Phylogenomics makes use of "large quantities of genetic data (not just entire genomes) to build evolutionary trees, or phylogenies." The new discipline makes great claims, for it aims to "reshape systematics" using the extensive data sets emerging from genome mapping projects. One researcher explains its scope: "Genomes are giving a much better view of the tree of life on Earth" and "The revolution is just starting - every new genome is causing rethinking."
It may surprise some, but Linnaeus did not pioneer systematics with the tree of life in mind. It is not necessary to presuppose a common ancestor for all living things to be a scholar working in this field.
More importantly, waving "the banner of phylogenetics" must not be confused with delivering results. Because some say the revolution is just starting, this does not mean that they are right. "What has also become clear is that many problems cannot simply be battered into submission with more data."
To illustrate one problem: "Perhaps the most high-profile gaffe was the declaration by the Human Genome Project in 2001 that 100-200 genes in humans had come directly from bacteria." Lateral gene transfer (LGT) was invoked to explain the data. It was challenged by several "flabbergasted evolutionary biologists, [who] rapidly shot the claim down, showing that the genes in question were more likely to have been present in the common ancestor of humans and bacteria but then lost in other lineages."
What is surprising is that there has not been a similar response to the new explanation: for it implies that the relevant genes were present in the evolutionary descendants and were systematically lost in every branch and twig of the tree of life except for that leading to humans. This explanation is as contrived as LGT!
According to one expert quoted: "you can't do good genome analysis without evolutionary analysis." Linnaeus would not have agreed with this. He would have warned of the dangers of force-fitting the data into a predetermined mould. If you presuppose the tree of life, how could researchers ever conclude that they were studying a forest, not a tree?
Linnaeus at 300: We are family
Nature 446, 247-249, (15 March 2007) | doi:10.1038/446247a
Updating the tree of life needs both the skills of evolutionary biologists and the data from genome-crunchers - the two ignore each other at their peril.
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