Determination of the phylogenetic relationships among major groups of bacteria more difficult than determining the phylogenetic relationships among major groups of mammals because of frequent horizontal gene transfer.
In addition to being a key factor in the evolution of bacteria that can break down novel compounds like pesticides made by humans, horizontal gene transfer also plays a crucial role in the maintenance, transmission, and evolution of virulence. It is the main mechanism by which antibiotic resistance in bacteria spreads.
The evolution of Archaea and Bacteria involved horizontal gene transfer across the two domains, despite the fact that gene exchange is simpler in closely related organisms. If horizontal gene transfer prevents the reconstruction of phylogenetic relationships in the microbial world, it is debatable.
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