Topic 3 Neutral Theory and DNA variation

Question 1

What is genetic drift

Answer 1

• random changes in allele frequency that occur from generation to generation as a result of sampling effects

Question 2

What are the 5 assumptions of the Hardy Weinberg principle?

Answer 2

• mating is random
• population of infinite size
• no migration
• no mutation
• no selection

Question 3

What would happen if these assumptions were true

Answer 3

there would be evolution

Question 4

What are the 4 forces of evolutionary change

Answer 4

• genetic drift
• gene flow
• mutation
• selection

Question 5

What are the 5 principles of the Neutral theory

Answer 5

• the probability of fixation of an allele
• the rate of fixation of new alleles
• the time between fixation of new alleles
• the time it takes for a new allele to become fixed
• the amount of diversity in a population

Question 6

What is the probability of fixation

Answer 6

• the probability P that a neutral allele will eventually reach fixation is equal to its frequency at the time of consideration, p

Question 7

What is the application of the first principle?

Answer 7

• the probability of a new mutation eventually becoming fixed is P = 1/2N

Question 8

What is the rate of fixation of new mutations

Answer 8

• the rate at which new mutations are fixed in a population is mu.

Question 9

What is the time between fixation of new alleles

Answer 9

1/mu (reciprocal of the rate of fixation)

Question 10

What is the average time to fixation of a new allele

Answer 10

• time to fixation or loss depends on effective population size
• mutations that are destined to become fixed do so in 4Ne generations
• mutations that are destined to be lost are gone in (2Ne/N)ln (2N)

Question 11

What is Ne

Answer 11

effective population size - an idealized number which is usually smaller than the population count or census size because it only has successful breeders

Question 12

What is predicted gene diversity

Answer 12

at equilibrium, we can predict heterozygosity (H) as a function of population size and mutation rate: H = 4Nemu/4Nemu + 1

Question 13

What are some shortcomings of studying genetic variation with electrophoresis

Answer 13

• enzymes have variable functional constraints on their sequence characteristics
• not all proteins are enzymes
• not all amino acids are detectable by electrophoresis
• not all DNA changes cause amino acid changes
• proteins are unstable and difficult to work with

Question 14

How can we quantifying DNA sequence variation

Answer 14

• useful to quantify variation at the level of nucleotide
• simplest way to calculate the proportion of nucleotide sites that differ in a sample of genes
• pn = S/N
• where S = number of sites that are different, and N = number of sites compared

Question 15

How can we include the number of sequences that were observed in the sample that pn can’t

Answer 15

• if we account for the number of sequences observed we can obtain an unbiased estimate of the polymorphism per site as theta = pn/a