Red_Rep
A reduced representation approach to population genetic analyses and applications to human evolution
We have implemented an inexpensive reduced representation protocol for preparing re-sequencing targets and we have developed the analytical tools necessary for making population genetic inferences.  This approach can be applied to any species for which a draft or complete reference genome sequence is available. The new tools we have developed include methods for aligning reads, calling genotypes and incorporating sample-specific sequencing error rates in the estimate of evolutionary parameters.  Applied to 19 individuals from a total of 18 human populations, our approach allowed sampling largely overlapping regions across individuals and that are representative of the entire genome. The re-sequencing data was used to test the serial founder model of human dispersal and to estimate the time of the Out of Africa migration. Our results also represent the first attempt to provide a time frame for the colonization of Australia based on large-scale resequencing data.