A recent paper (Treangen, T.J. et al., “Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes,” PLoS Genetics, 7:e1101284, 2011.)
shows that horizontal gene transfer (from one species to another) plays
a much larger role in the evolution of protein families in bacteria
than was previously thought. This link is to a news piece in The Scientist, but you can find the original at PLoS Genetics.
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