Lecture 7: Evolution I I. Population Genetics A. Overview Sources of VariationAgents of Change MutationN.S. Recombinationmutation - crossing over - independent assortment VARIATION

G. Hardy and W. Weinberg Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population 1. Definitions - Evolution: a change in the genetic structure of a population - Population: a group of interbreeding organisms that share a common gene pool; spatiotemporally and genetically defined - Gene Pool: sum total of alleles held by individuals in a population - Genetic structure: Gene array and Genotypic array - Gene/Allele Frequency: % of alleles at a locus of a particular type - Gene Array: % of all alleles at a locus: must sum to 1. - Genotypic Frequency: % of individuals with a particular genotype - Genotypic Array: % of all genotypes for loci considered; must = 1.

AAAaaa Individuals708050(200) Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population 1. Definitions 2. Basic Computations

AAAaaa Individuals708050(200) Genotypic Array 70/200 = /200 =.4050/200 = 0.25 = 1 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population 1. Definitions 2. Basic Computations

AAAaaa Individuals708050(200) Genotypic Array 70/200 = /200 =.4050/200 = 0.25 = 1 ''A' alleles /400 = 0.55 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population 1. Definitions 2. Basic Computations

AAAaaa Individuals708050(200) Genotypic Array 70/200 = /200 =.4050/200 = 0.25 = 1 ''A' alleles /400 = 0.55 'a' alleles /400 = 0.45 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population 1. Definitions 2. Basic Computations

- Determining the Gene Array from the Genotypic Array a. f(A) = f(AA) + f(Aa)/2 = /2 = =.55 b. f(a) = f(aa) + f(Aa)/2 = /2 = =.45 KEY: The Gene Array CAN ALWAYS be computed from the genotypic array; the process just counts alleles instead of genotypes. No assumptions are made when you do this. Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population 1. Definitions 2. Basic Computations

Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 1. Goal: Describe what the genetic structure of the population would be if there were NO evolutionary change – if the population was in equilibrium.

Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 1. Goal: Describe what the genetic structure of the population would be if there were NO evolutionary change – if the population was in equilibrium. For a population’s genetic structure to remain static, the following must be true: - random mating - no selection - no mutation - no migration - the population must be infinitely large

AAAaaa Initial genotypic freq Gene freq. Genotypes, F1 Gene Freq's Genotypes, F2 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example:

AAAaaa Initial genotypic freq Gene freq.f(A) = p =.4 +.4/2 = 0.6f(a) = q =.2 +.4/2 = 0.4 Genotypes, F1 Gene Freq's Genotypes, F2 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example:

AAAaaa Initial genotypic freq Gene freq.f(A) = p =.4 +.4/2 = 0.6f(a) = q =.2 +.4/2 = 0.4 Genotypes, F1p 2 =.362pq =.48q 2 =.16 = 1.00 Gene Freq's Genotypes, F2 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example:

AAAaaa Initial genotypic freq Gene freq.f(A) = p =.4 +.4/2 = 0.6f(a) = q =.2 +.4/2 = 0.4 Genotypes, F1p 2 =.362pq =.48q 2 =.16 = 1.00 Gene Freq'sf(A) = p = /2 = 0.6f(a) = q = /2 = 0.4 Genotypes, F2p 2 =.362pq =.48q 2 =.16 = 1.00 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example: After one generation with these conditions, the population equilibrates

Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example 3. Utility: If no populations meets these conditions explicitly, how can it be useful?

Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 2.Example 3. Utility: If no populations meets these conditions explicitly, how can it be useful? For comparison, like a “perfectly balanced coin” AAAaaa Initial genotypic freq Gene freq.f(A) = p =.5 +.2/2 = 0.6f(a) = q =.3 +.2/2 = 0.4 HWE expections p 2 =.362pq =.48q 2 =.16 = 1.00 CONCLUSION:The real population is NOT in HWE.

Sources of VariationAgents of Change MutationN.S. RecombinationDrift - crossing overMigration - independent assortmentMutation Non-random Mating VARIATION So, if NO AGENTS are acting on a population, then it will be in equilibrium and WON'T change. Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 3. Utility: - if a population is NOT in HWE, then one of the assumptions must be violated.

-Also, If HWCE is assumed and the frequency of homozygous recessives can be measured, then the number of heterozygous carriers can be estimated. For example: If f(aa) =.01, then estimate f(a) =.1 and f(A) must be.9. f(Aa) = 2(.1)(.9) = Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 3. Utility: - if a population is NOT in HWE, then one of the assumptions must be violated.

Sources of VariationAgents of Change MutationN.S. RecombinationDrift - crossing overMigration - independent assortmentMutation Non-random Mating VARIATION So, if NO AGENTS are acting on a population, then it will be in equilibrium and WON'T change. Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model 3. Utility: - if a population is NOT in HWE, then one of the assumptions must be violated.

Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model D. Deviations from HWE 1. mutation 1. Consider a population with: f(A) = p = 0.6 f(a) = q = Suppose 'a' mutates to 'A' at a realistic rate of: μ = 1 x Well, what fraction of alleles will change? 'a' will decline by: qm =.4 x = 'A' will increase by the same amount. f(A) = p1 = f(a1) = q =

p1 = 0.2 q1 = 0.8 p2 = 0.7 q2 = 0.3 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model D. Deviations from HWE 1. mutation 2. migration suppose migrants immigrate at a rate such that the new immigrants represent 10% of the new population

p2 = 0.7 q2 = 0.3 p1 = 0.2 q1 = 0.8 Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model D. Deviations from HWE 1. mutation 2. migration M = 10% p(new) = p1(1-m) + p2(m) = 0.2(0.9) + 0.7(0.1) = = 0.25

AAAaaa offspring F1 D. Deviations from HWE 1. mutation 2. migration 3. Non-random Mating a. Positive Assortative Mating – “Like mates with Like”

AAAaaa offspringALL AA1/4AA:1/2Aa:1/4aaALL aa F1 D. Deviations from HWE 1. mutation 2. migration 3. Non-random Mating a. Positive Assortative Mating – “Like mates with Like”

AAAaaa offspringALL AA1/4AA:1/2Aa:1/4aaALL aa F D. Deviations from HWE 1. mutation 2. migration 3. Non-random Mating a. Positive Assortative Mating – “Like mates with Like”

D. Deviations from HWE 1. mutation 2. migration 3. Non-random Mating a. Positive Assortative Mating – “Like mates with Like” b. Inbreeding: Mating with Relatives Decreases heterozygosity across the genome, at a rate dependent on the degree of relatedness among mates.

D. Deviations from HWE 1. mutation 2. migration 3. Non-random Mating 4. Finite Population Sizes: Genetic Drift The organisms that actually reproduce in a population may not be representative of the genetics structure of the population; they may vary just due to sampling error

1 - small pops will differ more, just by chance, from the original population D. Deviations from HWE 1. mutation 2. migration 3. Non-random Mating 4. Finite Population Sizes: Genetic Drift

1 - small pops will differ more, just by chance, from the original population 2 - small pops will vary more from one another than large D. Deviations from HWE 1. mutation 2. migration 3. Non-random Mating 4. Finite Population Sizes: Genetic Drift

- “Founder Effect” The Amish, a very small, close-knit group decended from an initial population of founders, has a high incidence of genetic abnormalities such as polydactyly D. Deviations from HWE 1. mutation 2. migration 3. Non-random Mating 4. Finite Population Sizes: Genetic Drift

- “Founder Effect” and Huntington’s Chorea HC is a neurodegenerative disorder caused by an autosomal lethal dominant allele. The fishing villages around Lake Maracaibo in Venezuela have the highest incidence of Huntington’s Chorea in the world, approaching 50% in some communities.

- “Founder Effect” and Huntington’s Chorea HC is a neurodegenerative disorder caused by an autosomal lethal dominant allele. The fishing villages around Lake Maracaibo in Venezuela have the highest incidence of Huntington’s Chorea in the world, approaching 50% in some communities. The gene was mapped to chromosome 4, and the HC allele was caused by a repeated sequence of over 35 “CAG’s”. Dr. Nancy Wexler found homozygotes in Maracaibo and described it as the first truly dominant human disease (most are incompletely dominant and cause death in the homozygous condition).

- “Founder Effect” and Huntington’s Chorea HC is a neurodegenerative disorder caused by an autosomal lethal dominant allele. The fishing villages around Lake Maracaibo in Venezuela have the highest incidence of Huntington’s Chorea in the world, approaching 50% in some communities. By comparing pedigrees, she traced the incidence to a single woman who lived 200 years ago. When the population was small, she had 10 children who survived and reproduced. Folks with HC now trace their ancestry to this lineage.

- “Genetic Bottleneck” If a population crashes (perhaps as the result of a plague) there will be both selection and drift. There will be selection for those resistant to the disease (and correlated selection for genes close to the genes conferring resistance), but there will also be drift at other loci simply by reducing the size of the breeding population. European Bison, hunted to 12 individuals, now number over Cheetah have very low genetic diversity, suggesting a severe bottleneck in the past. They can even exchange skin grafts without rejection… Elephant seals fell to 100’s in the 1800s, now in the 100,000’s

Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model D. Deviations From HWE: 1. Mutation 2. Migration 3. Non-Random Mating: 4. Populations of Finite Size and Sampling Error - "Genetic Drift" 5. Natural Selection 1. Fitness Components:

D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: Fitness = The mean number of reproducing offspring / genotype - probability of surviving to reproductive age - number of offspring - probability that offspring survive to reproductive age

D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: Fitness = The mean number of reproducing offspring / genotype - probability of surviving to reproductive age - number of offspring - probability that offspring survive to reproductive age 2. Constraints: i. finite energy budgets and necessary trade-offs:

D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: Fitness = The mean number of reproducing offspring / genotype - probability of surviving to reproductive age - number of offspring - probability that offspring survive to reproductive age 2. Constraints: i. finite energy budgets and necessary trade-offs: GROWTH METABOLISM REPRODUCTION

Maximize probability of survival GROWTH METABOLISM REPRODUCTION GROWTH METABOLISM REPRODUCTION Maximize reproduction D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: 2. Constraints: i.finite energy budgets and necessary trade-offs: TRADE OFF #1: Survival vs. Reproduction

METABOLISM REPRODUCTION Lots of small, low prob of survival A few large, high prob of survival D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: 2. Constraints: i.finite energy budgets and necessary trade-offs: TRADE OFF #1: Survival vs. Reproduction TRADE OFF #2: Lots of small offspring vs. few large offspring

D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: 2. Constraints: i.finite energy budgets and necessary trade-offs: ii.Contradictory selective pressures: Leaf Size Photosynthetic potential Water Retention

D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: 2. Constraints: i.finite energy budgets and necessary trade-offs: ii.Contradictory selective pressures: Leaf Size Photosynthetic potential Water Retention Rainforest understory – dark, wet Big leaves adaptive

D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: 2. Constraints: i.finite energy budgets and necessary trade-offs: ii.Contradictory selective pressures: Leaf Size Photosynthetic potential Water Retention Desert – sunny, dry Small leaves adaptive

D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: 2.Constraints: 3.Modeling Selection: a. Calculating relative fitness p = 0.4, q = 0.6AAAaaa Parental "zygotes" = 1.00 prob. of survival (fitness) Relative Fitness0.8/0.8=10.4/0.8 = /0.8=0.25

p = 0.4, q = 0.6AAAaaa Parental "zygotes" = 1.00 prob. of survival (fitness) Relative Fitness Survival to Reproduction = 0.49 Freq’s in Breeding Adults0.16/0.49 = /0.49 = /0.49 = 0.18 = 1.00 Gene FrequenciesF(A) = 0.575F(a) = Freq’s in F1 (p 2, 2pq, q 2 ) = 1.00 D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: 2.Constraints: 3.Modeling Selection: a. Calculating relative fitness b. Modeling Selection

D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: 2.Constraints: 3.Modeling Selection: 4. Types of Selection

Some traits that decrease survival may be selected for because they have a direct and disproportional benefit on probability of mating. Intrasexual – competition within a sex for access to mates. Intersexual – mates are chosen by the opposite sex. D. Deviations From HWE: 5. Natural Selection 1.Fitness Components: 2.Constraints: 3.Modeling Selection: 4. Types of Selection Sexual Selection

Sources of VariationAgents of Change MutationNatural Selection RecombinationGenetic Drift - crossing overMigration - independent assortmentMutation Non-random Mating VARIATION Modern Evolutionary Biology I. Population Genetics A. Overview B. The Genetic Structure of a Population C. The Hardy-Weinberg Equilibrium Model D. Deviations From HWE E. Summary; The Modern Synthetic Theory of Evolution