effective population size - senecio7の日記

Karasov T, Messer PW & Petrov DA 2010 Evidence that adaptation in Drosophila is not limited by mutation at single sites. PloS Genet 6:e1000924.

the current effective population size of modern D. melanogaster populations is likely to be substantially larger (≥100-fold) than commonly believed.
estimates of the effective population size are generally derived from levels of standing variation and thus reveal long-term population dynamics dominated by sharp—even if infrequent—bottlenecks
the short-term effective population sizes relevant for strong adaptation, on the other hand, might be much closer to census population sizes
adaptation in Drosophila may therefore not be limited by waiting for mutations at single sites
complex adaptive alleles can be generated quickly without fixation of intermediate states
adaptive events should also commonly involve the simultaneous rise in frequency of independently generated adaptive mutations

the old estimates, based on standing levels of neutral genetic variation, are misleading in the case of rapid adaptation
levels of standing variation are strongly affected by infrequent population crashes or adaptations taking place in the vicinity of neutral sites
many standard assumptions about the adaptive process in eukaryotes need to be reconsidered

Drosophila and many other organisms undergo recurrent boom-bust cycles thereby reducing the long-term N_e strongly but allowing adaptation during the boom years to occur in populations of large short-term N_e
Drosophila appears to undergo pervasive adaptation [30, 31] with most common neutral polymorphisms estimated to have been affected by several selective sweeps in their genomic vicinity
such pervasive adaptation generates dynamics similar to recurrent bottlenecks and will also reduce the long-term N_e values even if the short-term N_e might be consistently large

strong adaptation should be much more rapid and generally result in soft sweeps
complex adaptations that require multiple changes can be generated without fixation of interim states and with an enhanced chance of crossing fitness valleys
this raises the question of whether the widespread use of the weak mutation, strong selection ("WMSS") model for the study of adaptation should be broadened to include cases of strong mutation

in our simulations of evolution at Ace in the strong mutation regime (Θ per site on the order of 1), the complex 3-mutation alleles generally evolve without fixation of intermediate 1- and 2-mutation alleles
the number of adaptive substitutions estimated using McDonald-Kreitman approaches should then be larger than the number of independent adaptive fixations
the prediction of the number of selective sweeps derived from the number of adaptive substitutions should be upwardly biased
all of these expectations hold especially well for strong selection because it operates over shorter time scales and is therefore less sensitive to recurrent but infrequent bottlenecks [37] and neighbouring selective sweeps

if one searches exclusively for hard sweeps, then complete soft sweeps might appear as ongoing hard sweeps
the polymorphisms associated with the most frequent haplotype would appear as the likeliest candidates for the adaptive mutation
the true adaptive mutation would be fixed in the population
soft sweeps might also be common in humans, with the soft sweep associated with lactase persistence providing the strongest signature of adaptation in humans [41, 42]
the possibility of pervasive soft sweeps needs to be taken seriously
recurrent boom-bust cycles are a general feature in population dynamics of most studied organisms
adaptation and recurrent selective sweeps reducing the long-term but not the short-term N_e might also be common
short-term and long-term N_e values are likely to be different as a rule
the shortest term N_e is only bounded by the census population size, which is often very large and can easily be in the billions, particularly for insects or marine organisms
strong adaptation at single sites may not be limited by mutation in many eukaryotes