1 27 2014 CHAPTER 3 Population Genetics and Evolutionary Forces M U T A T I O N G E N E F L O W G E N E T I C D R I F T N A T U R A L S E L E C T I O N Understanding of Population Genetics is Essential Processes of evolution Origin of genetic diversity Maintenance and loss of variation Genetic adaptation Population Genetics Population Genetics What is a Population Breeding Populations are groups of organisms that tend to choose mates from within the group and share a common gene pool Gene pool genes possessed by a population Human populations are most often defined on the basis of geographic and political boundaries Linguistics Ethnicity Religion A potential problem is determining the difference between total census and the breeding population Once a population is defined it is necessary to determine frequencies of genotypes and alleles within the population Genotype Frequencies Let s Try It Genotype Frequencies and Alleles A genotype frequency is a measure of the relative proportions of different genotypes Equal to number of individuals per genotype total population An allele frequency is a measure of the relative proportions of alleles within a population Equal to number of each allele total number of alleles Let us examine Mendel s Pea population In the P1 generation assume we have 300 plants 150 yellow 150 green P1 Genotype frequency Yellow YY 150 300 0 5 Green yy 150 300 0 5 F1 Allele frequency Y 300 600 0 5 y 300 600 0 5 Y Yy Yy Y Yy Yy y y 1 1 27 2014 Let s Try It Let us examine Mendel s Pea population In the F1 generation assume we have 300 plants F1 Genotype frequency Yy 300 300 1 Allele frequency Y 300 600 0 5 y 300 600 0 5 Remember that evolution is the change in allele frequency across time F1 y y Y Yy Yy Y Yy Yy Importance of determining gene frequencies Characterize genetic variation of a population Compare gene pools Common origin migration isolation Use in models of evolutionary change Signatures of selection gene flow genetic drift and mutation Utility of SNP in GWAS Remember we want to include polymorphisms not mutations Check for genotyping errors Hardy Weinberg Equilibrium Mathematics of Probability Mathematical statement relating observed genotype frequencies to the expected genotype frequencies in the next generation Independently developed in 1908 by GH Hardy a mathematician and W Weinberg a physician The Hardy Weinberg model makes certain assumptions Random mating with respect to the gene of the study Infinite population size Random sampling No evolution gene flow mutation genetic drift selection Observed change means that one or more assumptions are incorrect Assume we have a two allele system with the frequency of each allele represented by p and q p q 1 If we want to examine genotype frequencies we must consider the combination of p and q 2 alleles combined 2 at a time 22 p q 2 12 p q p q 1 FOIL p2 pq qp q2 1 p2 2pq q2 1 Test of HWE Significance Population Genetics Investigators are often interested in testing the statistical significance of HWE After data collection we can apply Pearson s chi square test of significance 2 Observed Expected 2 Expected 1 degree of freedom test 2 needs to be 3 85 df genotypes number of alleles Null hypothesis Alleles are segregating independently HWE Hardy Weinberg Equilibrium The Hardy Weinberg equilibrium model is a mathematical statement relating allele frequencies to the expected genotype frequencies in the next generation The Hardy Weinberg model makes certain assumptions Random mating with respect to the locus of the study Infinite population size Random sampling No evolution gene flow mutation genetic drift selection Observed change means that one or more assumptions are incorrect 2 Population Genetics Hardy Weinberg Equilibrium Hardy Weinberg Equilibrium The population may not be in Hardy Weinberg equilibrium for two basic reasons the effects of evolutionary forces mutation natural selection genetic drift or gene flow or nonrandom mating Evolutionary forces are the only mechanisms that can cause allele frequencies to change over time Nonrandom mating involves patterns of mate choice that influence the distributions of genotype and phenotype frequencies Genotype frequencies can change without altering allele frequencies This is NOT evolution HWE Non random mating Inbreeding Increases the Probability of Expressing Rare Recessive Alleles Inbreeding is a form or nonrandom mating that occurs when there is mating between biologically related individuals Genetic effects of inbreeding are often harmful but among humans overall rates of inbreeding are relatively low due to high mobility and cultural rules discouraging or prohibiting it Increases homozygosity within a population Endogamy the practice of marrying within one s socially defined group Often leads to inbreeding Assortative mating is another form of nonrandom mating that occurs when there is mating based on phenotypic similarity positive or dissimilarity negative e g blondes choosing blondes Nonrandom mating does not cause evolution but it can affect the rate of evolutionary change Non Random Mating Population Genetics 1 27 2014 3 Mutation N E W V A R I A T I O N The Evolutionary Forces Mutation Mutation introduces new alleles into a population and changes the frequency of different alleles over time If no further evolutionary change occurs allele frequencies will remain the same in future generations Mutations can also occur in reverse direction mutating back to the original form This is rare Mutations are vital to evolution but rates are low and by themselves they do not lead to major changes in allele frequencies Mutations Characteristics of Mutation Mutations are changes in the genetic code and the ultimate Must occur in the gametes to have an evolutionary effect source of all genetic variation Mutations can take place in any cell of the body To have evolutionary importance the mutation must occur in a sex cell Mutations are random There is no way of predicting when they will take place Mutations can have different effects depending on the specific type of mutation and the environment Mutations are sometimes advantageous leading to changes that improve the survival and reproduction of organisms A substance or agent that causes genetic mutations or chemical alteration of the genetic material DNA Ethidium bromide UV radiation X rays Caused by Mutagens Replication error Age heat Carcinogens Any cancer causing agent Radiation Teratogens A substance that