Population Genetics. Ben Hecht CRITFC Genetics Training December 11, 2013

Transcription

1 Population Genetics Ben Hecht CRITFC Genetics Training December 11,

2 Population Genetics The study of how populations change genetically over time under the influence of evolutionary forces By studying the frequency and interaction of alleles in populations 2

3 Allele Frequency The frequency of the occurrence of an allele from a target locus within a population A 1 A 2 3

4 Allele Frequency 1. Count number of individuals = Determine total number of alleles = 2 x 12 = Count number of each allele present: Number of A 1 = 6 Number of A 2 = 18 Verify that = Estimate frequency of each allele: Frequency of A 1 = 6/24 = 0.25 Frequency of A 2 = 18/24 = 0.75 Verify that = 1 Evolution = change in allele frequency over time 4

5 Evolutionary Forces 1. Natural Selection favors an allele that offers a fitness advantage 2. Sexual Selection (non-random mating) favors more attractive alleles (eye color, feather pattern, etc.) 3. Mutation mistakes made by the cellular machinery when copying DNA, which introduces new alleles 4. Gene Flow introduction of new alleles through dispersal of individuals (immigration/emigration) 5. Genetic Drift random change in allele frequency due to a stochastic population decline (i.e. hurricane, fire, etc.) 5

6 Hardy-Weinberg Equilibrium (HWE) HWE = Allele and genotype frequencies in a population remain constant from generation to generation HWE Assumptions 1. No Natural Selection 2. No Sexual Selection A 1 A 2 3. No mutation 4. No migration 5. Infinite population size Allele frequency equation p + q = 1 Genotype frequency equation p 2 + 2pq + q 2 = 1 Provides an expectation to test hypotheses against 6

7 HWE Genotype Frequency 1. Determine observed genotype frequencies: Count the number of: A 1 A 1 = 1, A 1 A 2 = 4, A 2 A 2 = 7 *Verify that = Determine expected HWE genotype frequencies: Recall allele frequencies : A 1 = 6/24 = 0.25 = p and A 2 = 18/24 = 0.75 = q and plug them into the HWE equation: p 2 + 2pq + q 2 = 1 (0.25) 2 + 2(0.25)(0.75) + (0.75) 2 = 1 3. Convert frequency to expected number: p 2 = (0.25) 2 = , 12 x = pq = 2(0.25)(0.75) = 0.375, 12 x = 4.5 q 2 = (0.75) 2 = , 12 x = 6.75 *Verify that = 1 4. Compare observed to expected: Obs_A 1 A 1 = 1 vs Exp_A 1 A 1 = 0.75 Obs_A 1 A 2 = 4 vs Exp_A 1 A 2 = 4.5 Obs_A 2 A 2 = 7 vs Exp_A 2 A 2 =

8 EXCERCISE Estimate allele and genotype frequencies Determine if in HWE See effects of Natural Selection Genetic Drift Gene Flow Sexual Selection on allele frequencies 8

9 Genetic Diversity A measure of variation across the genome Genetic variation allows populations to adapt to changing environments Measured by estimating observed heterozygosity (Ho) Proportion of heterozygous (A 1 A 2 ) individuals in a population Populations with more diversity can adapt to changing environments Populations with low variation may not contain genetic material required to adapt 9

10 Genetic Distance (F ST ) The level of genetic divergence/similarity between populations High levels suggest divergence (distant relationship/isolation) Low levels suggest similarity (close relationship/gene flow) Divergence is due to allele frequency (p and q) differences among populations 10

11 Genetic Distance (F ST ) F ST = (H T H S )/ H T H T = Expected HWE heterozygosity of total population (multiple subpopulations considered as one) H S = Average HWE heterozygosity of subpopulations calculated as ((2p 1 q 1 + 2p 2 q 2 )/2) 11

12 Genetic Distance F ST = (HT HS)/ HT Obs. Genotype Frequency Allele Frequency Exp. Genotype Frequency Weir Lake A Lake B Weir A 1 A 1 A 1 A 2 A 2 A 2 A 1 (p) A 2 (q) A 1 A 1 A 1 A 2 A 2 A H S = ( )/2 = Wahlund effect H T = 2(0.5)(0.5) = 0.5 F ST = ( )/0.5 =

13 Neutral & Adaptive Genetic Variance 13

14 Neutral & Adaptive Genetic Variance Neutral variance genetic variation that has no effect on the fitness of an individual Natural selection does not act on this variation Genetic variation that does not change protein or expression profile of a gene Generally these are variations in non-coding regions of the genome Do not violate HWE assumptions 14

15 Neutral & Adaptive Genetic Variance Adaptive variance genetic variation that effects the fitness of an individual Natural selection acts on this variation Variations that change the protein, or that change the expression profile of a gene Generally variations near or within a gene Violate HWE assumptions 15

16 Questions? 16