavity known as a coelom, which is a characteristic feature of the two traditional groups of ‘higher’ animals: deuterostomes, including echinoderms and chordates, and protostomes, such as annelids, molluscs and arthropods.  Between these two extremes, according to the traditional view, lie the pseudoceolomate worms such as the nematodes, the body cavities of which lack the refinements of a true coelom.  This hierarchical view was shaken in the mid 1990s by a phylogenetic study of small subunit ribosomal (r)RNA genes.  This work elevated the acoelomate flatworms to a close relationship with the coelomate annelids and molluscs, in a group called the Lophotrochozoa, and pseudocoelomate nematodes moved close to the coelomate arthropods, creating a group called the Ecdysozoa.
    Opposing the ‘new animal phylogeny’, as this new scheme has been called, are several analyses of huge numbers of genes – close to 800 in the most recent – sampled from the few animals with completely sequenced genomes: fruitfly, nematode and various vertebrates.  These multigene analyses are unanimous in grouping coelomate arthropods and vertebrates to the exclusion of the pseudocoelomate nematodes, so reverting to traditional views of their relationships.
    The overwhelming number of genes supporting the old scheme might suggest that the new animal phylogeny was finished – an artefact of a small data set.  New work, however, suggests this conclusion is premature, and that the multigene result might itself be based on an artefact called long branch attraction.
  (Emphasis added in all quotes.)

Long branch attraction is a “pernicious effect” they say.  When “some species in a phylogenetic analysis have evolved much faster than others,” it makes them long branch species and confuses the tree.  What is the net effect?  “The result of this relatively common phenomenon is a tendency for all methods of tree reconstruction to group the long-branch species together regardless of their true relationship.”
    They provide examples of how the choice of “outgroup” (the distant species) and the tree-building method can produce radically different or counterintuitive results.  For example,

In common with previous studies Philippe et al. found that, using yeast as an outgroup, nematodes are located at the base of the tree with high statistical support.  The flatworms are long branched too, and they are also found at the base of the tree.  The change when short-branched Hydra is used instead of yeast is dramatic: both nematodes and flatworms jump up from the root of the tree to a position adjacent to the arthropods, strongly suggesting it was long branch attraction that placed them at the base.
    But this result is troubling, as there is now an unexpected close association between nematodes – which, as presumed ecdysozoans are appropriately close to the arthropods – and flatworms which, according to the new animal phylogeny ought to be grouped with annelids and molluscs in the Lophotrochozoa.

The authors describe efforts to counteract the effects of long branch attraction, some of which appear hopeful.  But much more data will need to be analyzed before any conclusions can be drawn.  Of the 28 animal phyla to be placed in the tree, only eight so far have genetic sequences available for analysis.

1Maximilian J. Telford, and Richard R. Copley, “Animal Phylogeny: Fatal Attraction,” Current Biology, Volume 15, Issue 8, 26 April 2005, Pages R296-R299, doi:10.1016/j.cub.2005.04.001.

What if the pieces of this huge puzzle don’t fit the picture Darwin drew on the box?  The very term “long branch attraction” comes from evolutionary assumptions.  When the organism should be on a certain branch in their a priori evolutionary mindset but the software puts it farther up, they can just assume it “evolved much faster” than its relatives.  But what if it did not evolve significantly at all?  What if animals are not related by common descent from a single cell?  It could be a complete exercise in futility.
    Science needs freedom to explore many possible avenues, some of which may become dead ends.  At what point do they give up and go the other direction?  What if complete representative genomes from all 28 animal phyla still don’t match expectations and produce “troubling” results for Charlie?  If a driver cannot read the dead-end sign, he might drive the wrong way forever.  Evolutionists know how to translate any warning sign into Darwinese.  It allows them to ignore No Trespassing signs and wander endlessly in storyland.
    This article illustrates how phylogenomics is like a perpetual metaphysical research programme.  Every parameter is tweakable except the notion of Darwinian common ancestry.  Notice the evolutionary assumptions embedded in their phrase, “a tendency for all methods of tree reconstruction to group the long-branch species together regardless of their true relationship.”  Phylogeny is the art of forcing uncooperative data into the “true relationship” received from Pope Charlie’s scriptures (see 02/13/2004 commentary).  And you thought only religious people operated under dogma.

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