This is a note for the book Population Genetics: A Concise Guide (Second Edition). Page 31 Problem 2.9 Graph -ΔNH and ΔuH as function of H for N = 104 and u = 5×10-5. Do the lines intersect where you expect them to? Note: Output: In this situation, 4Nu = 4×104×10-5 = 2, when H > […]
This is a note for the book Population Genetics: A Concise Guide (Second Edition). Page 30 Problem 2.8 Graph Equation 2.7 as a function of 4Nu. What value of 4Nu gives a reasonable fit to the average heterozygosity for proteins as described by electrophoretic studies in humans? Note: Equation 2.7: Set t = 4Nu Output: Proteins
This is a note for the book Population Genetics: A Concise Guide (Second Edition). Page 30 Problem 2.7 How many different alleles are one mutational step away from an allele at a locus that is 3000 nucleotides in extend? How many are two mutational step away? Note: One nucleotide has one of the three possibilities of
This is a note for the book Population Genetics: A Concise Guide (Second Edition). Page 28 Problem 2.6 g is almost the same as the homozygosity of the population, G. Suppose we were to define the homozygosity of a population as the probability that two alleles chosen at random from the population with replacement are identical
This is a note for the book Population Genetics: A Concise Guide (Second Edition). Page 28 Problem 2.5 Graph simultaneously both Formula 2.4 and Formula 2.5 as a function of N for N from 1 to 100. Is the approximation to your liking? Formula 2.4 Formula 2.5 Code: Output: So we can trust that Formula 2.5
This is a note for the book Population Genetics: A Concise Guide (Second Edition). Page 27 Problem 2.4 Graph Ht and Gt for 100 generations with H0 = 1 and population sizes of 1, 10, 100, and 1,000,000. Note: According to the formula: Output: This indicates that genetic drift has a greater impact on small populations
This is a note for the book Population Genetics: A Concise Guide (Second Edition). Page 25 Problem 2.3 Convince yourself that the average time for the population to become homozyggous is , in fact, two generations. Note: The model is discussed here is a single hermaphroditic A1A2 heterozygote individual, wich means: (1) the population is
Page 24 Problem 2.2 If you know how to program a computer, write a simulation of genetic drift. Note: The simulation model: 1. Choose an allele at random from among the 2N (N is the number of the diploid individuals) alleles in the parent generation. 2. Make an exact copy of the allele. 3. Place
Page 22 Problem 2.1 What is the probability that a particular allele has at least one copy in the next generation? The surprising answer quickly becomes independent of the population size as N increases. Note: The probability that a particular allele has at least one copy in the next generation is equal to one minus
Page 16 Problem 1.7 Derive the Hardy-Weinberg law for a sex-linked locus. Let the initial frequency of A1 in the females be pf and in the males, pm. Follow the two alleles frequencies in successive generations until you understand the allele-frequency dynamics. Then, jump ahead and find the equilibrium genotype frequencies in females and males.
Page 16 Problem 1.6 Perform a Chi-squared test for agreement of the data in Table 1.2 with the predictions of the Hardy-Weinberg law. Note: Table 1.2 see #note Population Genetics A Concise Guide (4) Run Chi-squared test in Python: Output:
Page 15 Problem 1.5 Graph the ratio of the frequencies of A1A2 heterozygotes to A2A2 homozygotes as a function of q using both the exact and the approximate formulae. Note: Exact formula by using Python: Output: Approximate formula by using Python: Output: