BSCI222 – Lecture 12 (10/15/13)- Chapter 25, Population Genetics- Early work in population genetics happened at the same time as early work in Mendellian. Mendel was rediscovered in 1901, and almost immediately the genetic field was split.o Morgan’s lab (mutants in drosophila, genetic maps -> structure of DNA, molecular biology, one thread of genetics). o But people with agricultural genetics didn’t find simple Mendellian traits, worked in a more quantitative field, developed statistics a lot, studied how alleles segregate in populations. o These 2 subfields remained largely separate for over a hundred years, until molecular techniques for maps and genomics.- How do alleles pass through populations? (like how genes pass through families)o Frequency of allele A1 = p, frequency of allele A2 = q. (no implication of dominance or recessiveness)o Do not confuse dominance with frequency! The most frequent allele might be recessive to a dominant allele that is rarer- Calculate allele frequencies from genotypic frequencies:o Total number of individuals (100 individuals = 200 alleles, diploid). P = frequency A = (2*(AA) + Aa)/total number of individuals.o 1 = p + q- Hardy-Weinberg expectation:o How do alleles come together in a population? Is it random? Frequency of alleles in males versus in females (normally same frequency in each sex as in total population)o fAA = p^2, fAa = pq, faa = q^2o This is how we expect gametes to combine at random in the population. If not conforming, have to go find why.o Genotypic proportions vary with allele frequency. If high frequency for p, A, thenalmost all people in the population are homozygous for AA. Right in the middle, get 50% Aa, 25% AA, and 25% aa. o (p+q)^2 = p^2 + 2pq + q^2 = 1o How would you expand the H-W expectation for 3 alleles? (p+q+r)^2 (squared because diploid) = p^2 + 2pq + q^2 + 2qr + r^2 + 2pr = 1 (TEST)o 2 alleles in a triploid organism? (p+q)^3. Ploidy is in the exponent, variables are alleles.o Sex chromosomes: X-linked alleles, females are normal, but males are either just p or just q, because always have the Y. o First thing you do in a population genetics study is check to see if the Hardy-Weinberg expectation is being met, are they mating randomly or is there somesystem underneath. Generate expected frequencies for the amount of individuals and ploidy and number of alleles, compare to observed frequencies. Chi-square test for significance [(observed-expected) ^2 /expected]. Mendellian genetics, 2 degrees of freedom. BUT, here, generating hypothesis from allele frequencies from data, so losing another degree of freedom: 1 degree of freedom. Chi-square critical p value is 0.05, at df = 1 is 3.84. If the sum of deviations are smaller than 3.84, then they are expected by chance and meet the Hardy-Weinberg expectation,accept the null hypothesis, meaning that the population is conforming to random gamete mating. Don’t have to go looking for an explanation for a deviation. What would cause a deviation? What sorts of natural forces?- Non-random mating, migration, mutation in one direction, natural disaster (if it wipes out indiscriminately then no, but if it is differential killing then yes). - The 4 forces: random genetic drift, mutation, migration, and selection. Inbreeding does not alter allele frequencies, only how the alleles are combined in the genotype.- Inbreedingo Selfing: organism produces male and female gametes and they combine. Extreme case. AA x AA -> AA offspring, p^2. Aa x Aa -> AA, Aa, and aa offspring -> after one generation of selfing, lost half of the heterozygosity. 2pq. aa x aa -> aa offspring, q^2. Always decreases heterozygosity, increases homozygosity. More AA and aa frequency, less and less Aa until no Aa at all. Losing half of the Aa, heterozygosity, every generation. Ultimately wind up with population composed of only the homozygotes. Only takes about 6 generation of selfing to make an organism completely homozygous. Mating of siblings: get to complete homozygosity in 14-16 generations. - Want to make an inbred line of anything, have to go about twenty generations to makes sure that the mice (or whatever) are completely homozygous and can be a research tool because genetically identical. Mating of first cousins: After about 15 generations, gone about a third of the way to homozygosity.  F is the inbreeding coefficient; it is the probability that 2 alleles in an individual are identical by descent, came from a common ancestral allele. Have to follow up through the pedigree. What is the chance that an individual inherits two identical alleles through this pedigree? How do you get an F of 0.25 from brother-sister matings? 2 alleles in eachparent, ¼. Population geneticists try to measure F, in part with deviation from the H-W expectation, can indicate that there is some inbreeding going on. Famous study: after dropping bombs on Japan in WWII, funded a long term study in Japan to see effects of radiation on breeding. Unrelatedindividuals with zero inbreeding, had a mortality rate of about 8%. Individuals whose parents were second cousins had a 10% mortality rate. Parents who were first cousins, children had an 11.4% mortality rate through 12 year olds. Deleterious alleles because made homozygous through inbreeding.  These effects of inbreeding are seen in all species. Corn in the U.S. is all hybrid, crossing homozygous lines. F close to 1, tiny corn ears; F close to 0, bigger. We all have a few mutations in a few enzymes; if we make those mutations homozygous, then we don’t have that enzyme activity anddon’t grow as well. Inbreeding depression. Terrestrial slug is fully inbred, completely homozygous, self-fertilizing hermaphrodite and still fully capable of chewing up lawns. But most species can’t do this.  Inbreeding did NOT change allele frequencies, only how they were combined in genotypes.o Random Genetic Drift Random fluctuations in allele frequency due to sampling small numbers ofgametes each generation. Flipping a coin simulates a population where p = q, 0.5 chance of getting heads and tails. But getting a small sample, probably won’t get data that perfect. The most likely result when you flip a coin is that you won’t get 50/50. Same thing in a population, only sampling finite number of alleles, not perfect sampling, not infinite.  Study with drosophila eye color over nineteen generations: start clustered in the middle around 0.5, over the