Science Literature

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Post details: Tree of Life, Bush of Life or Forest of Life?

12/07/06

Permalinkby David Tyler 12:31:20 pm, Categories: Literature - Articles, 563 words   English (UK)

Tree of Life, Bush of Life or Forest of Life?

Rokas and Carroll have produced a most interesting paper on the results of genome analyses designed to resolve questions about the tree of life (TOL). They draw attention to a prediction made by Richard Dawkins:

“… there is, after all, one true tree of life, the unique pattern of evolutionary branchings that actually happened. It exists. It is in principle knowable. We don't know it all yet. By 2050 we should – or if we do not, we shall have been defeated only at the terminal twigs, by the sheer number of species.”

However, the signs from the expanding research base suggest that this outcome is not likely to be reached. The analyses are producing bushes, not trees. “The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted.”
Examples are given of these bushes. Of great interest to us as humans is the gorilla/chimp/human analysis. Based on 98 genes, the results show that ~55% of genes support a human-chimpanzee clade, 40% are evenly split among the two alternative topologies, eith the remaining genes being uninformative.” The results for this clade and others are not as expectated, and the authers explore different ways of reconciling the data with the TOL model. Homoplasy is identified as a major contributor to this “lack of resolution”. They write: “the observed patterns … give cause for concern that the extent of homoplasy is much greater than expected under widely accepted models of sequence evolution and the attendant consequences for the limits to phylogenetic resolution are not sufficiently appreciated.” They conclude by submitting that Dawkins’ prediction will be fulfilled if we end up with “an arborescent bush of life”.
The situation then becomes remarkably similar to the problems of convergent evolution in palaeontology: how do we know what are primitive and what are derived characters? How do we avoid a situation where the data are interpreted through a TOL filter? As is so often the case in evolutionary theory, the empirical evidence does not confirm the theory, but the theory is used to bring “integration” to the data.
What if there is not a TOL, how could we ever know it using contemporary evolutionary theories? What we need are either theoretical approaches that do not presume the outcomes (i.e. presumption as illustrated by the Dawkins’ quote) or the adoption of multiple hypotheses to allow testing of alternative scenarios. In the interests of healthy science, alternatives to common ancestry should be welcomed by the research community.

Bushes in the tree of life
Rokas, A. and Carroll, S.B.
PLoS Biology, 2006, 4(11): e352, 1899-1904

First para: Genome analyses are delivering unprecedented amounts of data from an abundance of organisms, raising expectations that in the near future, resolving the tree of life (TOL) will simply be a matter of data collection. However, recent analyses of some key clades in life's history have produced bushes and not resolved trees. The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted. Here we examine how the combination of the spacing of cladogenetic events and the high frequency of independently evolved characters (homoplasy) limit the resolution of ancient divergences. Because some histories may not be resolvable by even vast increases in amounts of conventional data, the identification of new molecular characters will be crucial to future progress.

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