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They have relied on sampling populations that have been identified beforehand because most population genetics methods have required discrete populations.
Though most population genetics analyses of adaptive protein divergence treat entire proteins as single units, some analyses have addressed the question of the functional units within proteins that are the primary targets of directional selection (e.g. [5] [7]).
Many natural populations have overlapping generations, whereas most population genetics theory assumes discrete generations and ignores age structure.
However, the expense of sequencing a large number of individual genomes remains a limitation for most population genetics studies.
The first is that DiyABC and in fact most population genetics models assume nonoverlapping generations, which is unlikely to hold for long-living organism such as the olive tree.
RC and SR performed all resequencing experiments and analysed the data; MF and UP performed most population genetics analyses; MS, MF, RC, GPC and UP analysed and interpreted the data; NB participated in the study coordination.
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Most present population genetics analyses rely on coalescent theory, representing the genetic history of a random set of gene copies with genealogical trees where nodes represent coalescent events, that is when two evolutionary lines of descent reach a common ancestor [1] (Figure 1A; see Table 1 for a summary of notations).
Because population samples included in this study (as in most human population genetics studies) are not optimal for the population genetics inferences to be addressed, it is important to consider the limitations of our results.
Two families of analyses have been proposed recently in order to partially release the underlying assumptions of most classical population genetics data analyses, and take better advantage of the information contained in a given dataset.
Most stochastic population genetics models, including the classic coalescent (Kingman 1982), consider the extreme case where selection is so weak that the fate of an allele is determined entirely by random genetic drift.
On the other hand, most work on population genetics considers finite populations and includes stochastic effects, whereas quasispecies theory is first and foremost a deterministic description of infinite populations.
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