Population Genetics Lecture Notes PDF

Population Genetics Reading: Chapter 23 Review genotypes, phenotypes, alleles & mutation Dynamic Study Module: Chapter 23  First Week Feedback START: List one or more things I am not doing in the course that you would like me to do. STOP: List one or more things I am do...

Population Genetics Reading: Chapter 23 Review genotypes, phenotypes, alleles & mutation Dynamic Study Module: Chapter 23  First Week Feedback START: List one or more things I am not doing in the course that you would like me to do. STOP: List one or more things I am doing in the course you think I should stop doing. CONTINUE: List one or more things that I am doing in the course that you think is going well and I should continue.  Key Concepts Populations evolve, not individuals Genetic variation (mutation) makes evolution possible The Hardy-Weinberg equation tests if a population is evolving (= change in allele frequencies) Natural selection, genetic drift, and gene flow can alter allele frequencies in a population Natural selection is the only mechanism that consistently causes adaptive evolution  Evolution: What is it? How do we study it? Evolution Where does all this biological diversity come from? Where does all this biological diversity come from? Where does all this biological diversity come from? EVOLUTION (”big-picture” definition): All organisms on Earth are related by common ancestry and they have changed over time, and continue to change, via the major evolutionary forces.  Evolution at the ”small-scale” Evolution (”small-scale” definition): change in allele frequencies in a population from one generation to the next. Evolution and Population Genetics Evolution (”small-scale” definition): change in allele frequencies in a population from one generation to the next. Population genetics: ▪ Combines genetics and evolutionary biology to make predictions/inferences about populations ▪ We use math and models to predict the proportions of genotypes (e.g., A1/A1) of a whole population of offspring from one generation to the next…  The Smallest Unit of Evolution Microevolution is a change in allele frequencies in a population over generations Three mechanisms cause allele frequency change: – Natural selection – Genetic drift – Gene flow Only natural selection consistently causes adaptive evolution Populations Evolve, Not Individuals  The Hardy-Weinberg Equation can be used to Test Whether a Population is Evolving The first step in testing whether evolution is occurring in a population is to clarify what we mean by a population What is a population?  Genetic Variation Evolution acts on heritable traits that vary between organisms (genetic variation) Mendel discovered genes are basis for heritability http://biologos.org/blogs/dennis-venema-letters-to-the-duchess/encode-and-junk-dna-part-1-all-good-concepts-are-fuzzy  Genetic Variation (cont’d) Alternative versions of genes (alleles) account for variations in inherited characters – Organisms inherit 2 copies of Wikipedia each gene (1 from each parent) – If alleles differ, dominant determines appearance and recessive has no noticeable effect – Alleles separate during gamete formation, end up in different Figure 14.2 gametes (Law of Segregation)  Reminder: not all genetic variation results in phenotypic variation  Genetic Variation (cont’d) Sources of genetic variation: Sexual recombination = novel genotypes (Law of Independent Assortment) – No change in allele frequencies, but novel combinations natural selection can act upon Animation: Genetic Variation from Sexual Recombination Animation: Genetic Variation from Sexual Recombination Right-click slide / select “Play” Copyright © 2025 Pearson Canada, Inc. 23 - 18  Genetic Variation (cont’d) Sources of genetic variation: Sexual recombination = novel genotypes (Law of Independent Assortment) – No change in allele frequencies, but novel combinations natural selection can act upon Mutations = variation in alleles – Rare – Mostly in somatic cells (not passed on to next generation)  Review (Chap 17): Mutations Generate genetic variation by generating new alleles (e.g. point mutation)  Gene Pools and Allele Frequencies A population is a localized group of individuals capable of interbreeding and producing fertile offspring A gene pool consists of all the alleles for all loci in a population A locus is fixed if all individuals in a population are homozygous for the same allele  Allele Frequencies If there are two or more alleles for a locus, diploid individual may be either homozygous or heterozygous The frequency of an allele in population can be calculated: – For diploid organisms, the total number of alleles at a locus is the total number of individuals times 2 – The total number of dominant alleles at a locus is 2 alleles for homozygous dominant individual plus 1 allele for each heterozygous individual; the same logic applies for recessive alleles  Allele Frequencies By convention, if there are 2 alleles at a locus, p and q are used to represent their frequencies Frequency of all alleles in a population will add up to 1 – That is, p + q = 1  Allele frequencies What are the frequencies of the A1 and A2 allele, in this population?  Hardy-Weinberg Equilibrium In a given population where gametes contribute to the next generation randomly, and Mendelian inheritance occurs, allele and genotype frequencies remain constant from generation to generation Such a population is in Hardy-Weinberg equilibrium  Examples of recent applications of Hardy- Weinberg Equilibrium model  The Hardy-Weinberg Principle If p and q represent relative frequencies of only two possible alleles in a population at a particular locus, then – p2 + 2pq + q2 = 1 – where p2 and q2 represent the frequencies of the homozygous genotypes, and 2pq represents frequency of the heterozygous genotype Hardy-Weinberg equation calculates the expected frequency of genotypes from allele frequency So our whole p q population can be described as: p q  Allele frequencies What are the frequencies of the A1 and A2 allele, in this population? A1 : 25 copies A2 : 17 copies If p + q = 1, does that mean the population is in Hardy-Weinberg equilibrium? Example from previous slide: Total number of alleles in the population = 25 + 17 = 42 - freq(A1): 25/42 = ~0.60 A. Yes - freq(A2): 17/42 = ~0.40 B. No If our calculations are correct, the two frequencies should add up to 1: 0.60 + 0.40 = 1  Genotype frequencies If we assume mating is random, and allele frequencies don’t change: A1: 25 copies A2: 17 copies A1 A2 (0.6) (0.4) A1 (0.6) A2 (0.4)  Genotype frequencies If we assume mating is random, and allele frequencies don’t change: A1/A1: A1 A2 (0.6) (0.4) A1/A2: A1 (0.6) A1/A2: A2 (0.4)  Using “p” and “q” If we assume mating is random, and allele frequencies don’t change: A1/A1: 0.36 = p2 p q (0.6) (0.4) A1/A2: 0.48 = 2 × pq p (0.6) p×p p×q A1/A2: 0.16 = q2 q (0.4) p×q q×q If p2 + 2pq + q2 = 1, does that mean the population is in Hardy-Weinberg equilibrium? Example from previous slide: - freq(A1) = p = 0.60 - freq(A2) = q = 0.40 A. Yes Therefore: - freq(A1/A1) = p2 = 0.36 B. No - freq(A1/A2) = 2pq = 0.48 - freq(A2/A2) = q2 = 0.16 If our calculations are correct, the three frequencies should add up to 1: 0.36 + 0.48 + 0.16 = 1 What assumptions are we making when we predict offspring genotype frequencies this way? HWE Model assumptions:  IF the observed genotype frequencies were different from what we expected, does this mean that the population evolved? Maybe, but we need to know if that difference persists into the next generation. We can say this population is not in Hardy Weinberg equilibrium → means one of the assumptions is not met. Evolution: The change in allele frequencies at a genetic locus in a population from one generation to the next. Example: 300 flowers incompletely dominant for color – 40 homozygous dominant (CRCR) – 40 heterozygous (CRCW) – 220 homozygous recessive (CWCW) Number of alleles: – 300 individuals = ____alleles – CR = – CW = Allele frequency: – frequency of dominant allele CR = p = – frequency of recessive allele CW = q = – p+q=1  Hardy-Weinberg Principle Hardy-Weinberg equation calculates the expected frequency of genotypes from allele frequency p2 + 2pq + q2 = 1 CRCR =1 =1 Expected number of genotypes: R W (________) homozygous dominant (CRCR) = CC (________) heterozygous (CRCW) = (________) homozygous recessive (CWCW) = Observed number of genotypes : ___ homozygous dominant (CRCR) CWCW ___ heterozygous (CRCW) ___ homozygous recessive (CWCW)  How do we know if what we observed is different enough from what we expected? Scientists use statistics to decide if the differences between observed and expected are greater than can be expected by chance alone. Test is called a Chi-square (2 ) test Example: Genotype Observed frequencies Expected frequencies BB 0.385 0.464 Bb 0.594 0.434 bb 0.021 0.102 If n=1000 individuals, we observed 21 bb individuals, but expected to see 102 bb individuals. You were expecting 5x more bb!  Hardy-Weinberg Principle (cont’d) H-W principle: frequencies of alleles and genotypes in a population remain constant from generation to generation – If gametes contribute to the next generation randomly, allele frequencies will not change – Describes a population that is not evolving If principle does not hold, the population is evolving OR one of the assumptions of the principle is not being met  Hardy-Weinberg Principle (cont’d) In real populations, allele and genotype frequencies do change over time 5 conditions for non-evolving populations rarely met in nature 1. No mutations 2. Random mating 3. Large population size 4. No gene flow 5. No natural selection  Evolution Three major factors alter allele frequencies and bring about most evolutionary change: – Natural selection – Genetic drift – Gene flow  Natural Selection Acts on phenotype – Favors certain genotypes by acting on phenotypes Adaptive evolution  Evolution by natural selection requires: reproduction variation in traits (differences in phenotypes) trait differences are heritable (genetic basis) variation in fitness (not all individuals succeed) and this variation is related to trait differences YouTube: Natural Selection  Relative Fitness The phrases “struggle for existence” and “survival of the fittest” are misleading as they imply direct competition among individuals Reproductive success is generally more subtle and depends on many factors  Relative Fitness Relative fitness is the contribution an individual makes to the gene pool of the next generation, relative to the contributions of other individuals Selection favours certain genotypes by acting on phenotypes of certain individuals  Directional, Disruptive, and Stabilizing Selection There are three modes of selection: – Directional selection favours individuals at one end of the phenotypic range – Disruptive selection favours individuals at both extremes of the phenotypic range – Stabilizing selection favours intermediate variants and acts against extreme phenotypes  Evolution (cont’d) Natural Selection (cont’d) Figure 23.13 Directional selection: extreme phenotype favoured Disruptive selection: phenotypic extremes favoured Stabilizing selection: intermediate phenotypes favoured  The Evolution of Populations THINK-PAIR-SHARE Peppered moths were predominately light coloured. During Industrial Revolution their habitat was darkened by soot so light coloured moths stood out and were easily preyed upon. What type of selection is this an example of?  Evolution (cont’d) Genetic Drift Chance changes in allele frequencies – Reduces genetic variation through loss of alleles – Important in small populations Figure 23.9  Evolution (cont’d) Genetic Drift (cont’d) Small populations result from: The founder effect – A few individuals isolated from larger population – Allele frequencies in founder population different from parent population The bottleneck effect – Sudden reduction in population size – Resulting gene pool different from parent population  The Bottleneck Effect Figure 23.10 The bottleneck effect. Copyright © 2025 Pearson Canada, Inc. 23 - 52 Effects of Genetic Drift: A Summary 1. Genetic drift is significant in small populations 2. Genetic drift can cause allele frequencies to change at random 3. Genetic drift can lead to a loss of genetic variation within populations 4. Genetic drift can cause harmful alleles to become fixed  Evolution (cont’d) Gene Flow Movement of alleles among populations due to movement of fertile individuals or gametes (e.g. pollen) Reduces variation among populations over time  Example Question In a non-evolving population, 9% of the individuals are homozygous for the recessive allele. What is the frequency of heterozygous individuals in the population? What do we know? …  Example Question In a non-evolving population, 9% of the individuals are homozygous for the recessive allele. What is the frequency of heterozygous individuals in the population? p2 + 2pq + q2 = 1 p+q=1 What do we know? … – q2 = 0.09 (frequency of homozygous recessive) q = √0.09 = 0.3 (frequency of recessive allele) – p+ q = 1 p + 0.3 = 1 p = 1 – 0.3 = 0.7 (frequency of dominant allele in population) – Frequency of heterozygotes = 2pq = 2(0.7)(0.3) = 0.42 FOR NEXT CLASS READ Chapter 24