Lecture 8 From Inheritance to Population Genetics

1. Lecture 8From Inheritance to Population Genetics • Dominance and co-dominance • Mendelian inheritance • Hardy-Weinberg equilibrium • Population differentiation

2. Direct Code of life Basis of inheritance Obtain lots of characters Independent 800-1000 characters Can distinguish mutations Synonymous vs. non-synonymous Transitions vs. transversions Relatively short section Inherited as one unit Biased sample Need primers ‘Heterologous’ primers Indirect Only part of variation detected Important part? Mutation rate may be v. high Mini-, microsatellites Several (many) loci surveyed Or longer fragment Recombination Creation of variability Good coverage of genome Selected loci Genome mapping Independent gene lineages Primers Varies between markers Direct vs indirect sequence detection

3. RAPDRandom Amplified Fragment Polymorphism • Arbitrary primers • 8-10 bp long • V. little development • PCR • Amplification where primers on opposite strands are close • Variability • Point mutations • Insertions / deletions • Low stringency • Annealing temp: 35-45oC

4. X BB AA Co-dominant X AB AB AB AB AA AB AB BB Dominant X BB AA X AB AB AB AB AA AB AB BB Dominant and co-dominant AA AB BB • Estimation of allele frequencies ? • Analysis of 1 / 0 • Phenotypic trait

5. Locus 2 Locus 3 Locus 4 Locus 1 4 loci Dominant Minisatellites Single Locus Multilocus Ind. 1 Ind. 2

6. Types of mutations Substitutions Synonymous / non-synonymous Codon position Transition / transversion Mutation rates Accumulation of mutations Multiple hits Transitions 3rd codon positions Direct sequencing Indirect sequence detection Lots of methods Different parts of sequence diversity RAPD Reproducibility dominance Direct vs. indirect sequence detection Review of key concepts

7. X X Mendelian inheritance • If patterns of inheritance follow Mendelian laws • Mendelian inheritance

8. Mendelian inheritance The Hardy Weinberg Law male • Punnett Square • Add frequencies • f(A)=0.3 • f(B)=0.7 female males females

9. Mendelian inheritance The Hardy Weinberg Law • Punnett Square • Add frequencies • p2 + 2pq + q2 • Hardy Weinberg Law male female • Assumptions – ideal population • Diploidy • Sexual reproduction • Random mating • No selection • No mutation • Large populations size • No inbreeding

10. Allele frequency Allele frequency 0.250 1.000 0.900 0.200 0.800 0.700 0.150 0.600 Frequency Frequency 0.500 0.100 0.400 1.00 0.300 0.050 0.200 0.80 0.100 0.000 0.000 AA 1 1 2 2 3 3 4 4 5 5 0.60 AB Allele Allele Genotype Frequency BB 0.40 0.20 0.00 0.00 0.20 0.40 0.60 0.80 1.00 Allele Frequency (A) Why is this important? • Calculation of heterozygosity • Observed heterozygosity (Ho) • Frequency of heterozygotes • Expected heterozygosity (He) • Frequency of heterozygotes expected under HW • He=1-Σpi2

11. Dominant X BB AA X AB AB AB AB AA AB AB BB Why is this important? • What about dominant markers? AA AB BB

12. Why is this important? • Test • Data • Mis-scoring • Non-genetic variation • Locus under selection • Biology of the population • Mixture or panmictic • Inbreeding • Sexual reproduction • Selection

13. 30 30 25 25 20 20 15 15 10 10 5 5 0 0 105/105 105/105 105/107 105/107 107/107 107/107 Deviations from HWexample • Population mixture (N=50) • Pop 1 • p(105)=0.8, q(107)=0.2 • Pop 2 • p(105)=0.2, q(107)=0.8 • Mixture • p(105)=0.5, q(107)=0.5 x2=7.445 P=0.006 • Wahlund effect • Can we go further than that?