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 2 o 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 then almost 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 1 o 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 some system 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 Inbreeding o 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 each parent 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 Unrelated o Random Genetic Drift individuals 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 and don 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 Random fluctuations in allele frequency due to sampling small numbers of gametes 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 generations spread to the boundaries allele A1 or A2 until they re fixed for an allele S2 p The variance in allele frequency from one generation to the next pq allele frequencies 2N population size When p q that s when the numerator is the biggest Nearly fixed for an allele means not much room for missampling Ne size of an