lecture 24/25 pop_gen

Transcript

1. Population Genetics
2. Evolution • Natural Selection • Mutation • Genetic Drift • Gene Flow • Balancing Selection • Purifying Selection Models of evolution Lamarck The more you study the smarter your child will be! Mendel Proposed a mechanism for change (without the change) Darwin/Wallace Population sizes don't change(much) , or death rates must be high. Variation Inheritance "Survival of the Fittest" *Evolution is not guided!*
3. Alleles Two or more versions of one gene Wild Type/Mutant Reference/Alternative SNPs, mutations and alleles Polymorphic
4. Natural Selection Mutation Dominant/Recessive Alleles Inheritance Homozygous/Heterozygous Punnet Square *Vastly oversimplified*
5. Mutation • Incorrect base pairing ◦ Tautomers • Deamination • DNA polymerase makes errors • Meiosis is not perfect • Free Radicals or why the members of Jersey Shore are going to get skin cancer. • Point Mutations, ◦ Silent ◦ Missense ◦ Nonsense ◦ Frame-shift ◦ Many others • Indels
6. Mutation Cont... • Necessary for Evolution • Germline vs. Somatic Cells • Heritable change
7. Gene Flow • Neanderthals and Denisovans https://www.23andme.com/ • Isolated populations • Different (closely related) species
8. Genetic Drift Probability Alleles Neutral alleles/ non-neutral Segregating alleles script example
9. Hardy Weinberg Equilibrium Requirements • Mating is random • Population size is very large • There is no migration • There is no mutation • Natural selection does not affect the alleles under consideration • 2 chromosomes
10. HWE Cont... p = Allele frequency of A q = Allele Frequency of a p = 2N AA + N Aa /2N q = 2N aa + N Aa /2N p + q = 1 p2 + 2pq + q2 = 1
11. Distributions • Null hypothesis • Alternative hypothesis • When do we reject null? • Test statistic • p-value • Normal Distribution ◦ Lots of others • If distribution is known ◦ Use it • What if distribution is unknown? ◦ Bootstrap
12. 1000 genomes vcf files