First, simulations of bottlenecks of variable sizes and ages, resulting in the same amounts of genetic diversity as observed in current populations, cannot produce statistics (Tajima's D, Fu and Li's F*) as high as those observed on real data for C. guianensis, unless moderate to strong and recent bottlenecks are assumed.
The effect of such bottlenecks depends upon the effective size of the ancestral population, its initial variation, the duration of the bottleneck, and the nature of the marker under study.
Villages are of variable size.
The variable sizes of the loops accommodate variable numbers and sizes of genes.
The relatively modest decline in genetic diversity observed in this study (5 10%), with a more variable size across generations, suggests the absence of important bottlenecks events during the evolution of our laboratory populations.
In situations where the timing of coalescence is more certain, for example, shortly after a bottleneck of size 1 (a "strict" bottleneck), a pure Poisson approximation (Equation 5) may be more appropriate.
To evaluate the effect of a variable population size on the performance of the method, simulations were repeated with a more limited set of parameters (σ0∈{0.025, 0.05}, U∈{5×10−8, 1×10−7, 2×10−7}) for a population with initial size 10, which repeatedly doubled in size each generation for eight generations before undergoing a bottleneck at ratio 1 256.
The absolute magnitude of the copy number bottleneck is not critical: a range of bottleneck sizes can give rise to observed dynamics.
Co-author Heidi Parker, a geneticist at NHGRI, says that because humans initially bred dogs for specific traits—say, smaller body size or calm temperament selection created a population "bottleneck" that narrowed the genetic variation in offspring, leaving them with just a few specific clusters of variable genetic regions.
Although one could argue that the genetic diversity differences could be attributed to variable bottleneck size, an MOI of 0.01 in these studies still requires approximately 1 million WNV particles.
With respect to non-African populations, we tested for the occurrence of bottlenecks of varying intensities (βOoA, being the ratio between the population sizes before and after the bottleneck event), including the constant size model (βOoA = 1) (Figure 3C).
