Abstract
The emerging fields of microbial population genetics and genomics provide an avenue to study the ecological rules that govern how communities form, function, and evolve. Our struggle to understand the causes and consequences of microbial diversity stems from our inability to define ecologically and evolutionarily meaningful units of diversity. The 16S rRNA-based tools that have been so useful in charting microbial diversity may lack sufficient sensitivity to answer many questions about the ecology and evolution of microbes. Examining genetic diversity with increased resolution is vital to understanding the forces shaping community structure. Population genetic analyses enabled by whole genome sequencing, multilocus sequence analyses, or single-nucleotide polymorphism analyses permit the testing of hypotheses pertaining to the geographic distribution, migration, and habitat preference of specific microbial lineages. Furthermore, these approaches can reveal patterns of gene exchange within and between populations and communities. Tools from microbial population genetics and population genomics can be used to increase the resolution with which we measure microbial diversity, enabling a focus on the scale of genetic diversity at which ecological processes impact evolutionary events. This tighter focus promises to improve our understanding of the causes and consequences of microbial community structure.
Highlights
According to Greek mythology, Proteus knew of all things past, present, and future, but only shared this knowledge if captured
We argue that our comprehension of microbial communities is severely hampered by our inability to recognize ecologically and evolutionarily meaningful units of diversity
Population genetics and population genomics both focus on the evolutionary dynamics of populations
Summary
According to Greek mythology, Proteus knew of all things past, present, and future, but only shared this knowledge if captured. The most common unit of diversity employed in analyses of microbial community structure is the operational taxonomic unit (OTU) based on the 16S rRNA gene. Units of diversity defined by rRNA genes are valuable in terms of discovering and characterizing new lineages, charting the scope of microbial diversity, and resolving evolutionary relationships at temporal scales ranging approximately from 107 to 109 years.
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