[Paleopsych] SW: On the Scheme of Animal Phyla
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Evolutionary Biology: On the Scheme of Animal Phyla
http://scienceweek.com/2005/sw050603-3.htm
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
--------------------------------
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
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