Small variations in phenotypic characteristics (the length or shape of a bird’s beak or the color of its plumage, the timing of flowering in plants, the level of resistance to disease) have been used as markers to trace evolutionary processes in macroorganisms since Darwin’s Origin of Species (Darwin 1859). Until recently, microbiologists have had difficulty recognizing evolutionary processes in natural microbial populations because phenotypic characters and adaptations unique to certain populations have been virtually impossible to identify at the individual scale. High-resolution molecular techniques, such as multi-locus sequence analysis and environmental genomics, today provide the means to survey...

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