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Human Population Genetics

Human Population Genetics. Human population migrations. Out of Africa, Replacement Single mother of all humans (Eve) ~150,000yr Single father of all humans (Adam) ~70,000yr Humans out of Africa ~40000 years ago replaced others (e.g., Neandertals ) Evidence: mtDNA , Y chromosome

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Human Population Genetics

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  1. Human Population Genetics

  2. Human population migrations • Out of Africa, Replacement • Single mother of all humans (Eve) ~150,000yr • Single father of all humans (Adam) ~70,000yr • Humans out of Africa ~40000 years ago replaced others (e.g., Neandertals) • Evidence: mtDNA, Y chromosome • Multiregional Evolution • Fossil records show a continuous change of morphological features • Proponents of the theory doubt mtDNA and other genetic evidence

  3. Why humans are so similar A small population that interbred reduced the genetic variation Out of Africa ~ 40,000 years ago Out of Africa

  4. Migration of Humans

  5. Migration of Humans http://info.med.yale.edu/genetics/kkidd/point.html

  6. Migration of Humans

  7. Migration of Humans http://info.med.yale.edu/genetics/kkidd/point.html

  8. Human Variation in the Y Chromosome

  9. Some Key Definitions Mary: AGCCCGTACG John: AGCCCGTACG Josh: AGCCCGTACG Kate: AGCCCGTACG Pete: AGCCCGTACG Anne: AGCCCGTACG Mimi: AGCCCGTACG Mike: AGCCCTTACG Olga: AGCCCTTACG Tony: AGCCCTTACG G/G G/G G/T G/G G/G G/G G/G T/T T/G T/G Mom Dad Recombinations: At least 1/chromosome On average ~1/100 Mb • Heterozygosity: • Prob[2 alleles picked at random with replacement are different] • 2*.75*.25 = .375 • H = 4Nu/(1+4Nu) Alleles: G, T Major Allele: G Minor Allele: T Linkage Disequilibrium: The degree of correlation between two SNP locations

  10. The Fall in Heterozygosity

  11. The HapMap Project

  12. The HapMap Project

  13. The HapMap Project – Haplotype Blocks

  14. The HapMap Project – LD

  15. Fixation, Positive & Negative Selection How can we detect negative selection? How can we detect positive selection? Negative Selection Neutral Drift Positive Selection

  16. Conservation and Human SNPs Neutral CNS CNSs have fewer SNPs SNPs have shifted allele frequency spectra

  17. How can we detect positive selection? Ka/Ks ratio: Ratio of nonsynonymous to synonymous substitutions Very old, persistent, strong positive selection for a protein that keeps adapting

  18. How can we detect positive selection?

  19. EHH test

  20. Long Haplotypes –iHS test

  21. Some highly selected loci

  22. Example: Microencephalin gene

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