Chapter 6 The ways of change drift and

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Chapter 6 The ways of change: drift and selection

Chapter 6 The ways of change: drift and selection

Population genetics n Study of the distribution of alleles in populations and causes of

Population genetics n Study of the distribution of alleles in populations and causes of allele frequency changes

Key Concepts n Diploid individuals carry two alleles at every locus Homozygous: alleles are

Key Concepts n Diploid individuals carry two alleles at every locus Homozygous: alleles are the same n Heterozygous: alleles are different n n Evolution: change in allele frequencies from one generation to the next

Hardy-Weinberg equilibrium n Population allele frequencies do not change if: n Population is infinitely

Hardy-Weinberg equilibrium n Population allele frequencies do not change if: n Population is infinitely large n Genotypes do not differ in fitness n There is no mutation n Mating is random n There is no migration

Predictions from Hardy-Weinberg n Allele frequencies predict genotype frequencies p 2 + 2 pq

Predictions from Hardy-Weinberg n Allele frequencies predict genotype frequencies p 2 + 2 pq + q 2 = 1

Key Concepts n Hardy-Weinberg theorem proves that allele frequencies do not change in the

Key Concepts n Hardy-Weinberg theorem proves that allele frequencies do not change in the absence of drift, selection, mutation, and migration n Mechanisms of evolution are forces that change allele frequencies

Populations evolve through a variety of mechanisms

Populations evolve through a variety of mechanisms

Key Concept n Hardy-Weinberg serves as the fundamental null model in population genetics

Key Concept n Hardy-Weinberg serves as the fundamental null model in population genetics

Genetic Drift n Peter Buri started 107 cultures with 8 males and 8 females

Genetic Drift n Peter Buri started 107 cultures with 8 males and 8 females all heterozygous for bw 75 red eye and for bw white eye n bw / bw 75 heterozygous orange parents n All H-W assumptions met except large population size n 19 generations – each generation started with: n Randomly selected: 8 males and 8 females n Many populations had alleles that went to Extinction n Fixation Other populations ranged between two extremes n n What happened?

Genetic drift causes evolution in finite populations

Genetic drift causes evolution in finite populations

Genetic drift causes evolution in finite populations

Genetic drift causes evolution in finite populations

Genetic drift results from random sampling error Sampling error is higher with smaller sample

Genetic drift results from random sampling error Sampling error is higher with smaller sample

Drift reduces genetic variation in a population n Alleles are lost at a faster

Drift reduces genetic variation in a population n Alleles are lost at a faster rate in small populations n Alternative allele is fixed

Key Concepts n Genetic drift causes allele frequencies to change in populations n Alleles

Key Concepts n Genetic drift causes allele frequencies to change in populations n Alleles are lost more rapidly in small populations

Evolutionary biologists have debated the importance of natural selection and genetic drift R. A.

Evolutionary biologists have debated the importance of natural selection and genetic drift R. A. Fisher Natural Selection and Statistics Sewel Wright Genetic Drift Important Motoo Kimura also emphasized Genetic Drift

Bottlenecks reduce genetic variation Northern Elephant Seals – killed for tusks (ivory) and then

Bottlenecks reduce genetic variation Northern Elephant Seals – killed for tusks (ivory) and then for museums! A bottleneck causes genetic drift

Rare alleles are most likely to be lost during a bottleneck

Rare alleles are most likely to be lost during a bottleneck

Founder Effect Mutiny on the Bounty –Pitcairn Islands Founder effects cause genetic drift

Founder Effect Mutiny on the Bounty –Pitcairn Islands Founder effects cause genetic drift

High incidence of migraine headaches attributed to founder effects on Norfolk Island in Pitcairn

High incidence of migraine headaches attributed to founder effects on Norfolk Island in Pitcairn Islands

Genotypes, Phenotypes and Selection n Alleles are selectively neutral if they have no effect

Genotypes, Phenotypes and Selection n Alleles are selectively neutral if they have no effect on the fitness of their bearers. This phenomenon often occurs when genetic variation at a locus does not effect the phenotype of an individual. n Selection acts on whole phenotypes of individuals.

Key Concept n Even brief bottlenecks can lead to a drastic reduction in genetic

Key Concept n Even brief bottlenecks can lead to a drastic reduction in genetic diversity that can persist for generations

Key Concept n Alleles are selectivity neutral if they have no effects on the

Key Concept n Alleles are selectivity neutral if they have no effects on the fitness of their bearers. This phenomenon often occurs when genetic variation at a locus does not affect the phenotype of an individual. Selectively neutral n S = selection coefficient used to express how much genotypes differ in fitness n n Selection acts on whole phenotypes of individuals n So must affect fitness

The concept of fitness n Fitness: the reproductive success of an individual with a

The concept of fitness n Fitness: the reproductive success of an individual with a particular phenotype n Components of fitness: n Survival to reproductive age n Mating success n Fecundity n Relative fitness: fitness of a genotype standardized by comparison to other genotypes

Selection Changes Allele Frequencies n Average excess fitness: difference between average fitness of individuals

Selection Changes Allele Frequencies n Average excess fitness: difference between average fitness of individuals with allele vs. average fitness of those without Average excess of fitness Change in frequency due to selection p is frequency of A 1 allele Average fitness of the population n Use this to predict how the frequency of the allele will change from one generation to the next

Natural selection more powerful in large populations n Drift weaker in large populations n

Natural selection more powerful in large populations n Drift weaker in large populations n Selection weaker in small populations n Small advantages in fitness can lead to large changes over the long term

Pleiotropy may constrain evolution n Pleiotropy: mutation in a single gene affects many phenotypic

Pleiotropy may constrain evolution n Pleiotropy: mutation in a single gene affects many phenotypic traits Can be antagonistic n Net effect on fitness determines outcome of selection n

Pesticide resistance and pleiotropy • Ester 1 - mosquitoes resistant to insecticide, but more

Pesticide resistance and pleiotropy • Ester 1 - mosquitoes resistant to insecticide, but more vulnerable to spider predation. Ester 1 higher fitness on coast; away from coast much lower fitness (no insecticide) • Ester+4 less protection from mosquitoes at coast, but more common than Ester 1. . Higher fitness inland because less cost of predation. BUT higher costs due to overproduction of esterases. • Antagonistic Pleiotropy

Pesticide resistance and pleiotropy

Pesticide resistance and pleiotropy

Antagonistic Pleiotropy n Effects of mutation have opposite effects on fitness Ester 1 has

Antagonistic Pleiotropy n Effects of mutation have opposite effects on fitness Ester 1 has benefit along the coast but n Inland, benefit declines because there are fewer mosquitoes, and cost increases due to increased chance of predation by spiders n

Key Concept n Hardy-Weinberg serves as the fundamental null model in population genetics Condition

Key Concept n Hardy-Weinberg serves as the fundamental null model in population genetics Condition that we try to falsify n Test populations to see if they are in H-W equil. n n These are the null model frequencies n Ex: Hemoglobin (Box 6. 3) n Cavalli-Sforza - Nigeria n Hg A and S (based on difference in β-globin) n Results: More SA and AA and fewer SS than HW would predict

Why are there so many hemoglobin A alleles in the population? n Heterozygote Advantage

Why are there so many hemoglobin A alleles in the population? n Heterozygote Advantage n n n S = sickle cell disease hemoglobin n SS = sickle cell disease n Low fitness A = normal hemoglobin n AA = Susceptible to malaria n Low fitness AS n Protected from malaria n Protected from sickle cell disease n Survive and reproduce – higher fitness

Testing the Null Model Cavalli-Sforza, 2007

Testing the Null Model Cavalli-Sforza, 2007

Heterozygote advantage and sickle-cell anemia

Heterozygote advantage and sickle-cell anemia

Founder effect n Amish of Lancaster, PA n Ellis-van Creveld Syndrome: mutation causes dwarfism

Founder effect n Amish of Lancaster, PA n Ellis-van Creveld Syndrome: mutation causes dwarfism and polydactylism n n General population at levels less than 0. 1%, Lancaster Amish the allele’s level is approximately 7%. Absence of upper incisors and conical lower incisors

Ellis-van Creveld n Inherited disorder of bone growth: n Very short stature (dwarfism). n

Ellis-van Creveld n Inherited disorder of bone growth: n Very short stature (dwarfism). n Short forearms and lower legs n Narrow chest with short ribs. n Extra fingers and toes (polydactyly), n Malformed fingernails and toenails n Dental abnormalities. n More than half of affected individuals are born with a heart defect, which can cause serious or life-threatening health problems.

Founder effect n Nonrandom Mating n sibling matings - Inbreeding n reduces variation §

Founder effect n Nonrandom Mating n sibling matings - Inbreeding n reduces variation § Fig Wasps § Naked Mole rats § Human Eyebrow Mites (Demodex folliculorum)

Experimental evolution provides important insights about selection • Richard Lenski started 1988 • Started

Experimental evolution provides important insights about selection • Richard Lenski started 1988 • Started culture with 1 E. coli cell • Started 12 cloned populations • Grow in 10 m. L cultures with small amount of glucose

Natural selection in action Alleles that lower fitness experience Negative Selection Alleles that increase

Natural selection in action Alleles that lower fitness experience Negative Selection Alleles that increase fitness experience Positive Selection

Results n All cultures adapted to low glucose availability n Accumulated adaptations that made

Results n All cultures adapted to low glucose availability n Accumulated adaptations that made them more efficient at growing under the experimental conditions n Rate of increase in fitness has slowed but still condinues to rise after 60 K generations

Comparison of wild and adapted strains n Transfer segments of DNA from one cell

Comparison of wild and adapted strains n Transfer segments of DNA from one cell of generation 10 K into ancestral cultures of the same line n Then mixed each line of engineered bacteria with unmanipulated ancestral bacteria n Results: Saw increased fitness with one particular engineered line DNA segment n Help synthesize cell membrane n Transferred one nucleotide into ancestral bacteria and increased fitness by 5% n

Comparison of wild and adapted strains n Tested generation 500 for mutation – not

Comparison of wild and adapted strains n Tested generation 500 for mutation – not present n Tested generation 1000 and found that mutation was present in 45% of population n Generation 1500 97% of bacteria had it n This rapid spread is typical of a mutation that enhances fitness n Mutation may allow cell to make thinner membranes while reproducing faster n Found epistatic genes (interact with other alleles)

Relationships among alleles at a locus n Additive: allele yields twice the phenotypic effect

Relationships among alleles at a locus n Additive: allele yields twice the phenotypic effect when two copies present Especially vulnerable to selection n Favorable alleles can go to fixation if additive allele is present n n n Fitness order: Heterozygotes – homozygotes – those without the allele Deleterious alleles can go extinct n Fitness order: – homozygotes -those without the allele – heterozygotes - homozygotes with the allele

Relationships among alleles at a locus n Dominant and recessive alleles are not additive

Relationships among alleles at a locus n Dominant and recessive alleles are not additive n Dominance: dominant allele masks presence of recessive allele in heterozygote n Dominant allele has same effect whether present in one or two copies

Effects of selection on different types of alleles

Effects of selection on different types of alleles

Mutation generates variation n Mutation rates for any given gene are low n But,

Mutation generates variation n Mutation rates for any given gene are low n But, considering genome size and population size many new mutations arise each generation n Estimate in humans: 8. 5 billion new mutations n Source of variation for selection and drift to act on

Mutation-selection balance n Equilibrium frequency reached through tug-of- war between negative selection and new

Mutation-selection balance n Equilibrium frequency reached through tug-of- war between negative selection and new mutation n Explains persistence of rare deleterious mutations in populations

Balancing selection n Some forms of selection maintain diversity in populations: n n Negative

Balancing selection n Some forms of selection maintain diversity in populations: n n Negative frequency-dependent selection n Fitness is high when phenotype is rare n Fitness is low when phenotype is common Heterozygote advantage

Negative frequency-dependent selection

Negative frequency-dependent selection

Key Concepts n Selection occurs when genotypes differ in fitness n Outcome of selection

Key Concepts n Selection occurs when genotypes differ in fitness n Outcome of selection depends on frequency of allele and effects on fitness n Population size influences power of drift and selection Drift more powerful in small population n Selection more powerful in large population n

Key Concepts n Alleles may have pleiotropic effects n When fitness effects oppose each

Key Concepts n Alleles may have pleiotropic effects n When fitness effects oppose each other environment determines direction of selection n Laboratory evolution studies reveal how alleles rise and spread through populations n Rare alleles almost always carried in a heterozygous state Recessive alleles invisible to selection n Selection cannot drive dominant to fixation n

Key Concepts n Mutations are the source of new genetic variation in populations n

Key Concepts n Mutations are the source of new genetic variation in populations n Can be many in a large population n Balancing selection maintains multiple alleles in populations Negative frequency-dependent n Heterozygote advantage n

Inbreeding and the Hapsburg dynasty

Inbreeding and the Hapsburg dynasty

Inbreeding coefficient n Probability that two alleles are identical by descent

Inbreeding coefficient n Probability that two alleles are identical by descent

Inbreeding depression results in reduced fitness- inbreeding and selection n Rare deleterious alleles more

Inbreeding depression results in reduced fitness- inbreeding and selection n Rare deleterious alleles more likely to combine in homozygotes

Key Concepts n Alleles are identical by descent if they both descended from a

Key Concepts n Alleles are identical by descent if they both descended from a single mutational event n Inbreeding increases percentage of loci that are homozygous for alleles identical by descent n Genetic bottlenecks often go hand in hand with inbreeding and selection n Recessive alleles exposed to selection

How Genetic Variation is Lost n Effects of Population size n Genetic Drift: fixation

How Genetic Variation is Lost n Effects of Population size n Genetic Drift: fixation or loss of alleles n Population bottlenecks n causes § habitat destruction or fragmentation § introduced competitors or predators § disease n affects Mendelian (discontinuous) characters more severely than quantitative (continuous) characters

Genetic Drift n ex. Cheetahs Acinonyx jubatus n Large scale climate change about 10,

Genetic Drift n ex. Cheetahs Acinonyx jubatus n Large scale climate change about 10, 000 years ago n Most populations of cheetahs went extinct in North America, Europe, Asia, and much of Africa n Current animals are the result of inbreeding among the surviving few animals (perhaps a single preganant female? ) n Little genetic variability especially among immune system genes

Genetic Drift n Habitat encroachment and poaching have further reduce cheetah numbers, consequently snuffing

Genetic Drift n Habitat encroachment and poaching have further reduce cheetah numbers, consequently snuffing out even more genetic variation and leaving cheetahs even more vulnerable to extinction.

10, 000 ya

10, 000 ya

Slides excerpted from:

Slides excerpted from:

Cheating Cheetahs n 2007 study, female cheetahs seem to be at least as promiscuous

Cheating Cheetahs n 2007 study, female cheetahs seem to be at least as promiscuous as their male counterparts. n Females frequently mate with several different males while they are fertile and are then likely to bear a single litter of cubs fathered by multiple males making many of the cubs within a single litter only half-siblings. n This discovery has important implications for the conservation of these endangered animals. n Though it conflicts with the idea that cheaters never prosper, evolutionary theory suggests that, in this case, cheating may be beneficial

Cheating Cheetahs n Three hypotheses for evolution of cheating 1. Even if several of

Cheating Cheetahs n Three hypotheses for evolution of cheating 1. Even if several of her cubs were killed by a new disease, succumbed to a novel environmental stress, or just didn't have what it took to make a living in the Serengeti, a female with a variable litter could still hope that one of her cubs would have "the right stuff" to survive. n Biologists refer to this as "bet-hedging" — not putting all your eggs (or in this case, cubs) in one basket.

Cheating Cheetahs 2. Perhaps, multiple mating is really a strategy to avoid expending extra

Cheating Cheetahs 2. Perhaps, multiple mating is really a strategy to avoid expending extra energy fending off would-be suitors. In other words, maybe females mate multiple times not because it ensures genetic variation in offspring, but because it's so much easier than fighting off males right and left. n Web info from Berkeley evolution education site http: //evolution. berkeley. edu/evolibrary/news/07070 1 cheetah

Cheating Cheetahs 3. Perhaps multiple mating evolved as a way to deter infanticide. In

Cheating Cheetahs 3. Perhaps multiple mating evolved as a way to deter infanticide. In some big cats (and in many other species), males try to kill cubs that are not their own. However, if a mother mates with many different males, it is more difficult for a male to tell whether or not a cub is his own — and the male would likely be deterred from killing the cub. This third hypothesis suggests that multiple mating was favored by natural selection because it discouraged infanticide against a female's cubs, not because it increased the litter's genetic variation. n This third hypothesis fits with the observation that wild cheetah males seem to rarely (if ever) commit infanticide, though it is common in lions and other big cats.

Cheating Cheetahs n Gottelli, D. , Wang, J. , Bashir, S. , and Durant,

Cheating Cheetahs n Gottelli, D. , Wang, J. , Bashir, S. , and Durant, S. M. (2007). Genetic analysis reveals promiscuity among female cheetahs. Proceedings of the Royal Society B 274(1621): 1993 -2001. http: //dx. doi. org/10. 1098/rspb. 2007. 0502 n Menotti-Raymond, M. , and O'Brien, S. J. (1993). Dating the genetic bottleneck of the African cheetah. Proceedings of the National Academy of Sciences 90(8): 3172 -3176. http: //www. pnas. org/content/90/8/3172. abstract

Natural Selection n Individuals vary in the expression of their phenotypes n This variation

Natural Selection n Individuals vary in the expression of their phenotypes n This variation causes some individuals to perform better than others Natural Selection happens when there is differential fitness

Modern definition: Natural Selection n The differential survival or reproduction, on the average, of

Modern definition: Natural Selection n The differential survival or reproduction, on the average, of different phenotypes in a population n Will lead to changes in frequencies of those phenotypes within a generation, that is, different age classes will have different phenotype frequencies. n n Within a generation - Darwin thought of many generations Evolution happens between generations n Note: NS does not have to lead to evolution!

The concept of fitness n Fitness: the reproductive success of an individual with a

The concept of fitness n Fitness: the reproductive success of an individual with a particular phenotype n Ability to get genes into future generations n Components of fitness: n Survival to reproductive age n Mating success n Fecundity n Relative fitness: fitness of a genotype standardized by comparison to other genotypes

Measuring Fitness n Difficult, rarely possible to n Record lifetime reproductive success n Record

Measuring Fitness n Difficult, rarely possible to n Record lifetime reproductive success n Record how many of those offspring survive to reproduce themselves n Other problems n Can’t follow organisms for long time n Complex relationship b/w genotype and phenotype n Fitness is product of entire phenotype n Proxies for fitness n Probability of surviving to reproductive age n Measure number of offspring in a season

Fitness Fecundity Survival Zygote t adult t Mating gametes zygotes t t+1 n t

Fitness Fecundity Survival Zygote t adult t Mating gametes zygotes t t+1 n t and t+1 = generations n Fecundity = ability to produce gametes n Contribution to the next generation = fitness n If different phenotypes are due to different genotypes, and have different fitnesses, then natural selection will act and the phenotype and genotype frequencies will change.

Fitness n Absolute fitness of a genotype = average reproductive rate of individuals with

Fitness n Absolute fitness of a genotype = average reproductive rate of individuals with that genotype n n Absolute Fitness = W Subscripts = genotypes A 1 A 1 W 11 A 1 A 2 W 12 A 2 A 2 W 22

Fitness n Absolute fitnesses determine whether a population will increase or decrease in size

Fitness n Absolute fitnesses determine whether a population will increase or decrease in size n If average absolute fitness of all individuals in the population is >1 then population increases in size n If average absolute fitness is <1 then population decreases in size

Fitness n Population geneticists use value W n W = all fitness components: survival,

Fitness n Population geneticists use value W n W = all fitness components: survival, mating success and fecundity n Describes relative contribution of individuals with one genotype compared with the average contribution of all individuals in the population n Relative Fitness n Average excess fitness: difference between average fitness of individuals with allele vs. those without Δp = p x (a. A 1/ϖ)

Contribution of alleles to fitness n Average excess fitness can be used to predict

Contribution of alleles to fitness n Average excess fitness can be used to predict how the frequency of the allele will change from one generation to the next