The coalescent framework also assumes neutral evolution and several studies have shown that the pol gene is under both positive and negative selection [22] [25].
The REHH value of this core haplotype was further compared with numerous data points generated by simulation that assumes neutral evolution [81].
The IM model also assumes neutral genetic variation, freely recombining unlinked loci and no intragenic recombination or gene conversion [ 42].
In this regard, it should be noted that the model developed here assumes neutral evolution of gene sequences and may not be suitable for analysis of gene loci under selection.
Although Kimura's model assumes neutral rates of nucleotide substitutions, we use it as an approximation of the mutation rates of the GAPDH genes for the sake of consistency, perhaps yielding conservative estimates or upper bounds on the ages of pseudogenes.
The implementation of the coalescent in M igrate-N assumes neutral evolution, no recombination, and that population sizes, time since isolation, and number of demes are finite and have remained constant for at least the previous 2 N ef generations (two times the effective female population size).
