Since discrete clusters are not necessarily the predicted product of other, more complex, demographic processes (e.g. isolation by distance or progenitor-derivative relationships), we have not modeled those important scenarios here, and leave them for future studies.
The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories.
The assumption made here, that individuals mix nearly homogeneously out of their household may be an appropriate approximation for describing transmission within a neighbourhood or even a city [20], but ultimately one should also consider developing the estimators for more complex demographic situations such as a hierarchy of organisations (household, to village, to region, to country, etc).
These studies may yield a more complex demographic model than the one tested here and illuminate the complex population structure of Caucasus populations.
Although the model of Zeng and Charlesworth (2009) could be further extended to incorporate more complex demographic models, this would introduce more parameters.
This new method has significantly fewer model assumptions and allows us to identify more complex demographic processes, such as multiple admixture events.
Through simulations, Yang et al. (2014) described the relationship between the projection and the derived allele frequency for more complex demographic models.
Hence, the population parameter analyses support the previous inference of repeated positive selection on Xpr1 [ 60], although other more complex demographic scenarios can not be ruled out.
We then tested our model's performance in the more complex demographic scenario depicted in Figure 2b, where a population splits into two subpopulations that grow at different exponential rates, interacting with asymmetric migration rates.
However the inclusion of a larger central forest sample in this study would suggest that this explanation is too simple and that African elephants were subject to a more complex demographic history.
