The Tree of One Percent- review


The article "The tree of one percent" by T. Dagan and W. Martin challenges the traditional view of the tree of life as a single, bifurcating tree. The authors argue that the vast majority of genes in microbial genomes are not universally distributed, but have been transferred between different lineages through lateral gene transfer (LGT). This means that the tree of life as we know it is based on only a small fraction of the genes in microbial genomes, and that the true evolutionary relationships between microbes are much more complex than a simple tree can represent.

The authors support their argument by analyzing the distribution of 5,833 human proteins in prokaryotic genomes. They found that only 31 of these proteins were universally distributed, meaning that they were present in all of the prokaryotic genomes that they analyzed. The remaining 5,797 proteins were either absent from some genomes, or were present in only a subset of genomes. This suggests that the vast majority of human proteins have been acquired through LGT, and that they do not reflect the true evolutionary relationships between microbes.

The authors conclude that the tree of life as we know it is a "tree of one percent". They argue that the traditional view of the tree of life is based on a very small fraction of the genes in microbial genomes, and that the true evolutionary relationships between microbes are much more complex than a simple tree can represent.

The article "The tree of one percent" has been influential in the field of microbial evolution. It has helped to challenge the traditional view of the tree of life, and has led to a new appreciation for the importance of LGT in microbial evolution. The article has also raised important questions about the nature of the tree of life, and the extent to which it can be used to represent the evolutionary relationships between microbes.

Article snippets:


Two significant evolutionary processes are fundamentally not tree-like in nature - lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes.

To incorporate such processes into the bigger picture of early evolution, biologists need to depart from the preconceived notion that all genomes are related by a single bifurcating tree.

Evolutionary biologists like to think in terms of trees.

Since Darwin, biologists have envisaged phylogeny as a tree-like process of lineage splittings

Evolutionary biologists are not debating whether LGT exists. But they are debating - and heatedly so - how much LGT actually goes on in evolution.

Biologists are also hotly debating how LGT should influence our approach to understanding genome evolution on the one hand, and our approach to the natural classification of all living things on the other.

These debates erupt most acutely over the concept of a tree of life

Here we consider how LGT and endosymbiosis bear on contemporary views of microbial evolution, most of which stem from the days before genome sequences were available.

When it comes to the concept of a tree of life, there are currently two main camps. One camp, which we shall call the positivists, says that there is a tree of life, that microbial genomes are, in the main, related by a series of bifurcations, and that when we have sifted out a presumably small amount of annoying chaff (LGT), the wheat (the tree) will be there and will still our hunger for a grand and natural system

The other camp, which we will call the microbialists, says that LGT is just as natural among prokaryotes as is point mutation, and that furthermore, it has occurred throughout microbial history. This means that even were we to agree on a grand natural classification, the process of microbial evolution underlying it would be fundamentally undepictable as a single bifurcating tree, because a substantial component of the evolutionary process - LGT - is not tree-like to begin with

The need to incorporate non-treelike processes into ideas about microbial evolution has long been evident

But mathematicians and bioinformaticians are just now beginning to explore the biological utility of graphs that can recover and represent non-treelike process that sometimes underlie patterns of sequence similarity in molecular data and patterns of shared genes.

These approaches can involve networks, rings, or simply tack inferred gene exchanges onto trees

These newer approaches aim to recover and depict both the tree-like (vertical inheritance through common descent) and the non-treelike (LGT and endosymbiosis) mechanisms of microbial evolution

So, are we close to having a microbial tree of life? Or are we closer to rejecting a single tree as the null hypothesis for the process of microbial genome evolution? All in all, the latter seems more likely, for if our search for the tree of life delivers the tree of one percent, then we should be searching for graphs and theories that fit the data better than a single bifurcating tree.

So, are we close to having a microbial tree of life? Or are we closer to rejecting a single tree as the null hypothesis for the process of microbial genome evolution

All in all, the latter seems more likely, for if our search for the tree of life delivers the tree of one percent, then we should be searching for graphs and theories that fit the data better than a single bifurcating tree.




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