Chapter 3, “Quantifying genetic variation at the molecular level,” introduces quantitative methods for measuring variation directly in DNA sequences to help decipher fundamental properties of populations and what they can tell us about evolution. It provides an overview of the evolutionary factors that contribute to genetic variation, like mutational input, effective population size, genetic drift, migration rate, and models of migration. This chapter surveys the principal ways to measure and summarize polymorphisms within a single population and across multiple populations of a species, including heterozygosity, nucleotide polymorphism estimators of θ, the site frequency spectrum, and F
ST, and by providing illustrative natural examples. Populations are where evolution starts, after mutations arise as the spark of population genetic variation, and Chapter 3 describes how to quantify the variation to connect observations to predictions about how much polymorphism there ought to be under different circumstances.
Long-Term Experimental Evolution in Escherichia coli. VI. Environmental Constraints on Adaptation and Divergence