[Paleopsych] SW: On the Domains of Life

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Evolutionary Biology: On the Domains of Life
http://scienceweek.com/2005/sw050610-3.htm

    The following points are made by D.A. Walsh and W.F. Doolittle
    (Current Biology 2005 15:R237):
    1) The key molecular player in microbial classification has been the
    RNA component of the small subunit of ribosomes (SSU rRNA, or 16S/18S
    rRNA), which Carl Woese picked in the early 1970s as a convenient and
    reliable "universal molecular chronometer". His goal was nothing less
    than a global Tree of Life, relating all living things, but most
    immediately his purpose was to sort out the prokaryotes. In 1977, he
    and his postdoc George Fox were ready to announce to the world that
    these could be unequivocally divided into two very distinct groups, on
    the basis of SSU rRNA sequence. The first group comprised mostly
    well-studied organisms, such as E coli, cyanobacteria and anthrax,
    which they called "eubacteria". The second was made up of less
    well-known types, such as methanogens and (as they soon discovered)
    extreme halophiles and some thermophilic acidophiles, which they named
    collectively "archaebacteria".
    2) That prokaryotes are diverse was no surprise, but that they could
    be so neatly divided into two, and only two, groups certainly was a
    surprise, and so the division was not widely accepted until other
    characteristics that distinguished the domain Archaea from the domain
    Bacteria (as they are now called) were described. By the early 1980s,
    such traits were known to include: the possession of RNA polymerases
    more like their eukaryotic than their bacterial counterparts in
    subunit composition and sequence; some features of translation shared
    specifically with eukaryotes; insensitivity to most antibacterial
    antibiotics; and unique membrane glycerolipids composed of isoprenols
    ether-linked to glycerol-1-phosphate, those of bacteria and eukaryotes
    being fatty acids ester-linked to glycerol-3-phosphate. Ether-linked
    lipids have, however, now been found in several thermophilic bacteria,
    and fatty acids were recently detected in an archaeon, leaving only
    the stereoisomeric form of the glycerol phosphate backbone as a
    diagnostic tool to differentiate absolutely between archaeal and
    bacterial membranes.
    3) In the early 1970s, only partial sequence information (catalogs of
    oligonucleotides generated by nucleases) could be obtained. Now, of
    course near complete genes are easily PCR-amplified, cloned and
    sequenced. The SSU rRNA database as of February 2005 included more
    than 125,000 entries. These continue to support the division of
    prokaryotes into two domains, each with subdivisions most commonly
    called "phyla". Archaea show so far only two or three major
    constituent groups (perhaps they should be "kingdoms"): the
    Euryarchaeota, the Crenarchaeota and (possibly) the Korarchaeota.
    4) Among Bacteria there are at least 52 phyla; some of these turn out
    to correspond closely to divisions of bacteria recognized in
    pre-molecular sequence days by molecular and cellular phenotype alone,
    such as cyanobacteria and spirochaetes. Some unexpected groupings that
    could not be easily unified by phenotypic similarities include the
    Chloroflexi assemblage and the Proteobacteria subdivisions. Even for
    previously recognized phyla, SSU rRNA sequencing provides the
    advantage of quick identification and the ability to define
    within-phylum phylogenetic relationships down to the level of
    'species' in a uniform way.[1-5]
    References (abridged):
    1. Allers, T. and Mevarech, M. (2005). Archaeal genetics - the third
    way. Nat. Rev. Genet. 6, 58-73
    2. Charlebois, R.L. and Doolittle, W.F. (2004). Computing prokaryotic
    gene ubiquity: rescuing the core from extinction. Genome Res. 14,
    2469-2477
    3. DeLong, E.F. and Pace, N.R. (2001). Environmental diversity of
    bacteria and archaea. Syst. Biol. 50, 470-478
    4. Esser, C., Ahmadinejad, N., Wiegand, C., Rotte, C., Sebastiani, F.,
    et al. (2004). A genome phylogeny for mitochondria among
    alpha-proteobacteria and a predominantly eubacterial ancestry of yeast
    nuclear genes. Mol. Biol. Evol. 21, 1643-1660
    5. Forterre, P., Brochier, C., and Philippe, H. (2002). Evolution of
    the Archaea. Theor. Popul. Biol. 61, 409-422
    Current Biology http://www.current-biology.com
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    Related Material:
    EVOLUTIONARY BIOLOGY: PHYLOGENETIC TREES AND MICROBES
    The following points are made by W. Martin and T. M. Embley (Nature
    2004 431:134):
    1) Charles Darwin (1809-1882) described the evolutionary process in
    terms of trees, with natural variation producing diversity among
    progeny and natural selection shaping that diversity along a series of
    branches over time. But in the microbial world things are different,
    and various schemes have been devised to take both traditional and
    molecular approaches to microbial evolution into account. For example,
    Rivera and Lake(1), based on analysis of whole-genome sequences, call
    for a radical departure from conventional thinking.
    2) Unknown to Darwin, microbes use two mechanisms of natural variation
    that disobey the rules of tree-like evolution: lateral gene transfer
    and endosymbiosis. Lateral gene transfer involves the passage of genes
    among distantly related groups, causing branches in the tree of life
    to exchange bits of their fabric. Endosymbiosis -- one cell living
    within another -- gave rise to the double-membrane-bounded organelles
    of eukaryotic cells: mitochondria (the powerhouses of the cell) and
    chloroplasts. At the endosymbiotic origin of mitochondria, a
    free-living proteobacterium came to reside within an archaebacterially
    related host. This event involved the genetic union of two highly
    divergent cell lineages, causing two deep branches in the tree of life
    to merge outright. To this day, biologists cannot agree on how often
    lateral gene transfer and endosymbiosis have occurred in life's
    history; how significant either is for genome evolution; or how to
    deal with them mathematically in the process of reconstructing
    evolutionary trees. The report by Rivera and Lake(1) bears on all
    three issues: Instead of a tree linking life's three deepest branches
    (eubacteria, archaebacteria and eukaryotes), they uncover a ring.
    3) The ring comes to rest on evolution's sorest spot -- the origin of
    eukaryotes. Biologists fiercely debate the relationships between
    eukaryotes (complex cells that have a nucleus and organelles) and
    prokaryotes (cells that lack both). For a decade, the dominant
    approach has involved another intracellular structure called the
    ribosome, which consists of complexes of RNA and protein, and is
    present in all living organisms. The genes encoding an organism's
    ribosomal RNA (rRNA) are sequenced, and the results compared with
    those for rRNAs from other organisms. The ensuing tree(2) divides life
    into three groups called "domains". The usefulness of rRNA in
    exploring biodiversity within the three domains is unparalleled, but
    the proposal for a natural system of all life based on rRNA alone has
    come increasingly under fire.
    4) Ernst Mayr(3), for example, argued forcefully that the rRNA tree
    errs by showing eukaryotes as sisters to archaebacteria, thereby
    obscuring the obvious natural division between eukaryotes and
    prokaryotes at the level of cell organization. A central concept here
    is that of a tree's "root", which defines its most ancient branch and
    hence the relationships among the deepest-diverging lineages. The
    eukaryote-archaebacteria sister-grouping in the rRNA tree hinges on
    the position of the root. The root was placed on the eubacterial
    branch of the rRNA tree based on phylogenetic studies of genes that
    were duplicated in the common ancestor of all life(2). But the studies
    that advocated this placement of the root on the rRNA tree used, by
    today's standards, overly simple mathematical models and lacked
    rigorous tests for alternative positions(4).
    5) One discrepancy is already apparent in analyses of a key data set
    used to place the root, an ancient pair of related proteins, called
    elongation factors, that are essential for protein synthesis(5).
    Although this data set places the root on the eubacterial branch, it
    also places eukaryotes within the archaebacteria, not as their
    sisters(5). Given the uncertainties of deep phylogenetic trees based
    on single genes(4), a more realistic view is that we still don't know
    where the root on the rRNA tree lies and how its deeper branches
    should be connected.
    References (abridged):
    1. Rivera, M. C. & Lake, J. A. Nature 431, 152-155 (2004)
    2. Woese, C., Kandler, O. & Wheelis, M. L. Proc. Natl Acad. Sci. USA
    87, 4576-4579 (1990)
    3. Mayr, E. Proc. Natl Acad. Sci. USA 95, 9720-9723 (1998)
    4. Penny, D., Hendy, M. D. & Steel, M. A. in Phylogenetic Analysis of
    DNA Sequences (eds Miyamoto, M. M. & Cracraft, J.) 155-183 (Oxford
    Univ. Press, 1991)
    5. Baldauf, S., Palmer, J. D. & Doolittle, W. F. Proc. Natl Acad. Sci.
    USA 93, 7749-7754 (1996)
    Nature http://www.nature.com/nature
    ScienceWeek http://scienceweek.com
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    Related Material:
    EVOLUTIONARY BIOLOGY: ON THE PRIMEVAL KINGDOMS
    Notes by ScienceWeek:
    During most of the past 100 years, the consensus view among biologists
    was that all life on Earth evolved from a universal common ancestor, a
    primitive cellular form that lived approximately 3.5 to 3.8 billion
    years ago. This view capped centuries of detailed classifications of
    living systems, with relationships between organisms deduced and
    revised and revised again as new discoveries were made. Detailed
    analysis of many traits indicated, for example, that primates in the
    human family (hominids) shared a common ancestor with apes, that this
    common ancestor shared an earlier common ancestor with monkeys, and
    that that common ancestor, in turn, shared an even earlier common
    ancestor with primitive primates (prosimians; e.g., lemurs), and so
    on.
    The view was thus of a "tree of life", with discrete branches rising
    ever higher, but with all branches deriving from a single primeval
    trunk. The known organisms that might have comprised the primeval
    trunk and its lowest branches, however, did not provide enough
    organismic information to define detailed relationships, so that
    biologists were left with apparent mysteries concerning radical
    evolutionary innovations between primitive cells and more complex
    cells, between the first biological cells and the appearance of
    multicellular fungi, plants, and animals.
    The following points are made by W. Ford Doolittle (Scientific
    American February 2000):
    1) In the mid-1960s, Zuckerkandl and Pauling proposed a revolutionary
    strategy that might supply the missing information concerning
    evolutionary branching. The essential idea was that instead of
    investigating anatomy and physiology, family trees of living organisms
    should be based on differences in the monomer sequences in selected
    genes or proteins. This approach became known as "molecular
    phylogeny", and its essential basis was that as a result of changes in
    genes caused by mutations, as two species diverge from an ancestor,
    the gene sequences they share will also diverge, and as time passes,
    the genetic divergence will increase. Researchers could thus
    reconstruct the evolutionary past of living species by assessing the
    apparent history of divergence of genes or proteins isolated from
    those species. Protein studies completed in the 1960s and 1970s
    demonstrated the general utility of molecular phylogeny by confirming
    and then extending the already established family trees of
    well-studied groups such as the vertebrates.
    2) A new research development occurred in the late 1970s, when Carl
    Woese proposed that the two-domain view of life that divided living
    organisms into a) bacteria and b) cells with internal membrane-bound
    organelles (eukaryotes) was no longer tenable on the basis of
    molecular analysis. Woese suggested that certain so-called "bacteria"
    formed a distinct third primary group -- the archaea -- and that
    members of this group were as different from other bacteria as
    bacteria were different from eukaryotes. Woese suggested that although
    certain cells without internal membrane-bound organelles (prokaryotes)
    classified as bacteria might look like bacteria, they were genetically
    much different, and their *ribosomal RNA (rRNA) supported an early
    evolutionary divergence.
    3) Once the idea of three rather than two primeval domains was
    accepted by researchers, an important question was which of the two
    structurally primitive groups -- bacteria or archaea --gave rise to
    the first eukaryotes? Because of evidence indicating an apparent
    kinship between the gene expression/protein synthesis machinery of
    archaea and eukaryotes, the consensus was that eukaryotes diverged
    from the archaea.
    4) One important result of research in molecular phylogeny during the
    past 15 years has been the production of strong evidence supporting
    the "endosymbiont hypothesis". In biology, the term "symbiosis" refers
    in general to an intimate and protracted association of individuals of
    different species, and "endosymbiosis" refers to a symbiotic
    association between cells of two or more different species in which a
    smaller cell inhabits a larger host cell. The endosymbiont hypothesis
    in evolutionary biology, now a consensus view, proposes that the
    mitochondria components of eukaryotes, so essential for eukaryote
    metabolism, formed when an early eukaryote engulfed and then retained
    one or more primitive bacteria of a certain type
    (alpha-proteobacteria). Eventually, these bacteria relinquished their
    ability to live on their own and transferred some of their genes to
    the nucleus of the host cell, and these bacteria then evolved into the
    extant mitochondria. In addition, and similarly, the hypothesis
    proposes that some mitochondria-bearing eukaryotes ingested bacteria
    capable of producing oxygen during photosynthesis (cyanobacteria), and
    these resident symbiotic bacteria subsequently evolved into the
    chloroplasts, the present internal structures that drive
    photosynthesis in certain eukaryotes (e.g., in plant cells).
    5) Until very recently, therefore, the consensus view in biology could
    be summarized as follows: The early descendants of the last universal
    common ancestor -- a small prokaryote cell --divided into two
    prokaryotic groups: the bacteria and the archaea. Later, the archaea
    gave rise to the eukaryotes. Subsequently, the eukaryotes gained
    valuable energy-generating organelles --mitochondria and (in the case
    of plants, for example) chloroplasts -- by taking up and retaining
    certain symbiotic bacteria.
    6) Several years ago, however, the consensus view stated above became
    complicated by a large amount of evidence concerning the phenomenon of
    "lateral gene transfer" (horizontal gene transfer). Biologists
    recognize two types of gene transfer from one organism to another:
    vertical and horizontal. Vertical gene transfer occurs between parents
    and offspring, and horizontal gene transfer is the transfer that may
    occur between organisms otherwise. It is in bacteria that horizontal
    gene transfer has been studied most extensively, particularly in the
    last decade. Three types of horizontal gene transfer are known:
    conjugation, transduction, and transformation. Conjugation is a type
    of sexual reproduction exhibited by some bacteria, the process
    involving the exchange of genetic material by means of a tube or
    bridge, the transfer of DNA occurring either in one direction or in
    both directions.
    7) Transduction involves the transfer of genetic material from one
    bacterium to another with the intermediation of a virus. Essentially,
    when the virus infects one bacterium, it often carries away pieces of
    that bacterium's genome, and those pieces, upon the infection of a new
    bacterium, become incorporated into the second bacterial genome.
    Finally, transformation is the process involving the uptake or
    incorporation of DNA fragments (plasmids) by a bacterium, first
    observed in 1944 by Oswald Avery. In this context, the important
    aspect of horizontal gene transfer is that in primitive cells such as
    prokaryotes it is now apparent that horizontal gene transfer readily
    occurs across species. As a consequence of the new evidence, the
    consensus view of the interrelations between the primeval three
    kingdoms has now been seriously destabilized.
    8) In general, the current situation concerning the evolutionary "tree
    of life" is as follows: The conceptual tree-like structure with
    discrete branches is retained at the top of the eukaryote domain, and
    also retained is the idea that eukaryotes obtained mitochondria and
    chloroplasts from bacteria. But the lower parts of the tree are now
    seen to involve an extensive anastomosis of branches -- branches
    joining other branches in a complex network of intersecting links --
    resulting from extensive horizontal gene transfer of single or
    multiple genes, the horizontal gene transfer known to be common in
    unicellular organisms. Thus, the author (Doolittle) suggests that the
    "tree of life" lacks a single organism at its base, and that "the
    three major domains of life probably arose from a population of
    primitive cells that differed in their genes."
    Scientific American http://www.sciam.com