[Paleopsych] SW: On the Great Chain of Being

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Evolution: On the Great Chain of Being
Subject: EVOLUTION: ON THE GREAT CHAIN OF BEING
http://scienceweek.com/2005/sw050624-3.htm

    The following points are made by Sean Nee (Nature 2005 435:429):
    1) For centuries the "great chain of being" held a central place in
    Western thought. This view saw the Universe as ordered in a linear
    sequence starting from the inanimate world of rocks. Plants came next,
    then animals, men, angels and, finally, God. It was very detailed
    with, for example, a ranking of human races; humans themselves ranked
    above apes above reptiles above amphibians above fish. This view even
    predicted a world of invisible life in between the inanimate and the
    visible, living world, long before Antonie van Leeuwenhoek's
    discoveries. Although advocates of evolution may have stripped it of
    its supernatural summit, this view is with us still.
    2) Common presentations of evolution mirror the great chain by viewing
    the process as progressive. For example, in their book THE MAJOR
    TRANSITIONS IN EVOLUTION, John Maynard Smith and Eors Szathmáry take
    us from the origin of life, through to the origin of eukaryotic cells,
    multicellularity, human societies and, finally, of language. They
    explicitly point out that evolution does not necessarily lead to
    progress, and even refer to the great chain by its Latin name, scala
    naturae. But it is impossible to overlook the fact that the "major"
    evolutionary transitions lead inexorably, step by step, to us.
    Similarly, in their recent essay in Nature, "Climbing the co-evolution
    ladder" (Nature 431, 913:2004), Lenton and colleagues illustrate their
    summary of life-environment interactions through the ages with a
    ladder whose rungs progress through microbes, plants, and, at the top,
    large animals.
    3) In his recent book THE ANCESTOR'S TALE, Richard Dawkins reverses
    the usual temporal perspective and looks progressively further back in
    time to find our ancestors. Like Maynard Smith and Szathmáry, he
    cautions us against thinking that evolution is progressive,
    culminating with us. He emphasizes that with whatever organism we
    begin the pilgrimage back through time, we all are reunited at the
    origin of life. But by beginning the journey with us and looking
    backwards along our ancestry, Dawkins generates a sequence of chapter
    titles that would read like a typical chain to a medieval theologian,
    albeit with some novelties and the startling omission of God.
    4) By starting with us, Dawkins regenerates the chain because species
    that are more closely related to us are more similar as well, and such
    similarity was an important criterion in determining the rankings in
    the classical chain. But there is nothing about the world that compels
    us to think about it in this way, suggesting, instead, that we have
    some deep psychological need to see ourselves as the culmination of
    creation. Illustrating this, when we represent the relationships
    between species, including ourselves, in a family tree, we
    automatically construct it so that the column of species' names forms
    a chain with us as the top, as in the first of the trees pictured. But
    the other construction is equally valid.
    References:
    1. Lovejoy, A. O. The Great Chain of Being (Harper and Row, New York,
    1965)
    2. Gee, H. Nature 420, 611 (2002)
    3. Maynard Smith, J. & Szathmáry, E. The Major Transitions of
    Evolution (W. H. Freeman & Co., Oxford, 1995)
    4. Dawkins, R. The Ancestor's Tale (Weidenfeld & Nicolson, New York,
    2004)
    5. Nee, S. Nature 429, 804-805 (2004).
    Nature http://www.nature.com/nature
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    Related Material:
    EVOLUTIONARY BIOLOGY: ON THE SCHEME OF ANIMAL PHYLA
    The following points are made by M. Jones and M. Blaxter (Nature 2005
    434:1076):
    1) Despite the comforting certainty of textbooks and 150 years of
    argument, the true relationships of the major groups (phyla) of
    animals remain contentious. In the late 1990s, a series of
    controversial papers used molecular evidence to propose a radical
    rearrangement of animal phyla [1-3]. Subsequently, analyses of
    whole-genome sequences from a few species showed strong, apparently
    conclusive, support for an older view[4-6]. New work [7] now provides
    evidence from expanded data sets that supports the newer evolutionary
    tree, and also shows why whole-genome data sets can lead
    phylogeneticists seriously astray.
    2) Traditional trees group together phyla of bilaterally symmetrical
    animals that possess a body cavity lined with mesodermal tissue, the
    "coelom" (for example, the human pleural cavity), as Coelomata. Those
    without a true coelom are classified as Acoelomata (no coelom) and
    Pseudocoelomata (a body cavity not lined by mesoderm). We call this
    tree the A-P-C hypothesis. Under A-P-C, humans are more closely
    related to the fruitfly Drosophila melanogaster than either is to the
    nematode roundworm Caenorhabditis elegans[5,6].
    3) In contrast, the new trees [1-3,7] suggest that the basic division
    in animals is between the Protostomia and Deuterostomia (a distinction
    based on the origin of the mouth during embryo formation). Humans are
    deuterostomes, but because flies and nematodes are both protostomes
    they are more closely related to each other than either is to humans.
    The Protostomia can be divided into two "superphyla": Ecdysozoa
    (animals that undergo ecdysis or moulting, including flies and
    nematodes) and Lophotrochozoa (animals with a feeding structure called
    the lophophore, including snails and earthworms). We call this tree
    the L-E-D hypothesis. In this new tree, the coelom must have arisen
    more than once, or have been lost from some phyla.
    4) Molecular analyses have been divided in their support for these
    competing hypotheses. Trees built using single genes from many species
    tend to support L-E-D, but analyses using many genes from a few
    complete genomes support A-P-C [5,6]. The number of species
    represented in a phylogenetic study can have two effects on tree
    reconstruction. First, without genomes to represent most animal phyla,
    genome-based trees provide no information on the placement of the
    missing taxonomic groups. Current genome studies do not include any
    members of the Lophotrochozoa. More notably, if a species' genome is
    evolving rapidly, tree reconstruction programs can be misled by a
    phenomenon known as long-branch attraction.
    5) In long-branch attraction, independent but convergent changes
    (homoplasies) on long branches are misconstrued as "shared derived"
    changes, causing artefactual clustering of species with long branches.
    Because these artefacts are systematic, confidence in them grows as
    more data are included, and thus genome-scale analyses are especially
    sensitive to long-branch attraction. Long branches can arise in two
    ways. One is when a distantly related organism is used as an
    "outgroup" to root the tree of the organisms of interest. The other is
    when one organism of interest has a very different, accelerated
    pattern of evolution compared with the rest.
    References (abridged):
    1. Aguinaldo, A. M. A. et al. Nature 387, 489-493 (1997)
    2. Winnepenninckx, B. et al. Mol. Biol. Evol. 12, 1132-1137 (1995)
    3. Adoutte, A., Balavoine, G., Lartillot, N. & de Rosa, R. Trends
    Genet. 15, 104-108 (1999)
    4. Mushegian, A. R., Garey, J. R., Martin, J. & Liu, L. X. Genome Res.
    8, 590-598 (1998)
    5. Blair, J. E., Ikeo, K., Gojobori, T. & Hedges, S. B. BMC Evol.
    Biol. 2, 7 (2002)
    6. Wolf, Y. I., Rogozin, I. B. & Koonin, E. V. Genome Res. 14, 29-36
    (2004)
    7. Philippe, H., Lartillot, N. & Brinkmann, H. Mol. Biol. Evol. 22,
    1246-1253 (2005)
    Nature http://www.nature.com/nature
    --------------------------------
    Related Material:
    EVOLUTION: GENOMES AND THE TREE OF LIFE
    The following points are made by K.A. Crandall and J.E. Buhay (Science
    2004 306:1144):
    1) Although we have not yet counted the total number of species on our
    planet, biologists in the field of systematics are assembling the
    "Tree of Life" (1,2). The Tree of Life aims to define the phylogenetic
    relationships of all organisms on Earth. Driskell et al (3) recently
    proposed a computational method for assembling this phylogenetic tree.
    These investigators probed the phylogenetic potential of ~300,000
    protein sequences sampled from the GenBank and Swiss-Prot genetic
    databases. From these data, they generated "supermatrices" and then
    super-trees.
    2) Supermatrices are extremely large data sets of amino acid or
    nucleotide sequences (columns in the matrix) for many different taxa
    (rows in the matrix). Driskell et al (3) constructed a supermatrix of
    185,000 protein sequences for more than 16,000 green plant taxa and
    one of 120,000 sequences for nearly 7500 metazoan taxa. This compares
    with a typical systematics study of, on a good day, four to six
    partial gene sequences for 100 or so taxa. Thus, the potential data
    enrichment that comes with carefully mining genetic databases is
    large. However, this enrichment comes at a cost. Traditional
    phylogenetic studies sequence the same gene regions for all the taxa
    of interest while minimizing the overall amount of missing data. With
    the database supermatrix method, the data overlap is sparse, resulting
    in many empty cells in the supermatrix, but the total data set is
    massive.
    3) To solve the problem of sparseness, the authors built a
    "super-tree" (4). The supertree approach estimates phylogenies for
    subsets of data with good overlap, then combines these subtree
    estimates into a supertree. Driskell et al (3) took individual gene
    clusters and assembled them into subtrees, and then looked for
    sufficient taxonomic overlap to allow construction of a supertree. For
    example, using 254 genes (2777 sequences and 96,584 sites), the
    authors reduced the green plant supermatrix to 69 taxa from 16,000
    taxa, with an average of 40 genes per taxon and 84% missing sequences!
    This represents one of the largest data sets for phylogeny estimation
    in terms of total nucleotide information; but it is the sparsest in
    terms of the percentage of overlapping data.
    4) Yet even with such sparseness, the authors are still able to
    estimate robust phylogenetic relationships that are congruent with
    those reported using more traditional methods. Computer simulation
    studies (5) recently showed that, contrary to the prevailing view,
    phylogenetic accuracy depends more on having sufficient characters
    (such as amino acids) than on whether data are missing. Clearly,
    building a super-tree allows for an abundance of characters even
    though there are many missing entries in the resulting matrix.
    References (abridged):
    1. M. Pagel, Nature 401, 877 (1999)
    2. A new NSF program funds computational approaches for "assembling
    the Tree of Life" (AToL). Total AToL program funding is $13 million
    for fiscal year 2004. NSF, Assembling the Tree of Life: Program
    Solicitation NSF 04-526 (www.nsf.gov/pubs/2004/nsf04526/nsf04526.pdf)
    3. A. C. Driskell et al., Science 306, 1172 (2004)
    4. M. J. Sanderson et al., Trends Ecol. Evol. 13, 105 (1998)
    5. J. Wiens, Syst. Biol. 52, 528 (2003)
    Science http://www.sciencemag.org