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| Hinxton,
Friday1 July 2005 |
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Trees, vines and nets Microbial evolution changes its face |
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![A bird's-eye view of the tree of life, showing the vines in red and the tree's branches in grey [Bacteria] and green [Archaea]. The last universal common ancestor is shown as a yellow sphere.](../../../../../images/press/press05/press1jul05spic.jpg) |
| A bird's-eye view of the tree of life, showing the vines in red and the tree's branches in grey [Bacteria] and green [Archaea]. The last universal common ancestor is shown as a yellow sphere. |
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Press
Release 1 July 2005 [PDF]
EBI researchers have changed our view of 4 billion
years of microbial evolution. Christos Ouzounis
and colleagues have gained intriguing quantitative
insights into how gene families are transferred,
not only 'vertically' through passage from one organism
to its progeny, but also 'horizontally' through
the exchange of genetic material between distantly
related organisms. This new view of the tree of
life could help us to better understand how disease-causing
bacteria manage to stay one step ahead of us in
our battle to tackle antibiotic resistance.
Since
the time of Darwin, the evolutionary relationships
between organisms have been represented as a tree,
with the common ancestors at the base of the trunk
and the most recently evolved species at the tips
of the branches. Microbiologists have argued for
a long time that this representation doesn't really
hold true for microbes, which often exchange genes
among different species. Their claim has been that
the evolution of these organisms is better represented
by a net. Unfortunately, no-one knew exactly where
to draw the horizontal lines in this net.
Victor Kunin, previously a PhD student in Christos
Ouzounis's group, and their colleagues have now
constructed a map of microbial evolution, going
back billions of years to the last universal common
ancestor, that includes these horizontal lines.
"Reassuringly, evolutionary trees constructed
by many independent methods and different research
groups are remarkably consistent with each other,
projecting the same story. We used these trees as
the scaffold of the net, on which we looked for
the evidence of horizontally transferred genes,"
explains Victor.
To get a grip on horizontal gene transfer, they
used a method called GeneTrace, previously developed
by Victor and Christos. GeneTrace infers horizontal
transfer from the patchy presence of a gene family
in distantly related organisms. The data generated
by GeneTrace allowed them to draw 'vines', representing
horizontal-genetransfer events, connecting branches
on the evolutionary tree. In all, more than 600,000
vertical transfers are observed, coupled with 90,000
gene loss events and approximately 40,000 horizontal
gene transfers. Thus, although the distribution
of most of the gene families present today can be
explained by the classical theory of evolution by
descent, anomalies of these patterns are revealed
by the 'minority report' of horizontal exchange.
To understand the influence of horizontal gene transfer
on the microbial tree of life, they focused on the
network of vines coursing through the tree's branches.
This behaves in a 'scale-free' manner, a term used
to describe networks that have an uneven distribution
of connectivity and a small number of hubs that
are far more connected than other nodes.
One property of scale-free networks is their 'small-world'
nature: travelling from one node to any other is
very fast. [Other small-world networks include social
networks, the internet and air-travel connections.]
These characteristics allow the hubs to serve as
bacterial 'gene banks', providing a medium to acquire
and redistribute genes in microbial communities.
"This has important implications for our understanding
of horizontal gene transfer because, in small-world
networks, the shortest path between any two network
nodes is relatively small: in other words, a gene
can rapidly be disseminated from organism to organism
through very few horizontal gene transfer events,"
explains Christos Ouzounis. A few species, including
beneficial nitrogen-fixing soil bacteria, appear
to be 'champions'of horizontal gene transfer; "it's
entirely possible that apparently harmless organisms
are quietly spreading antibiotic resistance under
our feet," concludes Christos Ouzounis. A bird's-eye
view of the tree of life, showing the vines in red
and the tree's branches in grey [Bacteria] and green
[Archaea]. The last universal common ancestor is
shown as a yellow sphere.
Source article
The net of life: Reconstructing the microbial phylogenetic
network
V. Kunin, L. Goldovsky, N. Darzentas, and C. A. Ouzounis
Genome Res. 1 July 2005.
Press Contacts
Cath Brooksbank PhD
EMBL-EBI Scientific Outreach Officer Wellcome Trust
Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Tel: +44 [0]1223 492525,
E-mail: cath@ebi.ac.uk
Trista Dawson
EMBL Press Officer, European Molecular Biology Laboratory,
Meyerhofstrasse 1, 69117 Heidelberg, Germany
Tel: +49 [0] 6221 3878452
E-mail: trista.dawson@embl.de |
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