EMBL-EBI Press Release
European Molecular Biology Laboratory
European Bioinformatics Institute
For immediate release
Trees, vines and nets – microbial evolution changes its face
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.
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.
Hinxton, July 1, 2005 – 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
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.
Source Article:
V. Kunin, L. Goldovsky, N. Darzentas, and C. A. Ouzounis. The net of life: Reconstructing the microbial phylogenetic network.
Genome Res. 1 July 2005.
Press Contacts:
Cath Brooksbank PhD, EMBL-EBI Scientific Outreach Officer, Hinxton, Cambridge Tel: +44 (0)1223 492525, www.ebi.ac.uk, [email protected]
Trista Dawson, EMBL Press Officer, Heidelberg, Germany, Tel: +49 6221 387 452, www.embl.org, [email protected]
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