Mait Metspalu et. al. The American Journal of Human Genetics , December 9, 2011

1. Shared and Unique Components of Human PopulationStructure and Genome-Wide Signals of PositiveSelection in South Asia Mait Metspalu et. al. The American Journal of Human Genetics, December 9, 2011 Population Genetics Journal Club Speaker: Hang Zhou 02/22/2012

2. Background

3. CEPH-HGDP L. Luca Cavalli-Sforza, NATURE REVIEWS | GENETICS, 2005

5. How to study a population? • Linguistics • Fst • PCA • STRUCTURE • ADMIXTURE • Selection • …

6. How to study a population? • Linguistics • Fst • PCA • STRUCTURE • ADMIXTURE • Selection • …

7. Most common Fst i – ith loci, {1, .. , n} k – kth population, {1, .. , d}

8. Unbiased Fst

9. Fst • Unbiased Fst could be influenced by sample sizes ratio; • Any other Fst estimator? • New Fst estimator.

10. Fst Matrix of Pairwise Mean Fst Values of Regional Groupings of the Studied Populations

11. PCA principal component analysis of the Eurasian populations

12. Admixture ADMIXTURE analysis at K = 8 and 12. What the number of K should we choose?

13. EHH iHS (integrated haplotype score) rs57291235, chr22, 20787332, C/T • EHH (extended haplotype homozygosity) based • iHH (integrated EHH)

14. EHH EHH Recombination & mutation time EHH Extended haplotype homozygosity (EHH) Tang, 2007

15. iHS (integrated haplotype score) rs57291235, chr22, 20787332, C/T • Group the haplotypes into ancestral and derived groups; (MAF >= 0.05) • Calculate the EHH site by site; (until EHH < 0.05) • Integrated them to iHH; • Compare iHH_A and iHH_D. http://hgdp.uchicago.edu/Software/

16. iHS iHS signal sharing between continental populations

17. EHH XP-EHH & lnRsb Cross population EHH rs57291235, chr22, 20787332 Pop1 EHH Pop2 • XP-EHH integrate one side, lnRsb integrate both sides; • XP-EHH until [0.03..0.05], lnRsb until < 0.1; • ln(iHH_1/iHH_2); http://hgdp.uchicago.edu/Software/

18. XP-EHH XP-EHH signal sharing between continental populations.

19. Questions

20. Thank you ~