Impact of human population history on distributions of individual-level genetic distance
- PDF / 1,518,327 Bytes
- 16 Pages / 609.449 x 790.866 pts Page_size
- 85 Downloads / 199 Views
Impact of human population history on distributions of individual-level genetic distance Joanna L. Mountain1,2* and Uma Ramakrishnan3 1
Department of Anthropological Sciences, Stanford University, Stanford, CA 94305-2117, USA Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA 3 National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore 560065, India *Correspondence to: Tel: þ 1 650 725 5009; Fax: þ 1 650 725 9996; E-mail: [email protected] 2
Date received (in revised form): 2nd December 2004
Abstract
Summaries of human genomic variation shed light on human evolution and provide a framework for biomedical research. Variation is often summarised in terms of one or a few statistics (eg FST and gene diversity). Now that multilocus genotypes for hundreds of autosomal loci are available for thousands of individuals, new approaches are applicable. Recently, trees of individuals and other clustering approaches have demonstrated the power of an individual-focused analysis. We propose analysing the distributions of genetic distances between individuals. Each distribution, or common ancestry profile (CAP), is unique to an individual, and does not require a priori assignment of individuals to populations. Here, we consider a range of models of population history and, using coalescent simulation, reveal the potential insights gained from a set of CAPs. Information lies in the shapes of individual profiles — sometimes captured by variance of individual CAPs — and the variation across profiles. Analysis of short tandem repeat genotype data for over 1,000 individuals from 52 populations is consistent with dramatic differences in population histories across human groups. Keywords: human population genetic structure, genetic similarity, short tandem repeats (STRs), multilocus genotypes
Introduction The collective human gene pool, consisting of the genomes of all living people, has much to reveal regarding human population history. Until recently, surveys of human genetic variation have been sparse, in that hundreds or thousands of individuals have been studied for a small number of genetic regions (eg blood groups, Human Lymphocyte Antigens (HLA), mitochrondrial DNA, Y chromosome1 – 3) and a few individuals have been studied for a large fraction of the genome (eg through the Human Genome Project). In the past few years, however, larger sets of individuals have been studied for hundreds of genetic regions4 and, concomitantly, new data analysis tools have been developed.5 With new data and new tools, we are rapidly gaining a more precise understanding of how genetically similar individuals are, and of how that similarity corresponds to other dimensions of human variation.
Summaries of human genetic variation
Most differences between genomes take the form of single nucleotide polymorphisms (SNPs) rather than DNA insertions, deletions or multiplications.6 For the autosomes, two
4
DNA sequences chosen at random appear to differ at an average of about one per 1,000– 1,500 nucleotide site
Data Loading...
