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Autosomal haplotypes as markers for the histories and structures of human populations

By Suzanne Patricia Lavelle

Abstract

The demographic history of humans is very complex. Populations have undergone bottlenecks, isolation, migration, admixture and expansions. All of these have added to the complexity of what makes a population and how that population has changed over time. A record of these events can be found in our DNA. \ud This project used autosomal DNA to trace the histories and structures of human populations by using a combination of a SNP (single nucleotide polymorphism) and an STR (short tandem repeat) – SNPSTR (Mountain et al. 2002). Forensic STRs formed the basis for the SNPSTR systems because their allelic diversity is well characterised, their mutation rates have been reliably measured and they are robust in PCR amplification. \ud Four SNPSTR systems were found, using SNPs which had been verified by HapMap and/or Perlegen and which were < 500 base pairs away from the forensic STRs. \ud These SNPSTRs were typed on DNAs from the HapMap project, the CEPH-HGDP, Cornwall, UK African Caribbeans, Danes and Greenland Inuit. They were analysed using an ABI3100 and GeneMapper software. Data from the combined SNPSTRs allowed inferences to be made about population structures, and also enabled the calculation of the TMRCA of the derived SNPs associated with the forensic STRs. \ud Population structure was evident in the MDS plots where rudimentary population groupings could be seen. The Americas were outliers, reflecting their later peopling some 15,000 years ago (Jobling et al. 2003). Haplogroup analysis highlighted population isolates, such as the Surui in Brazil. \ud The STRUCTURE analysis of the SNPSTR data has also provided some insights into the admixed nature of the autosomal DNA in known admixed populations such as the Greenland Inuit and to some extent, the African Caribbeans. \ud One SNPSTR was expanded into a larger haplotype block - a PHAX - Phylogeographically informative Haplotypes on the Autosomes and seX chromosomes, by means of a SNaPshot reaction. The preliminary data from this suggested that this would allow us to gain a more complete insight into the histories and structures of human populations

Publisher: University of Leicester
Year: 2010
OAI identifier: oai:lra.le.ac.uk:2381/8374

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