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Tracing Human Evolution with Genetics SELECTION June 9-17, 2007 SNPs Single Nucleotide Polymorphisms May or may not be in coding regions May or may not cause phenotypic changes Frequency of SNP distribution varies Seq 1 ATCGG AT C CA TG T AT CGATT Seq 2 AT G GG ATGCA TG T AT CGATT

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slide2
SNPs
  • Single Nucleotide Polymorphisms
    • May or may not be in coding regions
    • May or may not cause phenotypic changes
    • Frequency of SNP distribution varies

Seq 1 ATCGG ATCCA TGTAT CGATT

Seq 2 ATGGG ATGCA TGTAT CGATT

Seq 3 ATCGG ATGCA TGAAA CGATT

haplotype
Haplotype
  • Refers to either:
    • Genetic makeup of one set of chromosomes
    • An area of a chromosome defined by a set of associated SNPs
  • Based on statistical analysis and measurement of linkage disequilibrium (LD)
  • Sources of LD
    • Recombination
    • Genetic linkage
    • Random drift
    • Non-random mating
    • Interactions between genes
    • Population structure
important points
Important points…
  • Correlation of a SNP and a phenotype is just that – a correlation, not necessarily a cause.
  • Haplotypes often identify genes involved in polygenic traits.
    • No single site controls the phenotype.
    • Quantitative trait loci (QTLs) are genetic areas involved in modulating expression of polygenic traits.
haplotypes and evolution
Haplotypes and Evolution
  • Recent human evolution is visible in the genome as “selective sweeps”.
  • Selective sweeps are identified based on LD and haplotypes.
  • Articles:
    • Localizing Recent Adaptive Evolution in the Human Genome
    • Convergent adaptation of human lactase persistence in Africa and Europe
lactase persistence and pastoralism
Lactase Persistence and Pastoralism
  • Positive selective pressure
    • Liquid
    • Protein
  • Subsequent migration and spread of phenotype
    • Northern Europeans to North America
    • Southern migrations through Africa
lactase persistence
Lactase Persistence
  • Lactose malabsorption
  • Lactose tolerance
  • Lactase Persistence
    • Continued expression of lactase-phlorizin hydrolase (LPH) in mammals past weaning
global distribution of lactase persistence
Global Distribution of Lactase Persistence
  • Europeans
    • High levels in Scandinavians
    • Decreasing levels further south in Europe
  • Asian
    • Generally low levels in tested populations
    • High in Khazaks
  • African
    • High in Tutsi and Fulani
    • Low in other groups
genetics of lactase persistence
Genetics of Lactase Persistence
  • Northern Europeans
    • SNP identified
    • Enhanced expression of lactase gene
  • Africans
    • Not the same SNP
lactose tolerance test
Lactose Tolerance Test
  • Fast for 8-12 hours
  • Ingest 50g lactose
  • Take blood samples for two hours and test for a rise in blood glucose levels
  • Caveats:
    • Fasting?
    • Field conditions: Used finger pricks and strips for monitoring diabetes
evolutionary medicine
Evolutionary Medicine
  • Many common medical issues are polygenic
  • Traditionally required a large affected family to identify candidate genes
  • Genome Wide Association (GWA) Articles
    • Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    • Guilt by association
slide12
Case
  • A medical researcher is interested in the underlying causes of type II diabetes. Specifically, why do different people have different tendencies to develop diabetes? Obviously current lifestyle will have a major impact, but lifestyle is not a complete explanation. What about genetic history? Is there a way to use tools such as the HapMap or genome-wide association surveys to predict risk for populations and individuals?
  • How might this be useful for helping an American of mixed ancestry understand their risk for developing diabetes?
  • Would it be useful for a Han Chinese person?
  • What are the ethical considerations of collecting and using this kind of information?