Identifying Regions of the Human Genome that Exhibit Evidence for Positive Selection

Ryosuke Kimura, Tokai University School of Medicine, Isehara, Kanagawa, Japan
Jun Ohashi, University of Tokyo, Bunkyo, Tokyo, Japan

Published online: July 2008

DOI: 10.1002/9780470015902.a0020850

The recent availability of human genomic data has driven genome-wide scans for natural selection with different approaches based on comparative genetics and population genetics. Such studies have provided many candidates for targets of positive selection in the human genome, but the results should be interpreted with caution because of the inevitability of false positives. Here, approaches for identifying positive selection in the human genome are reviewed, and, especially, an up-to-date approach based on haplotype variation and linkage disequilibrium is explained in detail.

Keywords: positive selection; human genome; selective sweep; haplotype variation

Figure 1. Approaches for detecting natural selection and their applicable time scales.
Figure 2. Conservation of the haplotype harbouring a beneficial mutation.
Figure 3. Scheme of EHH. (a) Extended haplotypes. Dark and light grey boxes represent different alleles. Extended haplotypes are determined for each distance from the core SNP. (b) The decay of EHH. Relative EHH can be calculated at any arbitrary distance. X1, 100 kb of physical distance; X2, the point just before EHH for the test allele drops below 0.4 and X3, the point just after EHH for the test allele drops below 0.05. EHH can be integrated (iHH).
Figure 4. The patterns of EHHR/EHHT values around the selected loci. (a) The result of the simulation under neutrality. (b) The results of the simulations assuming the various frequencies (p) of the selected allele (2Nes=300). EHHR/EHHT values (y axis) of SNPs within 200 kb around the selected loci were counted for each bin of the allele frequency (x axis). Data from 500 replications were put together and counted.
Figure 5. Definition of blocks to cover the region under complete selective sweep in a population. (a) HH10.5. (b) HH10.9.
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Related Sub-Topics:

Adaptive Evolution | Selection and Variation | Human Evolution | Population Structure and Genetics | Evolution of Coding and Functional Modules
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Article Title: Identifying Regions of the Human Genome that Exhibit Evidence for Positive Selection
 
How to Cite close
Kimura, Ryosuke, and Ohashi, Jun(Jul 2008) Identifying Regions of the Human Genome that Exhibit Evidence for Positive Selection. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020850]