Evolution Study Guide Midterm 2
Evolution Study Guide Midterm 2 BIOL 3303
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Chapter 9 The history in our genes Molecular Homologies - the Genetic Code • Mutations can change the relationship between the codon and the amino acid it encodes. – which may be better than "our" code.des are possible, some of – Other codes are possible, but life on earth all uses the same code. • Unique codes would be advantageous. – They would isolate each species and prevent HIV for example from jumping from chimps to humans. • Most would not argue with the statement that a population that speaks the same language (for example, French) is related by common ancestry. The same is true for our genetic language. • The simplest explanation to the question of why we all share the same code is that we all inherited this code from a common ancestor. • The universality of the genetic code is an historic accident. 2http://www.pbs.org/wgbh/evolution/library/04/4/l_044_02.html Pbs_Videos_1\Evidence for Evolution\ The Common Genetic Code_l_044_02_300.mov 4 min 1 Genetic loci have their own genealogy Experimental phylogenetics validates methods Alleles in populations coalesce to a common ancestor Coalescence – the process by which, when looking backward in time, any pair of homologous alleles merges in a common ancestor Very useful in tracing descent Gene trees do not always match species trees • Top– gene tree matches species tree • Bottom – gene tree says “1” split from “2” and “3” first – For these 2 loci, coalescence was late – alleles diverged before any speciation occurred. Solution: Look at many loci not just one 3 Building a phylogeny with genetic data • Each nucleotide a potentially informative character • But, homoplasy common – shared trait not in common ancestor – Only four possible character states • Genes differ in rate of evolution – Slowly evolving genes useful for distantly related species – Rapidly evolving genes useful for closely related lineages Common methods • Maximum parsimony – Simplest explanation favored • Distance matrix (e.g. neighbor joining) – Clusters taxa based on genetic distance • Maximum likelihood – Finds most likely tree given specific model of molecular evolution • Bayesian methods – Looks at probability that a tree is correct given a specific model of molecular evolution Case study: origin of tetrapods Fossils and DNA agree: Lobe fins are closest to tetrapods Hundreds of sequences in 12 species match fossil record Case study: human evolution • Multiregional model of human origins – Hominins across Old World were a single species connected by gene flow “Multiregional” – Multiregional differences the result of local Regional adaptation H. erectusmayf interminglingile 5 Case study: human evolution • Out-of-Africa model of human origins – All human populations are derived from recent African ancestry Data supports Out-of-Africa model • All mitochondrial DNA of humans comes from Africa (Sarah Tishkoff) https://www.youtube.com/watch?v=G6r6P OHC8zg • Notice great diversity in African DNA – Migration is a bottleneck Case study: origin of Darwin’s finches Two possibilities: 1. Multiple colonizations by different finch species – Different Darwin’s species should have closest relatives elsewhere 2. Single colonization then diversification – Darwin’s finches should form monophyletic group – Colonization of Isla de Coco by Galapagos finches • Cocos finch to some Darwin’s finches versus others – Ancestor of all most likely from Ecuador black-faced grassquit (Tiaris bicolor) https://www.google.com/maps/place/Cocos+Islandemail@example.com,-87.294242,8z/data=!4m2!3m1!1s0x8f92e562200916c7:0xfa2018b7bcd96b87 Case study: human immunodeficiency virus (HIV) Sequenced HIV genomes What does this phylogeny tell us? 7 Neutral theory of molecular evolution • Most evolution at the molecular level is neutral – due to genetic drift (Motoo Kimura 1968) • Neutral substitutions – Should accrue in a clock-like fashion – “molecular clock”! • Different types of DNA should evolve at different rates – Pseudogenes have much higher mutation rates than do expressed genes Support for clock-like substitution • Cytochrome c mutations vs time since divergence Rate of evolution in different types of DNA does differ Molecular clock can be used to estimate diversification events • Mammalian diversification The molecular clock can be used to estimate date of common ancestor Detecting selection on DNA sequences • Synonymous substitutions: do not change protein – Should evolve at a neutral rate • Nonsynonymous substitutions: change protein – Faster evolution than synonymous sites indicates positive selection – Slower evolution than synonymous sites indicates purifying selection Signature of positive selection Positive selection on FOXP2 Positive Selection on the Breast Cancer Gene, BRCA1 When Nonsyn/Syn is >1, positive selection is dominating “Brings” the selected allele to higher frequency. 23 Genome alignments reveal conserved elements with important functions Conservation of sequence in genome comparisons: Indications of importance Graph shows human vs mouse DNA Red is unknown (important) protein indicated by conservation New lipid binding protein found (APOAV) Mouse knockout leads to much higher lipid in blood 12 Genomics as discovery science • Genome alignments provide valuable information about functionally important coding and non coding sequences • Genomic studies allow “unbiased” discoveries – The sequence shows what is important. Chapter 8 Natural selection: empirical studies in the wild Evolution by Natural Selection Definitions: Darwinian fitness: The ability of an individual to survive and reproduce in its environment. The offspring of fit individuals make up a greater percentage in the next generation. Adaptation: A trait or characteristic of an individual organism that increases its fitness relative to individuals without the trait. 2 Evolution by Natural Selection The Four postulates (review): (1) Individuals within populations are variable. (2) The variation among individuals can at least in part be passed from parent to offspring. (3) In every generation, some individuals are more successful at surviving and reproducing than others. (4) The survival and reproduction of individuals are not random. Survival and reproduction are tied to the variation among the individuals. Those individuals with the most favorable variations for survival and reproduction are naturally selected. 3 Reproductive Potential - In every population studied, more offspring are produced than survive to breed. Also known as biotic potential or fecundity. The number of progeny an organism or pair can produce under optimal conditions assuming no deaths in the offspring. In every population looked at, some individuals are more successful at mating and producing offspring than others. A sbreeding survivor is produced.wth and no decline) an average of 1 offspring per Postulate 3 - Individuals vary in survival and reproduction is universal4y true. 2 Does Natural Selection Work in Nature? Beak shape in Galápogos Finches – Originally studied by Darwin . – Since 1973 by Grant & Grant • Total of 15 species – All similar in size and color. • Size and shape of beaks shows much variation. – Variation reflects the diversity of foods utilized. Crushers biters probers 5 Medium Ground Finches on Isla Daphne Major Grant and Grant have studied these finches for over 30 years. Few finches move into or off the island. Population is small enough to be studied completely. By 1980 marked 100% of the population. Life span ~ 16 yrs.; generation time 4.5 yrs. Seed eaters Crack by grasping at base of bill and applying force. Correlation by beak size and seed size observed by many. 6 3 Medium ground finch • Variation in beak size influences efficiency at eating different types of seeds Beak size evolution 1. Beak size is variable 2. Beak size is heritable 3. Large beaked birds survived better in 1977 4. Survival and reproduction appears tied to favorable variation • Drought resulted in more hard, woody seeds – Favored larger beaked birds Natural selection is variable over time • Often selection is not constant Natural Selection is not Forward-Looking Selection never looks ahead to predict the (environmental) changes that will occur in the next generation. Evolution is always a generation behind any changes in the environment. Each generation is the product of selections that occurred in the previous generation. In this sense evolution is not a real-time system. It operates on a one-generation delay. 10 Variation in beak size: How does it work? Embryonic growth factors should control growth • G. magnirostris expresses BMP4 at 26 weeks – BMP4 = bone morphogenic protein 4 (a bone growth factor – detected by mRNA probes in embryo cross-sections). • Others express it much later. Chapter 10 p. 304-307 11 The Nature of Natural Selection Difficult to comprehend because the result is statistical. Changes in trait distributions in populations. 12 6 The Nature of Natural Selection • Natural selection acts on individuals but its consequences are on populations. – HIV selected for AZT- resistance – Finch selected for seed utilization No individual is changed. – Cheetah selected for Each individual either lives to sprint speed reproduce or does not survive to reproduce. 13 Evolution by Natural Selection Hummingbird Diversity Video \Pbs_Videos_1\Evolution of Diversity\Evolving Ideas How Does Evolution Really Work_e_s_4_7 minov http://www.pbs.org/wgbh/evolution/library/11/2/e_s_4.html Darwin’s Dangerous Idea Chapter 3 (20:00-32:57) 14 7 Coat color variation affects fitness • Oldfield mice on mainland or white sands • Differential predation rates Light coat color evolved independently in different populations • Different mutations responsible for light color in different populations • Geographic separation • Independent adaptations Evolution by Natural Selection The Four postulates (again!): (1) Individuals within populations are variable. (2) The variation among individuals can at least in part be passed from parent to offspring. (3) In every generation, some individuals are more successful at surviving and reproducing than others. (4) The survival and reproduction of individuals are not random. Survival and reproduction are tied to the variation among the individuals. Those individuals with the most favorable variations for survival and reproduction are naturally selected. 17 Natural selection can be variable across space • Gene flow can bring alleles to new locations – Alleles may increase or decrease fitness Aposematism (warning coloration) favored only in areas where coral snakes co-occur • Predators wary of coral snake venom • Mimics protected in overlapping geographies only • Geography plays a role in fitness Gall flies induce plants to produce galls Opposing selective forces • Gallflies lay eggs in the goldenrod and induce a gall to form (feeds the larvae) • Gall size is heritable trait of the fly • Bird predation – prefers large galls • Wasp predation – prefers small galls to lay eggs • Stabilizing selection for intermediate galls Key Concepts • Stabilizing selection results when agents of selection act in opposing directions Eda involved in production of lateral plates in stickleback Marine ancestral Eda form (ectodysplastin) Freshwater alleles control number of plates derived form • Common ancestor was marine (3 spines and armor plates protect from predation) • Some populations trapped in fresh water lakes after last ice age (2 spines, less plates) Low Eda allele favored in freshwater populations • Production of armor energetically costly – Little predation pressure to counterbalance • Low Eda allele present at low frequency in marine environment – Favored when introduced to freshwater Shift in dorsal spine length recorded in fossil record • Cost of armor is high • 110,000 years of fossils from the same lake beds • Shows influx of spines and then loss • COST is important! Ability to digest lactose as adults found in certain populations - For some humans, Lactase expression persists into adulthood - Correlates with domestication of cattle Frequency of Lactase persistence gene Pattern of genetic linkage indicates history of selective sweep • Hitchhiking effect – strong selection will sweep neighboring alleles as well as selected allele to high frequencies Strong evidence for positive selection on lactase persistence alleles • Hitchhiking effects in Africans (A) and Europeans (B) are large • Green and Orange shows lactose tolerance alleles neighboring regions are very large Artificial selection in crop production • First chapter of “Origins of Species” devoted to artificial selection • Selection performed by humans Domesticated Brassica Explained Suddith et al. sequenced the CAULIFLOWER (inflorescence) genes from a variety of Brassicas. They found loss of function in mutations in: – 2 of 11 alleles in wild cabbage – 3 of 7 alleles in kale – 8 of 9 alleles in broccoli – 10 of 10 alleles in cauliflower. It is likely that ancient farmers selected the larger and larger inflorescence traits caused by the loss of function alleles in CAULIFLOWER. Eventually, these alleles became very common in the populations. 29 Artificial selection in crop production 15 Gradual increase in cob size documented by archaeologists All from one site in Mexico – three main loci involved Teosinte Oldest ---- to ------ Youngest Co-evolution of humans and plants • Are the plants manipulating the humans so that the humans reproduce the plant? 32 Domestic dog diversity created in last 15,000 years Pesticides and herbicides act as agents of selection Resistance to pesticides in houseflies Rapid evolution of herbicide resistance Alteration in EPSPS enzyme leads to Roundup resistance Monsanto Roundup (glyphosphate) • Blocks EPSPS enzyme (amino acid biosynthesis) • Ryegrass (A) and goosegrass (B) point mutation in EPSPS creates resistance • Palmer amaranth (C) – gene duplication / up-regulation of EPSPS creates resistance Two mechanisms of resistance Creation of refuges can slow the evolution of resistance • Bt crops select for resistance in pests – Comes at a cost when Bt is not present • Creation of Bt-free refuges favors Bt- susceptible insects – resistanceution of • required by law – 20% for corn – 50% for cotton Evolution of shorter male horns due to “Trophy” hunting Cod fishing has influenced life-history evolution • Atlantic cod reach sexual maturity at a much smaller size (and younger age) than before industrial fishing with nets Important Concepts • The speed of evolution depends on amount of genetic variation and strength of selection – Leads to rapid resistance in pest populations • An understanding of evolutionary biology can lead to novel management practices Big Misconception Natural selection acts on individuals and the individuals do not do things for the good of the species. Nothing is ever done for the "good" of the species. If an allele existed that was truly altruistic, it would be strongly selected against. – Altruism: a behavior that reduced the fitness of the bearer and increased the fitness of others. – Bearer would have less offspring (altruistic allele frequency would decrease in the population). – Others would have more offspring (higher percentage would not have the allele). 42 Lions can be Anti-Altruistic • Competing males that defeat other males and take over a pride will immediately kill all infant cubs (infanticide). • This increases the winning males fitness because non- nursing females will become fertile much sooner than nursing females. • The winner will have offspring sooner. Infanticide is widespread among animals. • Clearly not for the good of the species. 43 Anti-altruism in humans? The graphs show the rate at which parents kill their children (biological parents compared with step-parents by age of child). Data shown was collected in Canada,1974 – 1983. (Canada is a relatively normal country in terms of its total homicide rate.) Is it the same infanticide seen in lions? Is this evidence that we hold our genes more carefully than those of others? Does it reflect some other social factors? Or is it some combination of biological and social factors? 44 22 Chapter 6 The ways of change: drift and selection The Synthetic Theory of Evolution Modern Synthesis – Neo-Darwinism – Synthetic Theory: A Combination of Darwin, Morgan and Mendel: (1) As a result of mutation creating new alleles, and segregation and independent assortment shuffling alleles into new combinations, individuals within populations are variable for many traits. (2) Individuals pass their alleles on to their offspring intact. (3) In every generation, some individuals are more successful at surviving and reproducing than others. (4) The individuals that survive and reproduce, or who reproduce the most, are those with the alleles and allelic combinations that best adapt them to their environment. Results in Evolution – alleles associated with higher fitness increase in frequency from one generation to the next. 2 1 Population genetics • Study of the distribution of alleles in populations and causes of allele frequency changes • Diploid individuals carry two alleles at every locus – Homozygous: alleles are the same – Heterozygous: alleles are different • Evolution: change in allele frequencies from one generation to the next Population Genetics • Mendelian genetics allows us to predict characteristics of the next generation within families • Population genetics allows us to predict the characteristics of the next generation in whole populations 4 The Hardy-Weinberg Equilibrium Model Begins with an ideal model of what happens to allele and genotype frequencies in an idealized system. • A population is a group of interbreeding individuals and their offspring. • Once we know how Mendelian genetics works in the ideal population, one can analyze real populations. 5 Hardy-Weinberg equilibrium • Population allele frequencies do not change if these 5 things are true: – Population is infinitely large (no genetic drift) – Genotypes do not differ in fitness (no selection) – There is no mutation – There is no migration – Mating is random Hardy-Weinberg Equilibrium No evolution = no allele frequency change Start with a population with genotypes in a ratio of 1:2:1. A simple Mendelian monohybrid cross with one gene, two alleles. Results in new generation (zygotes) with genotypes of A1 1 + 2 A A1 2A A 2 2 If there is no evolution, the allele frequencies will not change over generations. This square is for 2 individuals.der to find out if evolution We need to calculate genotypes andurred, we’ll have to allele frequencies for a wholealculate the frequencies population of individuals! of alleles. 7 Frequencies of the Genotypes First step – calculating the frequency of the genotypes of the zygotes Same method as with Punnett square analysis, but use the frequency of each allele instead of its identity to complete the crosses. freq (A1) = p freq (A2) = q Do the math (which is simpl8) 4 Calculating frequencies of Genotypes (Spelled out step by step) 1 Step: calculate the probability of combining one A gamete with 1 a second A 1amete: (homozygous A A )1 1 Probability of o1e A x Probability of a 1econd A = p x p = p 2 Step: calculate the probability of combining one A sperm with an A egg: (heterozygous A A ) 1 2 1 2 Probability of o1e A x Probability 2f an A = p x q = pq 3 Step: calculate the probability of combining one A 1gg with an A sperm: (heterozygous A A ) 2 1 2 Probability of o1e A x Probability 2f an A = p x q = pq 4 Step: calculate the probability of combining one A 2amete with a second A gamete: (homozygous A A ) 2 2 2 2 Probability of o2e A x Probability 2f an A = q x q = q Now we have the frequencies for the zygotes’ genotypes: 2 2 p + 2pq + q = 1.0 (for A 1 1 (for A 1 2 (for A A2)2 (equals total) 9 Part 2: calculate the allele frequencies of the new generation from the genotype frequencies The frequencies of genotypes in the next generation equal: A 1 1 + 2 A A1 2 + A 2 2 p2 + 2pq + q 2 Next step is to calculate the frequencies of each allele in the next generation. Start with allele A 1 10 5 Part 2 – Calculate allele frequencies Calculation of the frequency of allele A : 1 A 1lleles from genotype A A cons1it1te a proportion of the population equal to p . 2 A 1lleles from genotype A A cons1it2te a proportion of the population equal to ½ (2pq). The allele frequency for A is therefore equal to: 1 p + ½(2pq)= p + pq 2 We also know that p + q = 1 (total frequency of both alleles = 100%) Therefore q = 1 - p 11 Part 2 – Calculate allele frequency for A 1 p + ½(2pq)= p + pq q = 1 – p Substituting: p + pq = p + p(1-p) = p + p – p 2 = p Therefore, the allele frequency for A in this next generation (with 1 no selection, no genetic drift, no mutation, no migration and random mating) = p The allele frequency for A in the first generation started out = p. 1 When our assumptions are met (i.e. no selection, no genetic drift, no mutation, no migration and random mating), then there is no evolution. 12 6 Hardy-Weinberg Equilibrium – Summary The allele frequency for A in t1e second generation = p Similarly, we can solve for q and show that the allele frequency for A in the second 2 generation = q The allele frequency for A in t1e first generation started out = p and the allele frequency for A 2 in the first generation started out = q. No evolution has occurred. 13 Hardy-Weinberg Equilibrium Constitutes proof of the general case that allele frequencies do not change when there is no selection, no genetic drift, no mutation, no migration and random mating. Hardy-Weinberg Equilibrium Principle: no selection, no genetic drift, no mutation, no migration and random mating = No evolution. Important consequence is that the allele frequencies across generations can be stable (in equilibrium) at any value of p and q. 14 7 Predictions from Hardy-Weinberg • Allele frequencies predict genotype frequencies when assumptions are met: p + 2pq + q = 1 • Mechanisms of evolution are forces that change allele frequencies Populations evolve through a variety of mechanisms Summary • Hardy-Weinberg model serves as the fundamental null model in population genetics – If a population’s allele frequencies are not in “equilibrium” i.e. not as predicted by Hardy Weinberg, then evolution may be happening. Genetic drift results from random sampling error • Sampling error – a chance difference in the frequency of a trait in a subset of a population versus the frequency of the trait in the entire population. • Sampling error – larger for small samples than it is for large samples. Genetic Drift reduces variation in a population • Alleles are lost at a faster rate in small populations – Alternative allele is fixed • Genetic drift is a function of population size Genetic drift causes evolution in finite populations • Gen 0 – 175 populations of 16 bw/bw 75flies – Very small population size • Bred through 19 generations • Gen 19 – most populations “fixed one allele or the other Random Fixation of Alleles If genetic drift is the only evolutionary mechanism at work on a finite population, • then eventually one allele will become fixed (frequency = 1.0) • and one allele will be lost (frequency = 0). Mathematically, the probability that an allele will become fixed is equal to its initial frequency. 21 Loss of Heterozygosity – the Reality In 1931, Sewald Wright showed if genetic drift is the only evolutionary force acting on a population, then the loss of heterozygosity from one generation to is certain. Heterozygosity follows the relationship: H = H [1 - 1/(2N)] where N=population size Unless N = ▯, heterozygosity will decrease with every generation. If N is finite, 1/(2N) will be between ½ and 1, so heterozygosity will be lower in the next generation. If N is small, heterozygosity will decrease very rapidly. 22 11 Loss of Heterozygosity – a Proof Consequence of genetic drift: – random fixation and loss of alleles – frequency of heterozygotes decreases. From H.-W. the probability of heterozygote is 2(p)(q) If p is the frequency of allele A , then 1 End effect: – heterozygosity is maximal when p=0.5 – decreases as p becomes greater or less than 0.5 – eventual loss of one allele or the other 23 Dire consequences for species approaching extinction When only 50 animals left, and you can accomplish random mating, you will lose 1% heterozygosity per generation due to genetic drift. H g+1 = H g1 - 1/(2N)] If there are only 10 animals left, and you are brilliant enough to still accomplish random mating, you will lose 5% heterozygosity per generation. Genetic drift: Robs a species of the genetic diversity it may need to adapt and survive in a new environment at exactly the time it needs this diversity the most. 24 12 Bottlenecks reduce genetic variation via sampling errors Northern elephant seals 1800s hunting animals to 30 Bottleneck • event that reduces a population to a small number Genetic drift • (sampling errors) reduces genetic diversity drastically Lasts for a very long time Rare alleles are likely to be lost during a bottleneck Mobile elements reveal small population size in the ancient ancestors of Homo sapiens 13 Founder effect – another sampling error effect Pitcairn Island - 1789 Bounty – descendants now >2000 Founder effects cause loss of diversity via genetic drift (sampling errors) The concept of fitness • Fitness: the reproductive success of an individual with a particular phenotype • Components of fitness: – Survival to reproductive age – Mating success – Fecundity – Easiest way to measure: count offspring • Relative fitness: fitness of a genotype standardized by comparison to other genotypes Contribution of alleles to fitness • Average excess fitness: difference between average fitness of individuals with allele vs. those without Δp = p x (aA1ϖ) aA1= average excess fitness due to A1 ϖ = average fitness of population If A1 is “good”, Δp is positive. If A1 is “bad”, Δp is negative. Natural selection more powerful in large populations • Drift weaker in large populations, but can dominate in small populations • Small advantages in fitness can lead to large changes over the long term Pleiotropy may constrain evolution • Pleiotropy: mutation in a single gene affects many phenotypic traits – Can be antagonistic • Some positive effects + some negative effects – Net effect on fitness determines outcome of selection Pesticide resistance and pleiotropy • Ester1 – overproduces esterase enzymes – Resistance to insecticides – But! Easier caught by predators (spiders) • Overall effect is in both contexts Pesticide resistance and pleiotropy Ester4 (1986) – Slightly less insecticide resistance – Much less damaging in pleiotropy • Less drop off in low pesticide zones Experimental evolution provides important insights about selection Richard Lenski – since 1988 ~50,000 generations of E. coli Growth on limiting glucose Natural selection in action Alleles that lower fitness experience negative selection Alleles that increase fitness experience positive selection Lenski has been able to find some alleles responsible and determine when they arose. All by mutations Relationships among alleles at a locus • Dominance: dominant allele masks presence of recessive in heterozygote • Additive: allele yields twice the phenotypic effect when two copies present – HMGA1 “height” allele – Heterozygote is 0.5 cm taller – Homozygote is 1.0 cm taller • Recessive: shows phenotype only in homozygote Effects of selection on different types of alleles Dominant – fast, but does not go to fixation Additive – fast and often goes to fixation Recessive – slow and can go to fixation All with allelic selection coefficient of 0.05 Will AIDS Increase the CCR5-D32 Allele Frequency? (recessive allele) Modeling suggests: no real human population with a high enough initial CCR5- D32 allele frequency that is selected strong enough by HIV-mortality Non-real case: Ashkenazi Jews of Europe: CCR5-D32 = 0.2 Mortality rates in Botswana = 25% Even then, needs 40 generations (1000 years) 38 19 Will AIDS Increase the CCR5-D32 Allele Frequency? European Populations Ashkenazi Jews of Europe: Highest CCR5-D32 = 0.2 Mortality rates in Europe (very low) = 0.005 40 generations (1000 years) Sub-SaharanAfrican Low CCR5-D32 = 0.01 Mortality rates in S.Africa (very high) = 0.25 40 generations (1000 years) 39 Actual Conditions: CCR5-D32 Frequency in Sub-Saharan Africa Low CCR5-D32 = 0.01 to start. Mortality rates in S. Africa (very high) = 0.25 Needs >325 generations of persistent lethal selection to increase CCR5- D32 frequency to 1 This would theoretically take about 8500 years. 40 20 Mutation generates variation Mutation rates for any given gene are low But: – genome size is often huge – population size can be huge • Therefore: many new mutations arise each generation • Estimate in humans: – 1.1 x 10 mutations per position per haploid genome – Genome size is 3.5 billion • 70 mutations per baby – 140 million babies per year – 9.8 billion new mutations in humans per year ~ 3 mutations per position per year! • Mutations – Source of variation for selection and drift to act Cystic fibrosis • Most common lethal genetic disease among U.S. Caucasians – Thick mucus in bronchial passageways and pancreatic ducts interferes with the functioning of these organs. • Defect in a chloride ion transport protein within plasma membranes – when chloride moves, water normally follows – lack of water results in the thick mucus. 42 21 Most Natural Populations are Genetically Diverse DNA electrophoresis studies of the cystic fibrosis locus • Locus on chromosome 7 • Encodes a transmembrane protein called CFTR CFTR enables cells of the lung to ingest and destroy bacteria. Homozygous CFTR loss-of-function mutations suffer chronic Pseudomonas aeruginosa infections. – Leads to lung damage • Geneticists have sequenced the DNA for CFTR in over 15,000 cystic fibrosis patients. 43 Genetically Diversity at the CFTR Locus Graph shows the abundance and location of loss-of- function mutations in the CFTR gene. Over 300 different mutations have been found. 44 22 Mutation-selection balance • Equilibrium frequency reached through tug-of-war between negative selection and new mutation • Explains persistence of rare deleterious mutations in populations Mutation – Selection Balance Spinal muscular atrophy Neurodegenerative disease of voluntary muscles Caused by mutations in the telSMN gene 2nd most prevalent autosomal recessive lethal disease in Caucasians; even higher in African Americans and Hispanics telSMN alleles persist at a frequency of ~0.01 Selection coefficient (fitness value) against these alleles is 0.9 !!! Why do these alleles persist at the 1% frequency? They are created at a rate that is equal to their removal. Mathematical modeling shows that Mutation –Selection balance can account for the persistence of the telSMN mutant alleles in the population 46 Balancing selection • Some forms of selection maintain diversity in populations: – Negative frequency-dependent selection – Heterozygote advantage Frequency Dependent Selection Elderflower orchids come in 2 colors: purple and yellow. The flowers attract bees, but have no nectar. The bees visit one color then the other, apparently looking to the other for nectar after being disappointed. The bees visit equal numbers of purple and yellow flowers. 48 Negative frequency-dependent selection Male success Female success • When yellow is rare – higher fitness • When common, lower fitness Heterozygote advantage sickle-cell anemia Mutation – Selection Balance does not explain cystic fibrosis: needs something else CFTR mutant alleles • maintained at a frequency of 0.02 in Caucasian populations • simple mutation – selection balance cannot account for this high allele frequency – Needs a mutation rate of 10 ; best real estimates are 10 -8 51 Mutation – Selection Balance + Heterozygote Advantage Fitness costs suffered by cystic fibrosis alleles in the homozygote balanced by an advantage in the heterozygote. Pier et al 1998 hypothesized – that CF heterozygotes would be resistant to typhoid fever – and that this would balance the disadvantage in the homozygotes. Typhoid fever is caused by a bacterium Salmonella typhi that initiate infections by crossing the cells that line the gut. Pier hypothesized that Salmonella typhi cross this barrier by using the CFTR membrane protein. 52 26 Mutation – Selection Balance + Heterozygote Advantage Note the log scale Tested the hypothesis by constructing three lines of mouse cells with three different CFTR genotypes: +/+ +/DF508 DF508/DF508 After exposure to Salmonella typhi the number of bacteria found inside the mouse cells was measured. Results support the hypothesis Salmonella typhi resistance in the heterozygote balances out the negative fitness in the CFTR homozygotes. 53 Mutation is a weak force by itself Even though it is a weak force, over long periods of time (many generations), constant mutation can have a appreciable effect. After 1000 generations the frequency of A will be 0.81. For most genes (with lower mutation rates), this effect will be even less. Mutation alone usually cannot cause appreciable changes in allele frequency (evolution). 54 27 Mutation with Selection can be a potent force Mutation in combination with natural selection is a very important force in evolution. 55 Selection on Silent Mutations Question: Why is the rate of mutation in pseudogene appear to be higher than the rate of silent mutations in real genes? – pseudogene – duplicated gene with no gene expression – silent mutations - same amino acid / different codon It turns out that the amount of tRNAs in the cell for degenerate codons is not equal. Phenomenon called codon bias operates in expressed genes. 56 Selection on Silent Mutations Silent mutations to codons that are rare in proteins that are highly expressed, "run out" of the appropriate tRNA. Slows translation. These silent mutations can be negatively selected against. 57 Hitchhiking Effects on Silent Mutations This special effect occurs in the neighborhood of an advantageous amino acid substitution mutation that is strongly selected (positively). Neutral mutations or even slightly deleterious mutations that are very close to the positive mutation are "swept along" with the advantageous allele an also increase in frequency. These mutations hitchhike on the positive mutations success. 58 Migration Migration in an evolutionary sense is the movement of alleles between populations. It is not seasonal movements of populations from one area to another. Migration is the transfer of alleles from a gene pool of one population to the gene pool of another. Mechanisms of such "gene flow" can be many things: – Juvenile animal migration – Movement of pollen, seeds or spores by wind, water or animals 59 One Island Model of Migration Hardy-Weinberg analysis of two populations: One very small island pop. and a very large continental population. Assumptions: – Migration from island to continent is inconsequential to gene pool of continent. – Migration from continent to island is important to gene pool of the island population. Migration is effectively ONE-WAY. 60 30 Migration can alter allele and genotype frequencies An example: 800A A islanders. 1 1 Migration of 200 outsiders onto the island. Allele frequencies change from 100%A to1 80%A : 20%A 1 2 Genotype frequencies change from 100%A A to 80%A A : 20%A A 1 1 1 1 2 2 Migration has thrown the Hardy-Weinberg Equilibrium off . Hardy-Weinberg predicts that this population should have genotype frequencies of 0.64A 1 :10.32A A 1 2.04A A 2 2 61 Migration General Effects Migration will keep an island population more like the mainland population. Tends to homogenize allele frequencies across populations. If unopposed, migration will completely homogenize the allele frequencies Migrations tend to prevent the evolutionary divergence of populations. 62 31 Research on Migration Water snake populations in Lake Erie: Color bandedness is controlled by single gene with 2 alleles. Banded is dominant. Nerodia sipedon On the mainland, snakes are predominantly banded. On the islands, snakes are mostly unbanded. Appears to be due to predator selection: Island snakes bask on limestone rocks; less predation of unbanded snakes . Why isn't the banded allele selected out of the island gene pool? Answer appears to be migration of banded snakes from the mainland. 63 Lake Erie Snake Migration banded Ais unbanded; B and C are intermediate; D snakes are banded. Banded have disadvantage on the Islands. Migration is opposing natural selection in this example. (Note the trend away from mainland.) Migration is preventing the fixation of unbanded on the islands. 64 32 Random Mating Final assumption of Hardy-Weinberg Equilibrium Model This is often (almost always?) not the case. Nonrandom mating does not by itself cause evolution (change in allele frequencies over generations). It does have profound effects, however. 65 Inbreeding in the Malarial Parasite Plasmodium falciparum life cycle: Only the oocyst is diploid. Since it is likely that the original infection of the mosquito occurred with a single genotype, Brothers are usually mating with sisters. 66 Inbreeding in the Malarial Parasite If inbreeding is occurring then it should be detectible with high homozygosity. 67 Inbreeding in the Malarial Parasite Researchers checked 3 loci for allele frequencies in protein coding genes of the oocyst. Highly polymorphic. Should result in high heterozygosity if random mating occurs. 68 34 Inbreeding in the Malarial Parasite Researchers checked 3 loci for allele frequencies in protein coding genes of the oocyst. Highly polymorphic. Should result in high heterozygosity if random mating occurs. Any violation of H.-W. may be responsible for the disequilibrium. But! only nonrandom mating can easily create these excesses of homozygosity. 69 Inbreeding Most common type of nonrandom mating is inbreeding. – Inbreeding: mating among genetic relatives. Inbreeding increases the frequency of homozygotes. It does not change the allele frequencies. Start here! 70 35 Inbreeding Allele frequencies: A 1 500/1000 50% A 500/1000 50% 2 In all generations from 0 to 3, no change. No evolution occurs (no change in allele frequency). Nonrandom mating is not a mechanism of evolution. 71 Inbreeding Depression Inbreeding cannot directly change allele frequencies, but it affects the evolution of a population indirectly. – called Inbreeding Depression Occurs when the mean fitness of a population decreases because of higher homozygosity of deleterious recessive mutations. 72 36 Inbreeding Depression in Humans Grey line is expected relationship if inbreeding had no effect on child mortality rates. All points for mating "cousins" higher than unrelated pairs. Demonstrates negative selection of homozygous recessives. 73 Prairie Chicken Mating Two pound birds with extraordinary mating rituals: Males congregate in large breeding areas (leks) and stake out territory. Inflate bright air sacks, stomp their feet and spread their feathers. Make a noise audible for miles. Females visit, inspect and choose a mate. 74 Prairie Chicken Population 1933 25,000 1962 2,000 1972 500 1990 76 1994 ▯ 50 1994 5 males Habitat destruction from the introduction and use of the steel plow is the most likely cause of this mear extinction. Before steel plow: 60% prairie; today ▯ 0.01% 75 Prairie Chicken Population 1933 Ban on hunting Large scale population decline, 1962 Habitat 1 Protected then growth is a 1967 Habitat 2 Protected "bottleneck". 1970 – 1975 Populations grow, Mid-70s on, population crashes Why the success, then the looks good failure? 76 38 Prairie Chicken Population Decline In 1960s, the two populations were very small and geographically isolated. Perfect conditions for genetic drift. Genetic drift results in: Random fixation of alleles, Accumulation of Decreased heterozygosity deleterious recessives (genetic load) can through inbreeding. Decreases overall fitness. result in extinction. How can this be tested? 77 Prairie Chicken Decreased Fitness Egg hatching success, A measure of overall fitness. Throughout the 60s ▯90% In 1990s as low as 40%. If this is due to inbreeding and loss of heterozygosity decreasing genetic diversity, then this should also be observable. 78 39 Prairie Chicken Decreased Genetic Diversity Scientists measured with DNA technologies the number of different alleles in several different populations (including the threatened Illinois population). Prebottleneck = museum samples from 1930s. Genetic diversity has decreased significantly, even when compared to their own ancestors. 79 Prairie Chicken Population Increases Again If the problem is genetic diversity, then the solution would be to increase gene flow (migration). 1992 Prairie chickens trapped in MN, KS, NE were moved into Jasper Co. Illinois. Population resumed growth. Hatch rates are again over 90%. Inbreeding does not effect allele frequency (no evolution effect), but it does effect fitness. Selection can then operate on the population. 80 40 Hardy-Weinberg equilibrium Population allele frequencies do not change if these 5 things are true: – Population is infinitely large (no genetic drift) – Genotypes do not differ in fitness (no selection) – There is no mutation – There is no migration – Mating is random Chapter 6 The ways of change: drift and selection The Synthetic Theory of Evolution Modern Synthesis – Neo-Darwinism – Synthetic Theory: A Combination of Darwin, Morgan and Mendel: (1) As a result of mutation creating new alleles, and segregation and independent assortment shuffling alleles into new combinations, individuals within populations are variable for many traits. (2) Individuals pass their alleles on to their offspring intact. (3) In every generation, some individuals are more successful at surviving and reproducing than others. (4) The individuals that survive and reproduce, or who reproduce the most, are those with the alleles and allelic combinations that best adapt them to their environment. Results in Evolution – alleles associated with higher fitness increase in frequency from one generation to the next. 2 1 Population genetics • Study of the distribution of alleles in populations and causes of allele frequency changes • Diploid individuals carry two alleles at every locus – Homozygous: alleles are the same – Heterozygous: alleles are different • Evolution: change in allele frequencies from one generation to the next Population Genetics • Mendelian genetics allows us to predict characteristics of the next generation within families • Population genetics allows us to predict the characteristics of the next generation in whole populations 4 The Hardy-Weinberg Equilibrium Model Begins with an ideal model of what happens to allele and genotype frequencies in an idealized system. • A population is a group of interbreeding individuals and their offspring. • Once we know how Mendelian genetics works in the ideal population, one can analyze real populations. 5 Hardy-Weinberg equilibrium • Population allele frequencies do not change if these 5 things are true: – Population is infinitely large (no genetic drift) – Genotypes do not differ in fitness (no selection) – There is no mutation – There is no migration – Mating is random Hardy-Weinberg Equilibrium No evolution = no allele frequency change Start with a populatio
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