In Fig. 7c, d we show how well the model replicates the evolution of the income per capita (or economic growth) and the consumption per capita from 1850 to 2000.
The simulation over 2004 201313 for Siem Reap clinic does not replicate exactly the evolution of the chronic disease clinic in Siem Reap documented over the period 2002 200505.
The observed large number of retrotransposons indicates that such elements have been actively replicating during the evolution of this species.
The situation is different in the case of non-coding RNAs such as ribosomal RNA and tRNA, as these were able to replicate prior to the evolution of ribosomal protein synthesis.
These values, along with the estimated codon equilibrium frequency, ω distribution (p = 0.530, q = 0.758 for the β distribution), tree length (23.47 substitutions per codon site) and transition/transversion ratio (κ = 1.9375), were used to simulate 100 replicates of the evolution of 65 sequences.
The model based on amino-acid preferences inferred from the combined experimental data from the three replicates describes the evolution of the naturally occurring HA sequences far better than the alternative models, despite the fact that the latter have a variety of free parameters that are optimized to improve the fit.
A detailed agent-based model has been built to replicate the past evolution, accounting for structural diversity of farmers, heterogeneity in behaviour, and natural resource constraints.
A genetic algorithm, in its purest form, will try to replicate the concepts of natural evolution, in a controlled and mathematical environment.
Given the evolution of faster replicating parasites, units of replication that rely on helpers for survival, such as the master sequence, are counterselected and go extinct (as explained above).
The constraint we observed, the difference in model success between replicates from different species, and the evolution of traits outside the scope of the model are all consistent with this outlook.
