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Population Genetics 1 1 Population Genetics 1 1

The Gene Pool • Members of a species can interbreed & produce fertile offspring The Gene Pool • Members of a species can interbreed & produce fertile offspring Species have a shared gene pool Gene pool – all of the alleles of all individuals in a population • • 2 2

The Gene Pool • Different species do NOT exchange genes by interbreeding Different species The Gene Pool • Different species do NOT exchange genes by interbreeding Different species that interbreed often produce sterile or less viable offspring e. g. Mule • 3 3

Populations • A group of the same species living in an area No two Populations • A group of the same species living in an area No two individuals are exactly alike (variations) More Fit individuals survive & pass on their traits • • 4 4

Speciation • Formation of new species • One species may split into 2 or Speciation • Formation of new species • One species may split into 2 or more species A species may evolve into a new species Requires very long periods of time • • 5 5

Modern Evolutionary Thought Modern Evolutionary Thought

Modern Synthesis Theory • Combines Darwinian • • selection and Mendelian inheritance Population genetics Modern Synthesis Theory • Combines Darwinian • • selection and Mendelian inheritance Population genetics study of genetic variation within a population Emphasis on quantitative characters 7 7

Modern Synthesis Theory • 1940 s – comprehensive theory of evolution (Modern Synthesis Theory) Modern Synthesis Theory • 1940 s – comprehensive theory of evolution (Modern Synthesis Theory) Introduced by Fisher & Wright Until then, many did not accept that Darwin’s theory of natural selection could drive evolution • • S. Wright A. Fisher 8 8

Modern Synthesis Theory • Today’s theory on evolution • Recognizes that GENES are responsible Modern Synthesis Theory • Today’s theory on evolution • Recognizes that GENES are responsible for the inheritance of characteristics • Recognizes that POPULATIONS, not • individuals, evolve due to natural selection & genetic drift Recognizes that SPECIATION usually is due to the gradual accumulation of small genetic changes 9 9

Microevolution • Changes occur in gene pools due to • • • mutation, natural Microevolution • Changes occur in gene pools due to • • • mutation, natural selection, genetic drift, etc. Gene pool changes cause more VARIATION in individuals in the population This process is called MICROEVOLUTION Example: Bacteria becoming unaffected by antibiotics (resistant) 10 10

Allele Frequencies Define Gene Pools 500 flowering plants 480 red flowers 320 RR 160 Allele Frequencies Define Gene Pools 500 flowering plants 480 red flowers 320 RR 160 Rr 20 white flowers 20 rr As there are 1000 copies of the genes for color, the allele frequencies are (in both males and females): 320 x (80%) 160 x (20%) 2 (RR) + 160 x 1 (Rr) = 800 R; 800/1000 = 0. 8 R 1 (Rr) + 20 x 2 (rr) = 200 r; 200/1000 = 0. 2 r 11 11

Species & Populations • Population - a localized group of individuals of the same Species & Populations • Population - a localized group of individuals of the same species. • Species - a group of populations whose individuals have the ability to breed and produce fertile offspring. Individuals near a population center are, on average, more closely related to one another than to members of other populations. • 12 12

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Gene Pools • A population’s gene pool is the total of all genes in Gene Pools • A population’s gene pool is the total of all genes in the population at any one time. If all members of a population are homozygous for a particular allele, then the allele is fixed in the gene pool. • 14 14

The Hardy-Weinberg Theorem • Used to describe a non-evolving population. • Shuffling of alleles The Hardy-Weinberg Theorem • Used to describe a non-evolving population. • Shuffling of alleles by meiosis and random fertilization have no effect on the overall gene pool. Natural populations are NOT expected to actually be in Hardy. Weinberg equilibrium. • 15 15

The Hardy-Weinberg Theorem • Deviation from Hardy-Weinberg equilibrium usually results in evolution Understanding a The Hardy-Weinberg Theorem • Deviation from Hardy-Weinberg equilibrium usually results in evolution Understanding a non-evolving population, helps us to understand how evolution occurs • 16 16

Assumptions of the H-W Theorem 1. Large population size - small populations can have Assumptions of the H-W Theorem 1. Large population size - small populations can have chance fluctuations in allele frequencies (e. g. , fire, storm). 2. No migration - immigrants can change the frequency of an allele by bringing in new alleles to a population. 3. No net mutations - if alleles change from one to another, this will change the frequency of those alleles 17 17

Assumptions of the H-W Theorem 3. Random mating - if certain traits are more Assumptions of the H-W Theorem 3. Random mating - if certain traits are more desirable, then individuals with those traits will be selected and this will not allow for random mixing of alleles. 4. No natural selection - if some individuals survive and reproduce at a higher rate than others, then their offspring will carry those genes and the frequency will change for the next generation. 18 18

Hardy-Weinberg Equilibrium The gene pool of a non-evolving population remains constant over multiple generations; Hardy-Weinberg Equilibrium The gene pool of a non-evolving population remains constant over multiple generations; i. e. , the allele frequency does not change over generations of time. The Hardy-Weinberg Equation: 1. 0 = p 2 + 2 pq + q 2 where p 2 = frequency of AA genotype; 2 pq = frequency of Aa plus a. A genotype; q 2 = frequency of aa genotype 19 19

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But we know that evolution does occur within populations. Evolution within a species/population = But we know that evolution does occur within populations. Evolution within a species/population = microevolution. Microevolution refers to changes in allele frequencies in a gene pool from generation to generation. Represents a gradual change in a population. Causes of microevolution: 1) Genetic drift 2) Natural selection (1 & 2 are most important) 3) Gene flow 4) Mutation 22 22

1) Genetic drift = the alteration of the gene pool of a small population 1) Genetic drift = the alteration of the gene pool of a small population due to chance. Two factors may cause genetic drift: a) Bottleneck effect may lead to reduced genetic variability following some large disturbance that removes a large portion of the population. The surviving population often does not represent the allele frequency in the original population. b) Founder effect may lead to reduced variability when a few individuals from a large population colonize an isolated habitat. 23 23

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*Yes, I realize that this is not really a cheetah. 26 26 *Yes, I realize that this is not really a cheetah. 26 26

2) Natural selection As previously stated, differential success in reproduction based on heritable traits 2) Natural selection As previously stated, differential success in reproduction based on heritable traits results in selected alleles being passed to relatively more offspring (Darwinian inheritance). The only agent that results in adaptation to environment. 3) Gene flow -is genetic exchange due to the migration of fertile individuals or gametes between populations. 27 27

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4) Mutation Mutation is a change in an organism’s DNA and is represented by 4) Mutation Mutation is a change in an organism’s DNA and is represented by changing alleles. Mutations can be transmitted in gametes to offspring, and immediately affect the composition of the gene pool. The original source of variation. 29 29

Genetic Variation, the Substrate for Natural Selection Genetic (heritable) variation within and between populations: Genetic Variation, the Substrate for Natural Selection Genetic (heritable) variation within and between populations: exists both as what we can see (e. g. , eye color) and what we cannot see (e. g. , blood type). Not all variation is heritable. Environment also can alter an individual’s phenotype [e. g. , the hydrangea we saw before, and… …Map butterflies (color changes are due to seasonal difference in hormones)]. 30 30

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Variation within populations Most variations occur as quantitative characters (e. g. , height); i. Variation within populations Most variations occur as quantitative characters (e. g. , height); i. e. , variation along a continuum, usually indicating polygenic inheritance. Few variations are discrete (e. g. , red vs. white flower color). Polymorphism is the existence of two or more forms of a character, in high frequencies, within a population. Applies only to discrete characters. 32 32

Variation between populations Geographic variations are differences between gene pools due to differences in Variation between populations Geographic variations are differences between gene pools due to differences in environmental factors. Natural selection may contribute to geographic variation. It often occurs when populations are located in different areas, but may also occur in populations with isolated individuals. 33 33

Geographic variation between isolated populations of house mice. Normally house mice are 2 n Geographic variation between isolated populations of house mice. Normally house mice are 2 n = 40. However, chromosomes fused in the mice in the example, so that the diploid number has gone down. 34 34

Cline, a type of geographic variation, is a graded variation in individuals that correspond Cline, a type of geographic variation, is a graded variation in individuals that correspond to gradual changes in the environment. Example: Body size of North American birds tends to increase with increasing latitude. Can you think of a reason for the birds to evolve differently? Example: Height variation in yarrow along an altitudinal gradient. Can you think of a reason for the plants to evolve differently? 35 35

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Mutation and sexual recombination generate genetic variation a. New alleles originate only by mutations Mutation and sexual recombination generate genetic variation a. New alleles originate only by mutations (heritable only in gametes; many kinds of mutations; mutations in functional gene products most important). - In stable environments, mutations often result in little or no benefit to an organism, or are often harmful. - Mutations are more beneficial (rare) in changing environments. (Example: HIV resistance to antiviral drugs. ) b. Sexual recombination is the source of most genetic differences between individuals in a population. - Vast numbers of recombination possibilities result in varying genetic make-up. 37 37

Diploidy and balanced polymorphism preserve variation a. Diploidy often hides genetic variation from selection Diploidy and balanced polymorphism preserve variation a. Diploidy often hides genetic variation from selection in the form of recessive alleles. Dominant alleles “hide” recessive alleles in heterozygotes. b. Balanced polymorphism is the ability of natural selection to maintain stable frequencies of at least two phenotypes. Heterozygote advantage is one example of a balanced polymorphism, where the heterozygote has greater survival and reproductive success than either homozygote (Example: Sickle cell anemia where heterozygotes are resistant to malaria). 38 38

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Frequency-dependent selection = survival of one phenotype declines if that form becomes too common. Frequency-dependent selection = survival of one phenotype declines if that form becomes too common. (Example: Parasite-Host relationship. Co-evolution occurs, so that if the host becomes resistant, the parasite changes to infect the new host. Over the time, the resistant phenotype declines and a new resistant phenotype emerges. ) 40 40

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Neutral variation is genetic variation that results in no competitive advantage to any individual. Neutral variation is genetic variation that results in no competitive advantage to any individual. - Example: human fingerprints. 43 43

A Closer Look: Natural Selection as the Mechanism of Adaptive Evolution Evolutionary fitness - A Closer Look: Natural Selection as the Mechanism of Adaptive Evolution Evolutionary fitness - Not direct competition, but instead the difference in reproductive success that is due to many variables. Natural Selection can be defined in two ways: a. Darwinian fitness- Contribution of an individual to the gene pool, relative to the contributions of other individuals. And, 44 44

b. Relative fitness - Contribution of a genotype to the next generation, compared to b. Relative fitness - Contribution of a genotype to the next generation, compared to the contributions of alternative genotypes for the same locus. - Survival doesn’t necessarily increase relative fitness; relative fitness is zero (0) for a sterile plant or animal. Three ways (modes of selection) in which natural selection can affect the contribution that a genotype makes to the next generation. a. Directional selection favors individuals at one end of the phenotypic range. Most common during times of environmental change or when moving to new habitats. 45 45

Directional selection 46 46 Directional selection 46 46

Diversifying selection favors extreme over intermediate phenotypes. - Occurs when environmental change favors an Diversifying selection favors extreme over intermediate phenotypes. - Occurs when environmental change favors an extreme phenotype. Stabilizing selection favors intermediate over extreme phenotypes. - Reduces variation and maintains the current average. - Example = human birth weights. 47 47

Diversifying selection 48 48 Diversifying selection 48 48

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Natural selection maintains sexual reproduction -Sex generates genetic variation during meiosis and fertilization. -Generation-to-generation Natural selection maintains sexual reproduction -Sex generates genetic variation during meiosis and fertilization. -Generation-to-generation variation may be of greatest importance to the continuation of sexual reproduction. -Disadvantages to using sexual reproduction: Asexual reproduction produces many more offspring. -The variation produced during meiosis greatly outweighs this disadvantage, so sexual reproduction is here to stay. 50 50

All asexual individuals are female (blue). With sex, offspring = half female/half male. Because All asexual individuals are female (blue). With sex, offspring = half female/half male. Because males don’t reproduce, the overall output is lower for sexual reproduction. 51 51

Sexual selection leads to differences between sexes a. Sexual dimorphism is the difference in Sexual selection leads to differences between sexes a. Sexual dimorphism is the difference in appearance between males and females of a species. -Intrasexual selection is the direct competition between members of the same sex for mates of the opposite sex. -This gives rise to males most often having secondary sexual equipment such as antlers that are used in competing for females. -In intersexual selection (mate choice), one sex is choosy when selecting a mate of the opposite sex. -This gives rise to often amazingly sophisticated secondary sexual characteristics; e. g. , peacock feathers. 52 52

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Natural selection does not produce perfect organisms a. Evolution is limited by historical constraints Natural selection does not produce perfect organisms a. Evolution is limited by historical constraints (e. g. , humans have back problems because our ancestors were 4 -legged). b. Adaptations are compromises. (Humans are athletic due to flexible limbs, which often dislocate or suffer torn ligaments. ) c. Not all evolution is adaptive. Chance probably plays a huge role in evolution and not all changes are for the best. d. Selection edits existing variations. New alleles cannot arise as needed, but most develop from what already is present. 55 55

Genes Within Populations Genes Within Populations

Gene Variation is Raw Material Natural selection and evolutionary change Some individuals in a Gene Variation is Raw Material Natural selection and evolutionary change Some individuals in a population possess certain inherited characteristics that play a role in producing more surviving offspring than individuals without those characteristics. The population gradually includes more individuals with advantageous characteristics. 57 57

Gene Variation In Nature Measuring levels of genetic variation blood groups – 30 blood Gene Variation In Nature Measuring levels of genetic variation blood groups – 30 blood grp genes Enzymes – 5% heterozygous Enzyme polymorphism A locus with more variation than can be explained by mutation is termed polymorphic. Natural populations tend to have more polymorphic loci than can be accounted for by mutation. 15% Drosophila 5 -8% in vertebrates 58 58

Hardy-Weinberg Principle Population genetics - study of properties of genes in populations blending inheritance Hardy-Weinberg Principle Population genetics - study of properties of genes in populations blending inheritance phenotypically intermediate (phenotypic inheritance) was widely accepted new genetic variants would quickly be diluted 59 59

Hardy-Weinberg Principle Hardy-Weinberg - original proportions of genotypes in a population will remain constant Hardy-Weinberg Principle Hardy-Weinberg - original proportions of genotypes in a population will remain constant from generation to generation Sexual reproduction (meiosis and fertilization) alone will not change allelic (genotypic) proportions. 60 60

Hardy-Weinberg Equilibrium Population of cats n=100 16 white and 84 black bb = white Hardy-Weinberg Equilibrium Population of cats n=100 16 white and 84 black bb = white B_ = black Can we figure out the allelic frequencies of individuals BB and Bb? 61 61

Hardy-Weinberg Principle Necessary assumptions Allelic frequencies would remain constant if… population size is very Hardy-Weinberg Principle Necessary assumptions Allelic frequencies would remain constant if… population size is very large random mating no mutation no gene input from external sources no selection occurring 62 62

Hardy-Weinberg Principle Calculate genotype frequencies with a binomial expansion (p+q)2 = p 2 + Hardy-Weinberg Principle Calculate genotype frequencies with a binomial expansion (p+q)2 = p 2 + 2 pq + q 2 p 2 = individuals homozygous for first allele 2 pq = individuals heterozygous for alleles q 2 = individuals homozygous for second allele 63 63

Hardy-Weinberg Principle 2 2 p + 2 pq + q and p+q = 1 Hardy-Weinberg Principle 2 2 p + 2 pq + q and p+q = 1 (always two alleles) 16 cats white = 16 bb then (q 2 = 0. 16) This we know we can see and count!!!!! If p + q = 1 then we can calculate p from q 2 Q = square root of q 2 = q √. 16 q=0. 4 p + q = 1 then p =. 6 (. 6 +. 4 = 1) P 2 =. 36 All we need now are those that are heterozygous (2 pq) (2 x. 6 x. 4)=0. 48. 36 +. 48 +. 16 64 64

Hardy-Weinberg Equilibrium 65 65 Hardy-Weinberg Equilibrium 65 65

Five Agents of Evolutionary Change Mutation rates are generally so low they have little Five Agents of Evolutionary Change Mutation rates are generally so low they have little effect on Hardy-Weinberg proportions of common alleles. ultimate source of genetic variation Gene flow movement of alleles from one population to another tend to homogenize allele frequencies 66 66

Five Agents of Evolutionary Change Nonrandom mating assortative mating - phenotypically similar individuals mate Five Agents of Evolutionary Change Nonrandom mating assortative mating - phenotypically similar individuals mate Causes frequencies of particular genotypes to differ from those predicted by Hardy-Weinberg. 67 67

Five Agents of Evolutionary Change Genetic drift – statistical accidents. Frequencies of particular alleles Five Agents of Evolutionary Change Genetic drift – statistical accidents. Frequencies of particular alleles may change by chance alone. important in small populations founder effect - few individuals found new population (small allelic pool) bottleneck effect - drastic reduction in population, and gene pool size 68 68

Genetic Drift - Bottleneck Effect 69 69 Genetic Drift - Bottleneck Effect 69 69

Five Agents of Evolutionary Change Selection – Only agent that produces adaptive evolutionary change Five Agents of Evolutionary Change Selection – Only agent that produces adaptive evolutionary change artificial - breeders exert selection natural - nature exerts selection variation must exist among individuals variation must result in differences in numbers of viable offspring produced variation must be genetically inherited natural selection is a process, and evolution is an outcome 70 70

Five Agents of Evolutionary Change Selection pressures: avoiding predators matching climatic condition pesticide resistance Five Agents of Evolutionary Change Selection pressures: avoiding predators matching climatic condition pesticide resistance 71 71

Measuring Fitness is defined by evolutionary biologists as the number of surviving offspring left Measuring Fitness is defined by evolutionary biologists as the number of surviving offspring left in the next generation. relative measure Selection favors phenotypes with the greatest fitness. 72 72

Interactions Among Evolutionary Forces Levels of variation retained in a population may be determined Interactions Among Evolutionary Forces Levels of variation retained in a population may be determined by the relative strength of different evolutionary processes. Gene flow versus natural selection Gene flow can be either a constructive or a constraining force. Allelic frequencies reflect a balance between gene flow and natural selection. 73 73

Natural Selection Can Maintain Variation Frequency-dependent selection Phenotype fitness depends on its frequency within Natural Selection Can Maintain Variation Frequency-dependent selection Phenotype fitness depends on its frequency within the population. Negative frequency-dependent selection favors rare phenotypes. Positive frequency-dependent selection eliminates variation. Oscillating selection Selection favors different phenotypes at different times. 74 74

Heterozygote Advantage Heterozygote advantage will favor heterozygotes, and maintain both alleles instead of removing Heterozygote Advantage Heterozygote advantage will favor heterozygotes, and maintain both alleles instead of removing less successful alleles from a population. Sickle cell anemia Homozygotes exhibit severe anemia, have abnormal blood cells, and usually die before reproductive age. Heterozygotes are less susceptible to malaria. 75 75

Sickle Cell and Malaria 76 76 Sickle Cell and Malaria 76 76

Forms of Selection Disruptive selection Selection eliminates intermediate types. Directional selection Selection eliminates one Forms of Selection Disruptive selection Selection eliminates intermediate types. Directional selection Selection eliminates one extreme from a phenotypic array. Stabilizing selection Selection acts to eliminate both extremes from an array of phenotypes. 77 77

Kinds of Selection 78 78 Kinds of Selection 78 78

Selection on Color in Guppies are found in small northeastern streams in South America Selection on Color in Guppies are found in small northeastern streams in South America and in nearby mountainous streams in Trinidad. Due to dispersal barriers, guppies can be found in pools below waterfalls with high predation risk, or pools above waterfalls with low predation risk. 79 79

Evolution of Coloration in Guppies 80 80 Evolution of Coloration in Guppies 80 80

Selection on Color in Guppies High predation environment - Males exhibit drab coloration and Selection on Color in Guppies High predation environment - Males exhibit drab coloration and tend to be relatively small and reproduce at a younger age. Low predation environment - Males display bright coloration, a larger number of spots, and tend to be more successful at defending territories. In the absence of predators, larger, more colorful fish may produce more offspring. 81 81

Evolutionary Change in Spot Number 82 82 Evolutionary Change in Spot Number 82 82

Limits to Selection Genes have multiple effects pleiotropy Evolution requires genetic variation Intense selection Limits to Selection Genes have multiple effects pleiotropy Evolution requires genetic variation Intense selection may remove variation from a population at a rate greater than mutation can replenish. thoroughbred horses Gene interactions affect allelic fitness epistatic interactions 83 83

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Population genetics • genetic structure of a population • alleles • genotypes group of Population genetics • genetic structure of a population • alleles • genotypes group of individuals of the same species that can interbreed Patterns of genetic variation in populations Changes in genetic structure through time 85 85

Describing genetic structure • genotype frequencies • allele frequencies rr = white Rr = Describing genetic structure • genotype frequencies • allele frequencies rr = white Rr = pink RR = red 86 86

Describing genetic structure • genotype frequencies • allele frequencies 200 white 500 pink genotype Describing genetic structure • genotype frequencies • allele frequencies 200 white 500 pink genotype frequencies: 200/1000 = 0. 2 rr 500/1000 = 0. 5 Rr 300 red total = 1000 flowers 300/1000 = 0. 3 RR 87 87

Describing genetic structure • genotype frequencies • allele frequencies 200 rr = 400 r Describing genetic structure • genotype frequencies • allele frequencies 200 rr = 400 r 500 Rr= 500 r = 500 R 300 RR= 600 R allele frequencies: 900/2000 = 0. 45 r 1100/2000 = 0. 55 R total = 2000 alleles 88 88

for a population with genotypes: calculate: Genotype frequencies 100 GG 160 Gg 140 gg for a population with genotypes: calculate: Genotype frequencies 100 GG 160 Gg 140 gg Phenotype frequencies Allele frequencies 89 89

for a population with genotypes: 100 GG 160 Gg calculate: Genotype frequencies 260 100/400 for a population with genotypes: 100 GG 160 Gg calculate: Genotype frequencies 260 100/400 = 0. 25 GG 0. 65 160/400 = 0. 40 Gg 140/400 = 0. 35 gg Phenotype frequencies 260/400 = 0. 65 green 140/400 = 0. 35 brown 140 gg Allele frequencies 360/800 = 0. 45 G 440/800 = 0. 55 g 90 90

another way to calculate allele frequencies: Genotype frequencies 100 GG 160 Gg 0. 25 another way to calculate allele frequencies: Genotype frequencies 100 GG 160 Gg 0. 25 GG 0. 40 Gg 0. 35 gg G 0. 25 G 0. 40/2 = 0. 20 g 0. 35 Allele frequencies 140 gg 360/800 = 0. 45 G 440/800 = 0. 55 g OR [0. 25 + (0. 40)/2] = 0. 45 [0. 35 + (0. 40)/2] = 0. 65 91 91

Population genetics – Outline ü What is population genetics? üCalculate - genotype frequencies - Population genetics – Outline ü What is population genetics? üCalculate - genotype frequencies - allele frequencies Why is genetic variation important? How does genetic structure change? 92 92

Genetic variation in space and time Frequency of Mdh-1 alleles in snail colonies in Genetic variation in space and time Frequency of Mdh-1 alleles in snail colonies in two city blocks 93 93

Genetic variation in space and time Changes in frequency of allele F at the Genetic variation in space and time Changes in frequency of allele F at the Lap locus in prairie vole populations over 20 generations 94 94

Genetic variation in space and time Why is genetic variation important? potential for change Genetic variation in space and time Why is genetic variation important? potential for change in genetic structure • adaptation to environmental change - conservation • divergence of populations - biodiversity 95 95

Why is genetic variation important? variation global warming survival EXTINCTION!! no variation 96 96 Why is genetic variation important? variation global warming survival EXTINCTION!! no variation 96 96

Why is genetic variation important? north south variation north south no variation 97 97 Why is genetic variation important? north south variation north south no variation 97 97

Why is genetic variation important? north south divergence variation north south no variation NO Why is genetic variation important? north south divergence variation north south no variation NO DIVERGENCE!! 98 98

Natural selection Resistance to antibacterial soap Generation 1: 1. 00 not resistant 0. 00 Natural selection Resistance to antibacterial soap Generation 1: 1. 00 not resistant 0. 00 resistant 99 99

Natural selection Resistance to antibacterial soap Generation 1: 1. 00 not resistant 0. 00 Natural selection Resistance to antibacterial soap Generation 1: 1. 00 not resistant 0. 00 resistant 100

Natural selection Resistance to antibacterial soap Generation 1: 1. 00 not resistant 0. 00 Natural selection Resistance to antibacterial soap Generation 1: 1. 00 not resistant 0. 00 resistant Generation 2: 0. 96 not resistant 0. 04 resistant mutation! 101

Natural selection Resistance to antibacterial soap Generation 1: 1. 00 not resistant 0. 00 Natural selection Resistance to antibacterial soap Generation 1: 1. 00 not resistant 0. 00 resistant Generation 2: 0. 96 not resistant 0. 04 resistant Generation 3: 0. 76 not resistant 0. 24 resistant 102

Natural selection Resistance to antibacterial soap Generation 1: 1. 00 not resistant 0. 00 Natural selection Resistance to antibacterial soap Generation 1: 1. 00 not resistant 0. 00 resistant Generation 2: 0. 96 not resistant 0. 04 resistant Generation 3: 0. 76 not resistant 0. 24 resistant Generation 4: 0. 12 not resistant 0. 88 resistant 103

Natural selection cause populations to diverge north south divergence 104 Natural selection cause populations to diverge north south divergence 104

Selection on sickle-cell allele Hb. S – abnormal ß hemoglobin low very fitness sickle-cell Selection on sickle-cell allele Hb. S – abnormal ß hemoglobin low very fitness sickle-cell anemia Hb. A – normal ß hemoglobin intermed. fitness vulnerable to malaria Hb. AHb. S – both ß hemoglobins resistant to malaria high fitness Selection favors heterozygotes (Hb. AHb. S ). Both alleles maintained in population (Hb. S at low level 105

How does genetic structure change? • mutation • migration genetic change by chance alon How does genetic structure change? • mutation • migration genetic change by chance alon • natural selection • genetic drift • sampling error • misrepresentation • small populations • non-random mating 106

Genetic drift Before: 8 RR 0. 50 R 8 rr 0. 50 r After: Genetic drift Before: 8 RR 0. 50 R 8 rr 0. 50 r After: 2 RR 6 rr 0. 25 R 0. 75 r 107

How does genetic structure change? • mutation • migration • natural selection cause changes How does genetic structure change? • mutation • migration • natural selection cause changes in allele frequencies • genetic drift • non-random mating 108

How does genetic structure change? • mutation • migration • natural selection • genetic How does genetic structure change? • mutation • migration • natural selection • genetic drift mating combines alleles into genotypes • non-random mating non-random allele combinations 109

A A A a A A 0. 8 a 0. 2 AA 0. 8 A A A a A A 0. 8 a 0. 2 AA 0. 8 x 0. 8 a. A 0. 2 x 0. 8 aa x AA AA a 0. 2 Aa 0. 8 x 0. 2 aa 0. 2 x 0. 2 aa AA allele frequencies: A = 0. 8 A = 0. 2 genotype frequencies: AA = 0. 8 x 0. 8 = 0. 64 Aa = 2(0. 8 x 0. 2) = 0. 32 aa = 0. 2 x 0. 2 = 0. 04 110

Example: Coat color B__ = black bb = red Herd of 200 cows: 100 Example: Coat color B__ = black bb = red Herd of 200 cows: 100 BB, 50 Bb and 50 bb 111

Allele frequency No. B alleles = 2(100) + 1(50) = 250 No. b alleles Allele frequency No. B alleles = 2(100) + 1(50) = 250 No. b alleles = 2(50) + 1(50) = 150 Total No. = 400 Allele frequencies: f(B) = 250/400 =. 625 f(b) = 150/400 =. 375 112

genotypic frequencies f(BB) = 100/200 =. 5 f(Bb) = 50/200 =. 25 f(bb) = genotypic frequencies f(BB) = 100/200 =. 5 f(Bb) = 50/200 =. 25 f(bb) = 50/200 =. 25 phenotypic frequencies f(black) = 150/200 =. 75 f(red) = 50/200 =. 25 113

Previous example: counted alleles to compute frequencies. Can also compute allele frequency from genotypic Previous example: counted alleles to compute frequencies. Can also compute allele frequency from genotypic frequency. f(A) = f(AA) + 1/2 f(Aa) f(a) = f(aa) + 1/2 f(Aa) 114

Previous example, we had f(BB) =. 50, f(Bb) =. 25, f(bb) =. 25. allele Previous example, we had f(BB) =. 50, f(Bb) =. 25, f(bb) =. 25. allele frequencies can be computed as: f(B) = f(BB) + 1/2 f(Bb) =. 50 + 1/2 (. 25) =. 625 f(b) = f(bb) + 1/2 f(Bb) =. 25 + 1/2 (. 25) =. 375 115

Mink color example: B_ = brown bb = platinum (blue-gray) Group of females (. Mink color example: B_ = brown bb = platinum (blue-gray) Group of females (. 5 BB, . 4 Bb, . 1 bb) bred to heterozygous males (0 BB, 1. 0 Bb, 0 bb). 116

Allele frequencies among the females? f(B) =. 5 + 1/2(. 4) =. 7 f(b) Allele frequencies among the females? f(B) =. 5 + 1/2(. 4) =. 7 f(b) =. 1 + 1/2(. 4) =. 3 Allele frequencies among the males? f(B) = 0 + 1/2(1) =. 5 f(b) = 0 + 1/2(1) =. 5 117

Expected genotypic, phenotypic and allele frequencies in the offspring? 118 Expected genotypic, phenotypic and allele frequencies in the offspring? 118

Expected frequencies in offspring Genotypic Phenotypic . 35 BB. 50 Bb. 15 bb . Expected frequencies in offspring Genotypic Phenotypic . 35 BB. 50 Bb. 15 bb . 85 brown. 15 platinum 119

Allele frequencies in offspring f(B) = f(BB) +. 5 f(Bb) =. 35 +. 5(. Allele frequencies in offspring f(B) = f(BB) +. 5 f(Bb) =. 35 +. 5(. 50) =. 6 f(b) = f(bb) +. 5 f(Bb) =. 15 +. 5(. 50) =. 4 120

Also note: allele freq. of offspring = average of sire and dam f(B) = Also note: allele freq. of offspring = average of sire and dam f(B) = 1/2 (. 5 +. 7) =. 6 f(b) = 1/2 (. 5 +. 3) =. 4 121

Hardy-Weinberg Theorem Population gene and genotypic frequencies don’t change over generations it is at Hardy-Weinberg Theorem Population gene and genotypic frequencies don’t change over generations it is at or near equilibrium. Population in equilibrium means that the populations isn’t under evolutionary forces (Assumptions for Equilibrium*) 122

Assumptions for equilibrium large population (no random drift) Random mating no selection no migration Assumptions for equilibrium large population (no random drift) Random mating no selection no migration (closed population) no mutation 123

Hardy-Weinberg Theorem Under these assumptions populations remains stable over generations. It means: If frequency Hardy-Weinberg Theorem Under these assumptions populations remains stable over generations. It means: If frequency of allele A in a population is =. 5, the sires and cows will generate gametes with frequency =. 5 and the frequency of allele A on next generation will be =. 5!!!!! 124

Hardy-Weinberg Theorem Therefore: It can be used to estimate frequencies when the genotypic frequencies Hardy-Weinberg Theorem Therefore: It can be used to estimate frequencies when the genotypic frequencies are unknown. Predict frequencies on the next generation. 125

Hardy-Weinberg Theorem If predicted frequencies differ from observed frequencies Population is not under Hardy. Hardy-Weinberg Theorem If predicted frequencies differ from observed frequencies Population is not under Hardy. Weinberg Equilibrium. Therefore the population is under selection, migration, mutation or genetic drift. Or a particular locus is been affected by the forces mentioned above. 126

Hardy-Weinberg Theorem (2 alleles at 1 locus) Allele freq. Genotypic freq. f(A) = p Hardy-Weinberg Theorem (2 alleles at 1 locus) Allele freq. Genotypic freq. f(A) = p f(a) = q f(AA) = p 2 Dominant homozygous f(Aa) = 2 pq Heterozgous f(aa) = q 2 Recessive homozygous p + q = 1 Sum of alleles = 100% p 2 + 2 pq + q 2 = 1 Sum of all genotypes = 100% 127

Hardy-Weinberg Theorem Genotypic freq. f(AA) = p 2 Dominant homozygous f(Aa) = 2 pq Hardy-Weinberg Theorem Genotypic freq. f(AA) = p 2 Dominant homozygous f(Aa) = 2 pq Heterozgous f(aa) = q 2 Recessive homozygous p 2 + 2 pq + q 2 = 1 Sum of all genotypes = 100% Allele freq. f(A) = p f(a) = q p + q = 1 Sum of alleles = 100% Gametes A (p) a(q) A(p) AA (pp) Aa (pq) a(q) a. A (qp) aa (qq) AA = p*p = p 2 Aa = pq + qp = 2 pq Aa = q*q = q 2 128

Example use of H-W theorem 1000 -head sheep flock. No selection for color. Closed Example use of H-W theorem 1000 -head sheep flock. No selection for color. Closed to outside breeding. 910 white (B_) 90 black (bb) 129

Start with known: f(black) = f(bb) =. 09 =q 2 Then, p = 1 Start with known: f(black) = f(bb) =. 09 =q 2 Then, p = 1 – q =. 7 = f(B) f(BB) = p 2 =. 49 f(Bb) = 2 pq =. 42 f(bb) = q 2 =. 09 130

In summary: Allele freq. f(B) = p =. 7 (est. ) f(b) = q In summary: Allele freq. f(B) = p =. 7 (est. ) f(b) = q =. 3 (est. ) Genotypic freq. f(BB) = p 2 =. 49 (est. ) f(Bb) = 2 pq =. 42 (est. ) f(bb) = q 2 =. 09 (actual) Phenotypic freq. f(white) =. 91 (actual) f(black) =. 09 (actual) 131

Mink example using H-W Group of 2000 (1920 brown, 80 platinum) in equilibrium. We Mink example using H-W Group of 2000 (1920 brown, 80 platinum) in equilibrium. We know f(bb) = 80/2000 =. 04 = q 2 f(b) = (q 2) = . 04 =. 2 f(B) = p = 1 - q =. 8 f(BB) = p 2 =. 64 f(Bb) = 2 pq =. 32 132

Forces that affect allele freq. 1. 2. 3. 4. Mutation Migration Selection Random (genetic) Forces that affect allele freq. 1. 2. 3. 4. Mutation Migration Selection Random (genetic) drift Selection and migration most important for livestock breeders. 133

Mutation Change in base DNA sequence. Source of new alleles. Important over long time-frame. Mutation Change in base DNA sequence. Source of new alleles. Important over long time-frame. Usually undesirable. 134

Migration Introduction of allele(s) into a population from an outside source. Classic example: introduction Migration Introduction of allele(s) into a population from an outside source. Classic example: introduction of animals into an isolated population. others: new herd sire. opening herd books. “under-the-counter” addition to a breed. 135

Change in allele freq. due to migration pmig = m(Pm-Po) where Pm = allele Change in allele freq. due to migration pmig = m(Pm-Po) where Pm = allele freq. in migrants Po = allele freq. in original population m = proportion of migrants in mixed pop. 136

Migration example 100 Red Angus (all bb, p 0 = 0) purchase 100 Bb Migration example 100 Red Angus (all bb, p 0 = 0) purchase 100 Bb (pm =. 5) p = m(pm - po) =. 5(. 5 - 0) =. 25 new p = p 0 + p = 0 +. 25 = f(B) new q = q 0 + q = 1 -. 25 =. 75 = f(b) 137

Random (genetic) drift Changes in allele frequency due to random segregation. Aa . 5 Random (genetic) drift Changes in allele frequency due to random segregation. Aa . 5 A, . 5 a gametes Important only in very small pop. 138

Selection Some individuals leave more offspring than others. Primary tool to improve genetics of Selection Some individuals leave more offspring than others. Primary tool to improve genetics of livestock. Does not create new alleles. Does alter freq. Primary effect change allele frequency of desirable alleles. 139

Example: horned/polled cattle 100 -head herd (70 HH, 20 Hh, and 10 hh). Genotypic Example: horned/polled cattle 100 -head herd (70 HH, 20 Hh, and 10 hh). Genotypic freq. : f(HH) =. 7, f(Hh) =. 2, f(hh) =. 1 Allele freq. : f(H) =. 8, f(h) =. 2 Suppose we cull all horned cows. Calculate allele and genotypic frequencies after culling? 140

After culling f(HH) =. 7/. 9 =. 778 f(Hh) =. 2/. 9 =. 222 After culling f(HH) =. 7/. 9 =. 778 f(Hh) =. 2/. 9 =. 222 f(hh) = 0 f(H) =. 778 +. 5(. 222) =. 889 f(h) = 0 +. 5(. 222) =. 111 p =. 889 -. 8 =. 089 141

2 nd example Cow herd with 20 HH, 20 Hh, and 60 hh Initial 2 nd example Cow herd with 20 HH, 20 Hh, and 60 hh Initial genotypic freq. : . 2 HH, . 2 Hh, . 6 hh Initial allele frequencies: f(H) =. 2 + 1/2(. 2) =. 3 f(h) =. 6 + 1/2(. 2) =. 7 Again, cull all horned cows. 142

Genotypic freq (HH) =. 2/. 4 =. 5 freq (Hh) =. 2/. 4 =. Genotypic freq (HH) =. 2/. 4 =. 5 freq (Hh) =. 2/. 4 =. 5 freq (hh) = 0 Allele freq. f(H) =. 5 + 1/2(. 5) =. 75 f(h) = 0 + 1/2(. 5) =. 25 p =. 75 -. 3 =. 45 Note: more change can be made when the initial frequency of desirable gene is low. 143

3 rd example initial genotypic freq. . 2 HH, . 2 Hh, . 6 3 rd example initial genotypic freq. . 2 HH, . 2 Hh, . 6 hh. Initial allele freq. f(H) =. 3 and f(h) =. 7 Cull half of the horned cows. 144

Genotypic f (HH) =. 2/. 7 =. 2857 f (Hh) =. 2/. 7 =. Genotypic f (HH) =. 2/. 7 =. 2857 f (Hh) =. 2/. 7 =. 2857 f (hh) =. 3/. 7 =. 4286 Allele freq. f(H) =. 2857 + 1/2(. 2857) =. 429 f(h) =. 4286 + 1/2(. 2857) =. 571 p =. 429 -. 3 =. 129 Note: the higher proportion that can be culled, the more you can change allele freq. 145

Selection Against Recessive Allele Freq. A a. 1. 9. 3. 7. 5. 5. 7. Selection Against Recessive Allele Freq. A a. 1. 9. 3. 7. 5. 5. 7. 3. 9. 1 Genotypic Freq. AA Aa. 01. 18. 09. 42. 25. 50. 49. 42. 81. 18 aa. 81. 49. 25. 09. 01 146

Factors affecting response to selection 1. Selection intensity 2. Degree of dominance (dominance slows Factors affecting response to selection 1. Selection intensity 2. Degree of dominance (dominance slows progress) Initial allele frequency (for a one locus) Genetic Variability (Bell Curve) 147