MBE Advance Access published online on July 14, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh212
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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1 Department of Anthropological Sciences, Stanford University, Stanford, CA
* To whom correspondence should be addressed. E-mail: uramakri{at}stanford.edu.
Inference of intra-specific population divergence patterns typically requires genetic data for molecular markers with relatively high mutation rates. Microsatellites, or short tandem repeat (STR) polymorphisms, have proven informative in many such investigations. These markers are characterized, however, by high levels of homoplasy and varying mutational properties, often leading to inaccurate inference of population divergence. A SNPSTR is a genetic system that consists of an STR polymorphism closely linked (typically <500bp) to one or more single nucleotide polymorphisms (SNPs). SNPSTR systems are characterized by lower levels of homoplasy than are STR loci. Divergence time estimates based on STR variation (on the derived SNP allele background) should therefore be more accurate and precise. We use coalescent-based simulations in the context of several models of demographic history to compare divergence time estimates based on SNPSTR haplotype frequencies and STR allele frequencies. We demonstrate that estimates of divergence time based on STR variation on the background of a derived SNP allele are more accurate (3-7% bias for SNPSTR vs 11-20% bias for STR) and more precise than STR based estimates, conditional on a recent SNP mutation. These results hold even for models involving complex demographic scenarios with gene flow, population expansion, and population bottlenecks. Varying the timing of the mutation event generating the SNP revealed that estimates of divergence time are sensitive to SNP age, with more recent SNPs giving more accurate and precise estimates of divergence time. However, varying both mutational properties of STR loci and SNP age demonstrated that multiple independent SNPSTR systems provide less biased estimates of divergence time. Furthermore, the combination of estimates based separately on STR and SNPSTR variation provides insight into the age of the derived SNP alleles. In light of our simulations, we interpret estimates from data for human populations.
Original Articles
Precision and Accuracy of Divergence Time Estimates from STR and SNPSTR Variation
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