It isn’t often that the Hot Papers in Biology allow one
to focus on science for the pure joy of discovery. Even the most
esoteric investigations of detailed molecular biology usually tend
to be highly cited because of some anticipated medical value. Not
so the paper newly arrived at #7.
Casey Dunn, of Brown University in Rhode Island, and his colleagues
use a broad array of DNA sequencing and computational tools to
confirm a new view of the animal tree of life that contains quite a
few surprises for anyone who learned their zoology more than about
10 years ago. Older biologists, for example, will be familiar with
the group known as coelomates, animals with a fluid-filled body
cavity within the tissue known as mesoderm. The molecular trees
admit of no such thing.
Inferring the "true" structure of the tree of life—assessing
which species are more closely related to one another and which
more distant—has been part of the great project of biology
ever since The Origin of Species. The idea, essentially,
is to use similarities among living species and fossils to deduce
their evolutionary history.
The problems are many. Taxonomists can use shared characteristics,
such as an opposable thumb, to say that chimpanzees, gorillas, and
humans all share an ancestor that itself had an opposable thumb.
Evolution, however, can throw a spanner in the works, as it does in
the case of the panda’s thumb, made famous in an essay of the
same name by Stephen J. Gould.
A member of the ctenophores.
The panda’s "thumb" is not, in fact a true digit like yours
and mine. It is, instead, a modified wrist bone that would never
have fooled any anatomist into treating the giant panda as a great
ape and is, in any case, only a single character. The business of
phylogeny, however, is full of similar little traps that make
building an evolutionary tree on which all can agree
extraordinarily difficult.
One breakthrough was the realization that taxonomists could use
molecules as well as gross anatomy to examine phylogenies. This is
not a new idea—it goes back at least to the pioneering
studies of G.H.F. Nuttall in the early 1900s—and it received
a considerable boost from the work of Vincent Sarich and Allan
Wilson in the 1960s.
What is relatively new is the sheer deluge of molecular data that
taxonomists have to work with. Since the advent of high-speed
sequencing there has been a steady stream of papers re-examining
time-honored anatomically based family trees, especially those
where taxonomists could not agree, and generally trumping anatomy
with molecules. Nevertheless, disagreements remained, particularly
over some of the very early branches of the tree and how some large
groups were related.
Dunn and his colleagues systematically gathered molecular data from
29 different animal species belonging to 21 phyla, including 11
phyla that had not previously been included in studies of this
kind. The sequence data were derived from expressed sequence tags
(ESTs) that are associated with genuine working genes, rather than
random stretches of DNA, and so can be assumed to be reasonably
important. Software then uses the similarities and differences
among sequences to build phylogenetic trees, which confirm many of
the more important ideas about relationships.
For example, in 1997, using evidence from a ribosomal subunit, a
new clade (a clade groups together all taxa derived from a single
ancestor; it is one branch of the tree) called the Ecdysozoa was
proposed, grouping all animals that moult. This grouping, which
joins arthropods, tardigrades, nematodes, and others, was hotly
contested, but the new analysis confirms it is almost certainly a
correct reflection of evolutionary history. Although seemingly very
diverse, all those animals do in fact share a common ancestor.
The analysis also confirms another clade that at first glance seems
very odd. The Lophotrochozoa groups the annelid worms and molluscs
with bryozoans (moss animals) and phoronids (horseshoe worms, one
of the smallest and least well-known animal phyla). It also offers
a clear sub-division of the Lophotrochozoa into three distinct
clades.
In addition to confirming some older new hypotheses with stronger
data, the broad analysis by Dunn and his colleagues comes up with a
couple of new hypotheses that will repay further study. Perhaps the
most interesting is the identification of ctenophores, also known
as comb-jellies, as "the earliest diverging extant multicellular
animals." This gives the lie to a very common belief, that more
recently diverged animals are generally more complex. Ctenophones
are indeed morphologically much more complex than, say, sponges and
jellyfish (which the ctenophores used to be lumped with).
Dunn et al. are careful to say that their conclusion is
provisional, but that if confirmed "it would have major
implications for early animal evolution, indicating either that
sponges have been greatly simplified or that the complex morphology
of ctenophores has arisen independently from that of other
metazoans." In other words, molecular data have much to say, but to
really understand evolutionary history it would be nice to have
some fossils too.
Dr. Jeremy Cherfas is Science Writer at Bioversity
International, Rome, Italy.
Biology Top 10
Papers
Rank
Paper
Citations
This Period
(Nov-Dec 09)
Rank
Last Period
(Sep-Oct 09)
1
K. Takahashi, et al., "Induction of
pluripotent stem cells from adult human fibroblasts by
defined factors,"Cell, 131(5):
861-72, 30 November 2007. [Kyoto U., Japan; CREST,
Kawaguchi, Japan; Gladstone Inst. Cardio. Dis., San
Francisco, CA] *243MG
114
1
2
J.C. Barrett, et al., "Genome-wide
association defines more than 30 distinct
susceptibility loci for Crohn’s
disease,"Nature Genetics, 40(8):
955-62, August 2008. [31 institutions worldwide] *331QF
49
6
3
D. Baek, et al., "The impact of
microRNAs on protein output," 455(7209):
64-71, Nature, 4 September 2008. [Whitehead
Inst., Cambridge, MA; Howard Hughes Med. Inst., MIT,
Cambridge; Harvard Med. Sch., Boston, MA] *343XS
42
10
4
E. Zeggini, et al., "Meta-analysis of
genome-wide association data and large-scale
replication identifies additional susceptibility loci
for type 2 diabetes,"Nature
Genetics, 40(5): 638-45, May 2008. [5 U.S. and
U.K. institutions] *293WS
38
7
5
M. Selbach, et al., "Widespread
changes in protein synthesis induced by
microRNAs,"Nature, 455(7209): 58-63,
4 September 2008. [Max Delbruck Ctr. Molec. Med.,
Berlin, Germany; U. Glasgow, U.K.] *343XS
38
9
6
S.A. Mani, et al., "The
epithelial-mesenchymal transition generates cells with
properties of stem cells,"Cell,
133(4): 704-15, 16 May 2008. [8 U.S. and Swiss
institutions] *301NQ
38
†
7
C.W. Dunn, et al., "Broad phylogenomic
sampling improves resolution of the animal tree of
life,"Nature, 452(7188): 745-9, 10
April 2008. [13 institutions worldwide] *285QY
37
†
8
D.R. Bentley, et al., "Accurate whole
genome sequencing using reversible terminator
chemistry,"Nature, 456(7218): 53-9,
6 November 2008. [7 European and U.S. institutions]
*369DH
34
2
9
M. Nakagawa, et al., "Generation of
induced pluripotent stem cells without Myc from mouse
and human fibroblasts,"Nature
Biotech., 26(1): 101-6, January 2008. [Kyoto U.,
Japan; CREST, Kawaguchi, Japan; Gladstone Inst., San
Francisco, CA] *249IW
33
5
10
M.W. Karaman, et al., "A quantitative
analysis of kinase inhibitor selectivity,"Nature Biotech., 26(1): 127-32, January 2008.
[Ambit Biosciences, San Diego, CA; Tufts U., Boston,
MA] *249IW