Life on a Young Planet by Andrew H. Knoll Read Free Book Online

requires only one evolutionary change. (We could, of course, eliminate some possibilities if we knew for certain which traits characterized the last common ancestor, but we have no way of determining this.)
    A clever solution to the rooting problem was proposed in 1989. Two research groups headed by Naoyuki Iwabe and Peter Gogarten, respectively, independently recognized that while three sets of organisms cannot be joined into a rooted tree, some of the genes they contain can be. The genes in question share a specific property: they were present in duplicate sets in the last common ancestor. How does this help us? As shown in figure 2.2 , each of the two sister genes present in the last common ancestor diverged as the three domains differentiated. The resulting array of genes can be ordered into a tree. In toto, the tree is unrooted, but it consists of two component branches that can be rooted relative to each other. Both “half trees” have the same form: one branch that contains only bacteria and a second containing Archaea plus eukaryotes.
    This exercise has been repeated numerous times, using dozens of gene families. Many trees yield the root position shown in figure 2.2 , but others suggest different relationships among the three domains. No one tree satisfies all genetic data, forcing a startling conclusion. We think about genes being passed vertically through the tree from ancestor to descendant, but some genes must have been passed horizontally from one branch to another, perhaps by hopping a ride on a virus or by the uptake of DNA from dead cells. Contemporary organisms are, thus, genetic chimeras.

    Figure 2.2. Rooting the Tree of Life. Top: The genealogical relationships among Bacteria (B), Eucarya (E), and Archaea (A) are shown by the hollow cylindrical branches. Lines within the cylinders show the phylogeny of a gene that duplicated into forms A and B prior to the differentiation of the three domains from their last common ancestor. Bottom: The evolutionary relationships among the genes are shown here. Each half tree can be rooted relative to the other, allowing molecular biologists to reconstruct the genealogical relationships among eukaryotes, archaeans, and bacteria.
    This revelation potentially casts doubt on the entire endeavor of constructing phylogenies from gene sequences, because gene trees and organism trees will not coincide when horizontal transfer has occurred. According to some biological Cassandras, the genes of microorganisms have been swapped so often and so promiscuously that no meaningfultree of microbial organisms can be recovered from molecular comparisons. This possibility is both frustrating and tantalizing, but it may be overdrawn. Sorel Fitz-Gibbons of UCLA and Christopher House, now at Penn State, analyzed the distribution of all genes in the dozen or so organisms whose complete genomes had been sequenced by early 1999. The tree recovered by comparing universal gene distributions closely matches that inferred from ribosomal RNA gene sequences, suggesting that despite gene swapping, phylogenetic order underpins the genomes of bacteria and archaeans.
    James Lake and Maria Riviera, also of UCLA, have even hypothesized that certain rules govern the likelihood of horizontal transfer. Informational genes that code for basic features of cell biology appear to be unlikely candidates for lateral exchange—ribosomal RNA genes fall into this category. In contrast, operational genes, genes or groups of genes that encode specific metabolic functions, may be passed from one lineage to another with relative ease by means of viruses or other vectors. For example, we know that bacterial tolerance to heavy metals can be gained by the uptake of particular genes.
    Dawn is just breaking on the study of microbial genes and phylogeny, and as more and more genomes are sequenced in their entirety, new insights can be expected to topple current generalizations. For now, it is reasonable to view the Tree of Life