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Liu et al [ 19] proposed a multi-level two-part random effects logit-lognormal model; two nested random effects were included in each part to model the nested clustering structure in a data, assuming the respective random effects in the two parts followed a bivariate normal distribution.
This suggests the need to model the nested structure of data (Raudenbush & Bryk, 2002).
Because of the increased bottleneck severity between regions, unlike the modern serial founder model, the nested regions model also reproduces the larger differences in values of the three summary statistics observed between regions compared to values observed within regions.
However, as in the modern serial founder model, the nested regions model predicts small FST between pairs that are far from the source population, a pattern that is not observed for populations in the Americas (contrast Figure 4C and Figure 7C).
The new model, the Nested Inequalities Climate-Economy model or NICE, builds off the Regional Integrated Model of Climate and the Economy (RICE), which was developed by William Nordhaus of Yale University.
We used the likelihood ratio test to compare models including a given variable versus absence of the variable in the model (the nested model).
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For the second model's analyses (high-resolution modeling), the nested study Domains C and D that were characterized by grid size of 3 m and 1 m, respectively, were used.
As was seen with the modern serial founder model above, the nested regions model recovers most of the patterns observed in human population-genetic data.
Using coalescence-time densities in various special cases, we have found that the modern serial founder model and the nested regions model are consistent with geographic patterns of within- and between-population genetic diversity observed in human data.
After all runs were converged under the full model, which estimates the six demographic parameters, we tested the fit of the data to simpler demographic models using the nested model approach in the L-Mode option of IMa.
Here, we used three LRTs based on site-specific models comparing the nested models: M1a-M2a, M7-M8 and M8a-M8.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com