PubMed · 15032233
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Jane Bradbury. 2004-03-15. Pathogens maketh man.. https://doi.org/10.1016/s1359-6446(04)03032-6
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We propose a simple model of evolution at a pair of SNP loci, under mutation, genetic drift and recombination. The developed model allows to consider evolution of SNPs under different demographic scenarios. We applied it to SNP data containing polymorphisms spanning 19 gene regions. We initially matched the linkage disequilibrium (LD) data only, and then we reconciled both LD and heterozygosity data. The imbalance between LD and heterozygosity data, observed for some of the analyzed genomic regions, may be a signature of selection acting in these regions. However, assuming neutrality, we obtain estimates of the age of population expansion of modern humans, which are consistent with the consensus estimates. In addition, we are able to estimate the ages of the polymorphisms observed in different genomic regions and we find that they vary widely with respect to their age. Polymorphisms at loci implicated in human disease, seem to be younger than average. Our results supplement the conclusions originally obtained by Reich and co-workers for the same set of data.
Rates of approach to equilibrium values of F(ST)/R(ST) at various mutation rates and using different mutation models (K-allele model KAM and stepwise model SMM) were analyzed numerically for the finite island model and the one-dimensional stepping stone models of migration, using simulation. In the island model of migration and the KAM mutation model, the rate of approach to the equilibrium F(ST) value was appreciably higher and the equilibrium value was almost twofold lower at micro (mutation rate) = m (migration rate) than at micro << m. In the one-dimensional stepping stone model of migration and the KAM model of mutation, the mutation rate significantly affected both the rate of approaching F(ST) equilibrium and the equilibrium value. In both island and one-dimensional stepping stone models and SMM, R(ST) was not influenced by various mutation rates. The rate of approach to the equilibrium values of both F(ST) and R(ST) was lower for the stepping stone model than to the island model. RST was rather resistant to deviations from the SMM mutation model.
Using the structured coalescent model, it is shown that unequal migration rates between different pairs of subpopulations can increase the value of Wright's coefficient F(ST) and its dependence on the mutation rate, and decrease the effective level of gene flow. Two specific models of population structure are considered: (i) an 'island model with barrier' where migration rates between subpopulations on the same side of the barrier are higher than migration rates between subpopulations on opposite sides of the barrier, and (ii) the two-dimensional stepping-stone model with unequal migration rates in the two dimensions of the model.