dNdlogD

dNdlogD is a method used in evolutionary biology and population genetics to analyze patterns of genetic variation within and between populations. It specifically focuses on the relationship between the rate of synonymous nucleotide substitution (dN) and the logarithm of the effective population size (logD). The effective population size (D) is a theoretical measure representing the size of an ideal population that would experience the same amount of genetic drift as the actual population.

The dNdlogD framework is employed to investigate how demographic factors, such as population size changes and bottlenecks, might influence the rates at which neutral genetic changes accumulate. By examining the correlation or lack thereof between dN and logD, researchers can infer whether observed patterns of genetic diversity are consistent with neutral evolution or if they might be shaped by selection or other evolutionary forces.

This approach often involves analyzing DNA sequences from multiple individuals within a species or from closely related species. Statistical models are then used to estimate both dN and D, allowing for the quantification of their relationship. Deviations from expected neutral patterns in the dNdlogD relationship can provide clues about the evolutionary history of a population, including past expansions, contractions, or periods of stability. The interpretation of dNdlogD plots can help distinguish between demographic effects and the action of natural selection on genetic variation.