Basic concepts of population genetics - Bioversity International

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An example of three populations in Hardy- Weinberg equilibrium Popul. Pop. 1 Pop. 2 Pop. 3 Genotypes of G 0 A 1 A 1 0.6 0.49 0.4 A 1 A 2 0.2 0.42 0.6 A 2 A 2 0.2 0.09 0.0 p 0.7 0.7 0.7 Frequencies G 0 0.3 0.3 0.3 Copyright: IPGRI and Cornell University, 2003 Population genetics 18 q 18 Genotypes of G 1 A 1 A 1 0.49 0.49 0.49 A 1 A 2 0.42 0.42 0.42 A 2 A 2 Population genotype frequencies are given in rows. Generations (G 0 and G 1 ) are given in columns. Again, we have one gene with two alleles, A 1 and A 2 . The frequency of allele A 1 is p and the frequency of allele A 2 is q. Genotype frequencies are different for each population in generation 0 (e.g. the frequency of A 1 A 1 in population 1 is 0.6; in population 2, 0.49; and in population 3, 0.4, and so on for the other genotypes). We note, though, that the allele frequencies in the three populations are similar in G 0 (p = 0.7 and q = 0.3). In the next generation, G 1 , if all requirements of the H-W principle are met, the genotype frequencies in the three populations balance (now the frequency of A 1 A 1 is 0.49 in the three populations, and the same happens with the frequencies of A 1 A 2 and A 2 A 2 ). The allele frequencies are kept. 0.09 0.09 0.09 p 0.7 0.7 0.7 G 1 q 0.3 0.3 0.3
The chi-square test This hypothesis test is useful for determining whether the allelic frequencies are in H-W equilibrium The procedure is as follows: Define H 0 (and H a ) Define significance level Perform the statistical test Apply the decision criteria Copyright: IPGRI and Cornell University, 2003 Population genetics 19 H 0 = the hypothesis that says the allele frequencies for trait Q in a given population are in H- W equilibrium. H a = an alternative hypothesis that says the allele frequencies for trait Q are not in H-W equilibrium. We choose a significance level to give us a certain percentage of confidence in our results. The statistical test follows the formula: Where, ST = statistical test k = number of genotypic classes O = observed frequencies m = number of alleles E = expected frequencies df = degrees of freedom If our sample allows for only 1 degree of freedom, then the difference in frequencies is reduced by 0.5, a correction factor, such as: The decision criteria is applied as follows: Where, If 2 cal 2 tab then H0 is accepted; and, if 2 cal > 2 tab then H0 is rejected cal = the result of calculating ST with the data obtained in our sample tab = the value identified in the table (a 2 table may be found in Appendix 1, click here). 19 Oi Ei (Ei) 2 2 ST k mdf 2 Oi Ei 0.5 Ei
Page 1 and 2: Genetic diversity analysis with mol
Page 3 and 4: Definitions: Population genetics T
Page 5 and 6: Phenotypic variation Pink Pale crea
Page 7 and 8: Genotype is … The description of
Page 9 and 10: What is polymorphism? ‘Presence
Page 11 and 12: Population structure Three levels o
Page 13 and 14: Allele frequency Allele frequency
Page 15 and 16: Genotype frequency This is the fre
Page 17: Demonstrating the H-W principle Gen
Page 21 and 22: Calculating allele frequencies: Exa
Page 23 and 24: Locus A B D … with a codominant m
Page 25 and 26: Locus A Locus B Locus D … with a
Page 27 and 28: ... with a codominant gene having m
Page 29 and 30: Random mating Mating that takes pl
Page 31 and 32: Inbreeding coefficient It compares
Page 33 and 34: Forces shaping genetic diversity M
Page 35 and 36: Migration It is the movement of in
Page 37 and 38: Selection It is the inherited abili
Page 39 and 40: Effective population size Ne is th
Page 41 and 42: Consequences … (continued) A bot
Page 43 and 44: Appendix 1 Copyright: IPGRI and Cor
Page 45 and 46: By now you should know … The bas
Page 47:
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