This creates a drastic bottleneck equivalent to the effect of an instantaneous selective sweep.
We show that even weak levels of heterochrony (∼10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism θ, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck).
For most relevant sets of parameter values compatible with most classical aDNA analyses, i.e., limited time lapse with respect to the root of an intraspecific tree, heterochrony leads to a shift toward star-like trees, revealed by negative frequency statistics and a deficit of association between mutations, thus mimicking population expansion possibly following a drastic bottleneck (Fig. 6A).
Human migrations introduced a drastic bottleneck in the diffusion of these triploids, with only some suckers of the same clonal origin being exported and then spread.
According to the present study, the most drastic bottleneck underwent by the wild Atlantic salmon occurred hundreds of generations ago and was followed by another decrease these last decades in France, which favors the second hypothesis.
The usual targets of breeding programs are domesticated species that have been exposed to drastic bottleneck effect during domestication (probably even before domestication, see [ 46]) and can therefore be evolutionarily plastic.
In an attempt to reconstruct past demographic histories based on phylogenetic inferences, the tree in Fig. 1 suggests that a drastic bottleneck occurred during the Late Eurasian Saalian glacial (~130 160 ka ago) [ 36– 39], which is compatible with the age of the major macro-haplogroup A'B'C'D'G.
Given the distortion of the L-shaped distribution is transient, and likely to be detectable until genetic drift begin to re-establish mutation-drift equilibrium [ 7] we hypothesize that the extremely small Ne produced by the drastic bottleneck in EB, has allowed a rapid return of the population to genetic equilibrium.
These drastic population bottlenecks are believed to represent a major sieve for viral diversity, to reduce the efficacy of natural selection, and to favor the accumulation of deleterious mutations in viral genomes by random genetic drift (Chao, 1990; Escarmís et al., 2006).
The drastic population bottleneck that occurred after World War II and to a lesser extent the decline in popularity have limited the gene pool of ROT breed today, and may explain why its observed genetic diversity is not as high as the GR, despite the striking popularity of the ROT in the 1990s.
