http://www.genomenewsnetwork.org/articles/09_00/Buchnera.shtml

"Researchers have mapped the genomic evolution of a bacterium found in aphids. This parasite, called Buchnera, has shared a mutually beneficial relationship with the insect for about 250 million years. Buchnera does not behave like other bacteria because it relies on aphids for functions such as protection and reproduction. In return, the aphid depends on the bacteria to supply necessary proteins it cannot obtain on its own.

A team of researchers led by Hajime Ishikawa of the University of Tokyo's Graduate School of Science sequenced the Buchnera genome and found that it lacks the genes normally found in other bacteria. To find out why these differences have occurred, Ishikawa and his colleagues plotted the evolutionary position of Buchnera among other bacteria with a similar set of genes. Their results indicate that Buchnera fell away from the bacterial lineage of R. prowazekii, leaving Buchnera's closest relatives as E. coli and H. influenzae, with which it shares some genes. The results of this study are published in the current issue of Nature.

Buchnera is a small genome, resulting from years of evolutionary dependence on aphids. According to Ishikawa, "the gene repertoire of the Buchnera genome is so specialized to intracellular life that it cannot survive outside the eukaryotic cell."

"This study is the first case where genomic evolution of a mutualistic organism is revealed at the genomic level, " says Ishikawa in Nature."

From the :

"To evaluate the evolution of the characteristic gene set in Buchnera , we tried to reconstruct the history of Buchnera. First, we determined the evolutionary position of Buchnera among prokaryotes. We made orthologue groups of all ORFs in 23 complete prokaryotic genomes. For each group, we constructed a molecular phylogenetic tree and inferred the most plausible phylogeny of Buchnera and its relatives by searching for the most frequent sub-tree of the same topology that included one or more Buchnera genes or domains. The results indicate that after the speciation of R. prowazekii , Buchnera then diverged from the lineage to E. coli and H. influenzae, although a certain number of trees support the topology in which the closest relative of E. coli is Buchnera. To see whether the Buchnera genome is small because the genome of the last common ancestor (LCA) of Buchnera, E. coli and H. influenzae was as small as that of Buchnera, or because of gene loss in Buchnera after speciation, we inferred the gene set of the LCA. The gene set of Buchnera, excluding a few genes, is a small subset of that of the LCA, and many genes of the LCA were missing in Buchnera, such as those for non-essential amino-acid metabolism. In addition, no Buchnera -specific duplicated gene was found. These results strongly indicate that the small Buchnera genome is the result of reductive evolution."

- So yes, there is proof of evolution in bacterium, in a close relative of E. coli no less. Pick up a journal publication from the last few years and then we can discuss more.

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