W09L11_Population+Genetics

W09L11_Population+Genetics - QUESTION. You have a...

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Unformatted text preview: QUESTION. You have a self-compatible plant that exhibits three traits: flower color (yellow); leaf shape (entire); and seed shape (round). These are all dominant traits. You know that the recessive characters for these three traits. They are: a) flower color = white (aa); leaf shape = toothed (bb); and seed shape = flat (cc). You conduct a test cross with a homozygous recessive to genotype your unknown plant. You get lots of seed. The resulting F1 generation has the following results: approximately 100 each of: (1) yellow flowered, entire leafed, round seeded; (2) white flowered, entire leafed, round seeded; (3) yellow flowered, entire leafed, flat seeded; and (4) white flowered, entire leaved, flat seeded. Complications for SIMPLE traits 1. Interactions between alleles at the same locus Dominance vs. recessive traits (multiple genotypes lead to same phenotype) Multiple alleles for a single trait Co-dominance / incomplete / partial dominance (apparent blending) Effects on multiple traits: Pleiotropy 2. Environmental effects The unknown parental genotype is: 1: AABBCC 2:AABbCC 3: AABBCc 4: AaBBCC 5:AaBbCC 6: AaBBCc 7: AABbCc 8:AABbCc 9: AaBbCc Complications for not so simple traits 1. Epistasis You are here Interactions among genes Multiple genes controlling phenotyopic expression of a single trait 2. Polygenic traits How Do Genes Interact? N>1 Epistasis Epistasis: phenotypic expression of one gene is influenced by Epistasis another gene. Example: 2-locus control of coat color in Labrador retrievers. At B locus, allele B (black) dominant to b (brown) At E locus, allele E (pigment deposition) is dominant to e (no pigment deposition--yellow) The Mendelians The Mendelians believed that natural selection on continuous variation was ineffective, and could never produce truly new types. Mutations of major effect were necessary in the evolutionary process, especially the evolution of new evolution types/species. Wilhelm Waldeyer identifies CHROMOSOMES Weissmann proposes that hereditary particles reside on chromosomes Morgan eats crow & admits that CHROMOSOMES BEAR PARTICULATE UNITS OF INHERITANCE! Mendel proposes existence of HEREDITARY PARTICLES deVries, Correns, & von Seysennegg REDISCOVER MENDEL'S WORK Johannsen distinguishes between GENOTYPE VS PHENOTYPE 1865 1868 1889 1892 1897 1900 1902 1905 1909 1910 1915 Darwin proposes that gemmules transmit traits E. B. Wilson describes behavior of chromosomes during embryo development Wilson & Sutton identify sex chromosomes Morgan argues against role of chromosomes in inheritance Hugo de Vries develops concept of pangenes (special particles for every hereditary character) Wilson & students confirm MEIOSIS IS REDUCTION DIVISION FOR GAMETES If you're an ee homozygote at E locus, the B-locus genotype is irrelevant Development of a comprehensive theory of inheritance The Biometricians Biometricians held that all evolution proceeded by the gradual accumulation of small, incremental changes (as per Darwin), and considered Mendelian traits, with their large phenotypic effects, were special cases. Quantitative genetics/polygenic traits to the rescue! OBSERVATION Mendel's characters were discrete and qualitative. For more complex characters, phenotypes vary continuously over a range--quantitative variation, or continuous. This is common in nature. Wilhelm Waldeyer identifies CHROMOSOMES Weissmann proposes that hereditary particles reside on chromosomes Mendel proposes existence of HEREDITARY PARTICLES deVries, Correns, & von Seysennegg REDISCOVER MENDEL'S WORK Johannsen distinguishes between GENOTYPE VS PHENOTYPE Morgan eats crow & admits that CHROMOSOMES BEAR PARTICULATE UNITS OF INHERITANCE! CONCLUSION Most quantitative characters must be POLYGENIC, controlled by multiple genes. Also. (Quantitative variation is usually due to both genes and environment (environment can determine expression).) 1865 1868 1889 1892 1897 1900 1902 1905 1909 1910 1915 Darwin proposes that gemmules transmit traits E. B. Wilson describes behavior of chromosomes during embryo development Wilson & Sutton identify sex chromosomes Morgan argues against role of chromosomes in inheritance Hugo de Vries develops concept of pangenes (special particles for every hereditary character) Wilson & students confirm MEIOSIS IS REDUCTION DIVISION FOR GAMETES Development of a comprehensive theory of inheritance 1 Nilsson-Ehle (1909) : effects of multiple loci on wheat Nilssonchaff color 3 loci (A, B, & C), each with 2 alleles (A,A'; B,B'; C,C') each (A,A' B,B' C,C' contributes equally to the color of the chaff in wheat. How multiple loci lead to continuous/quantitative variation When a large enough number of genes influence a character, it will have a continuous, normal frequency distribution. Rescuing both the Mendelian and Darwinian perspectives Discrete phenotypic classes Continuous phenotypic variation Polygenic Traits Why might it be unlikely that apparently polygenic traits are tightly linked? Linkage Mutation Pleiotropy Multiple alleles Environmental effects Epistasis Polygenic What happens when "true breeding" breeding" individuals with two different forms of a trait (e.g. wrinkled vs. smooth) are crossed together? A. All F1 offspring look like one of the parents. B. Some F1 offspring look like one parent, some like the other. C. No F1 offspring have either parent's trait. parent' D. F1 offspring look like a mix between the two parents. Now where to? That was TRANSMISSION GENETICS. GENETICS Moving from individual genotypes to characteristics of populations Natural selection acts on the individual to create changes in the distribution of characters in the population. In order to understand natural selection, we need to be able to characterize the population. FROM TRANSMISSION GENETICS TO POPULATION GENETICS Darwin's concerns about evolution through natural Darwin' selection 1. How are the phenotypic traits that influence the # of descendants an organism leaves to future generations passed from parent to offspring? offspring? 2. Why doesn't natural selection consume all variation & doesn' evolution grind to a halt? Hence, POPULATION GENETICS 2 1. MENDEL, SEX, & MEIOSIS Fertilization: individual's get 1/2 their genes from their mother and 1/2 from their father Principle of Segregation: if there are 2 different alleles on each homolog, each will be allocated at random to 1N gametes When fertilization occurs, new allelic combinations (genotypes) will be formed that differ from those present in the parents Law of Independent Assortment: Genes on non-homologous chromosomes will be allocated at random to each gamete It is virtually impossible for all of the maternally derived or paternally derived homologs to stay together in a gamete Recombination: Through crossing over, novel combinations of alleles arise on the same homolog Toward a genetic definition of evolution Evolution = change in the heritable properties of groups of individuals over the course of generations 1. 2. What do we mean by heritable properties? properties? What do we mean by groups of individuals? individuals POPULATION: A group of individuals of the same species that lives & interbreeds in a particular place Individual organisms do NOT evolve POPULATIONS EVOLVE! 2. MUTATION is the source of all novel genetic variation (Darwin considered mutation a VERY rare event; mutations are generally considered to be biased toward deleterious traits (genetic load) Mutation slowly adds variation; Sexual reproduction shuffles the deck of genes Evolution is characterized by changes in allele frequencies within a population from one time period to the next ADAPTATION: increase in frequencies of heritable properties ADAPTATION: that improve individual survival &/or fecundity relative to other members of the population TWO Important Points Regarding Evolution ADAPTATION: increase in frequencies of heritable properties ADAPTATION: that improve individual survival &/or fecundity relative to other Second Important Point: members of the population. Natural selection is one of the primary ways that populations can evolve through time, but there are others (founder effects, drift, gene flow). But natural selection is the only one that causes adaptations FIRST POINT>>> Adaptations must patiently await the random chance of mutation. Second Important Point: Natural selection is one of the primary ways that populations can evolve through time, but there are others (founder effects, drift, gene flow). But natural selection is the only one that causes adaptations "Island" population Mainland population Population Genetics Why we study genotypes and not phenotypes Review terms 1. ___________: makes it difficult to detect ___________: the frequency of recessive alleles, and some individuals have the same phenotype and different genotypes 2. _____________: The phenotypic effects _____________: produced by a particular locus may vary according to the alleles at other loci 3. ____________________: the phenotype ____________________: produced by a given genotype may vary according to the environment in which the genes are expressed e.g., Founder effect 3 Two Scales of Evolution The process of evolution is studied at 2 different scales: Microevolution is the study of changes that occur within a population Evolution = Changes in the heritable properties of a population (allele frequencies) over the course of generations This is what we'll be talking about for the next few lectures... Macroevolution is the study of changes between populations that can lead to speciation speciation Populations may become subdivided, into subpopulations If different changes occur in the subpopulations, they may diverge diverge and eventually become distinct species (speciation) We'll talk about speciation later in the quarter... Population Genetics: Populations as gene pools POPULATION: A group of individuals of the same species that POPULATION: lives & interbreeds in a particular place Most species consist of multiple populations***. populations***. From an evolutionary perspective, we need to study populations because we are interested how alleles increase or decrease in frequency relative to other alleles in a group of interbreeding organisms, because this is where the "struggle for existence" plays out existence" To understand evolution, it makes no sense to compare the reproductive success/fitness of organisms that cannot exchange genes (like fruit flies vs. humans) Gene Pool: The collection of all copies of all alleles at all loci (or for some focal loci) in a population Evolutionary change involves changes in allele frequencies through through time in a gene pool *** What does that mean? Population Genetics Populations as gene pools Last week that we calculated the predicted offspring genotypes from a given cross using a Punnett square, or by probability NOW, we're predicting the distribution of we' offspring genotypes for the POPULATION, not POPULATION, just a particular cross between individuals So instead of pollen from one plant...we have all the pollen from all the male plants in the whole population...and all the ovules from all the female plants in the whole population Each reproductive event draws one pollen and one egg at from this bag of gametes, which is the GENE POOL Population Genetics Populations as gene pools; Gene pools as M&Ms Breeding rules for M&M's M&M' 1. Each color represents an allele (n = 6 alleles) for 1 locus 2. Frequencies of each color/allele range from 0 to1 3. We make a 2N (diploid) zygote by combining two 1N (haploid) gametes gametes There are 21 unique genotypes! 4. All gametes are randomly picked 5. A package represents a gene pool Gametes can only be picked from the same package Picking gametes from different packets would be like gene flow Predicting GENOTYPE frequencies: HOMOZYGOUS GENOTYPES 1. p(RedRed) = p(Red) x p(Red) p(RedRed) p(Red) p(Red) 2. p(GrnGrn) = p(GrnGrn) 3. Same rule for all other homozygotes HETEROZYGOUS GENOTYPES 1. p(RedGrn) = p(Red) x p(Grn) + p(Grn) x p(Red) = 2 x p(Red) x p(Grn) p(RedGrn) p(Red) p(Grn) p(Grn) p(Red) p(Red) p(Grn) 2. p(RedBlu) = p(RedBlu) 3. Same rule for all other heterozygotes Simple, simple, simple COLOR Red Burgundy TOTAL Package 1 25 (0.50) 25 (0.50) 50 Package 2 25 (0.50) 25 (0.50) 50 COLOR Red Green Yellow Blue Orange Brown TOTAL (n) Less Simple Package 1 21 (0.123) 33 (0.193) 25 (0.146) 30 (0.175) 33 (0.193) 29 (0.170) 171 Package 2 14 (0.081) 47 (0.273) 25 (0.145) 37 (0.215) 24 (0.139) 15 (0.087) 172 Package 1 Package 2 .081 x .081 = .0066 .273 x .273 = .0745 1. 2. 3. 4. 5. p(RedRed) = p(Red) x p(Red) = .50 x .50 p(RedRed) p(Red) p(Red) p(BrgBrg) = p(Brg) x p(Brg) = .50 x .50 p(BrgBrg) p(Brg) p(Brg) .50 p(RedBrg) = p(Red) x p(Brg) = .50 x .50 p(RedBrg) p(Red) p(Brg) p(BrgRed) = p(Brg) x p(Red) = .50 x .50 p(BrgRed) p(Brg) p(Red) Prob (heterozygote) = = = = = 1. p(RedRed) = p(Red) x p(Red) = p(RedRed) p(Red) p(Red) 2. p(GrnGrn) = p(Grn) x p(Grn) = p(GrnGrn) p(Grn) p(Grn) .123 x .123 = .0015 .193 x .193 = .0372 1. p(RedGrn) = [p(red) x p(grn)] + [p(grn) x p(red)] = 2[p(red) x p(grn)] = ???? p(RedGrn) [p(red) p(grn)] [p(grn) p(red)] 2[p(red) p(grn)] 2. p(RedBlu) = [p(red) x p(blu)] + [p(blu) x p(red)] = 2[p(red) x p(blu)] =???? p(RedBlu) [p(red) p(blu)] [p(blu) p(red)] 2[p(red) p(blu)] 4 Population Genetics The Hardy-Weinberg Equilibrium Hardy5 30 Population Genetics The Hardy-Weinberg Equilibrium HardyN = 50 individuals At locus A, there are 2 alleles (A1 & A2) in this gene pool A1A2 A1A1 A1A2 A1A2 A1A2 A1A2 A1A2 A1A1 A2A2 A1A2 A1A2 A1A2 A1A2 A1A2 A1A2 A1A2 A1A2 A1A1 A1A1 A1A2 A1A2 A1A2 A1A2 A1A2 A1A1 A1A1 The M&M example is to illustrate the concept of the gene pool But a population is not a bowl of gametes; it is a group of individuals of the same species that lives & interbreeds in a particular place place A2A2 15 A1A2 A1A1 A1A1 A1A2 A1A1 A2A2 A1A2 A2A2 A1A2 A1A1 A1A2 A1A1 A1A2 Let p = freq(A1) freq(A Let q = freq(A2) freq(A There are 3 genotypes in the population: A1A1, A1A2,A2A2 f(A1A1) = 15/50 = 0.30 f(A1A2) = 30/50 = 0.60 f(A2A2) = 5/50 = 0.10 Total = _______ From this we can calculate the allele frequencies p = f(A1) = 0.30 + (0.60) = 0.6 f( q = f(A2) = 0.10 + (0.60) = 0.4 f( p + q = 1, so q = 1 - p A1A1 A1A2 A1A2 A1A2 A2A2 So now we want to create a general model that will allow us to predict allele frequencies and/or genotypes of individuals in a population gene pool. A1A1 We'll use a simpler population with 1 focal locus and just 2 alleles We' alleles (The population genetics of the M&M population with 6 alleles for 1 for locus is more complicated than we'll tackle here, but the same way we' that the sameprinciples apply to the two color bag of M&M's and the ' M&M 6 color bag, so do these rules for estimating the frequency of allele allele combinations in populations.) A1A2 A1A2 A1A1 A1A1 Population Genetics The Hardy-Weinberg Equilibrium HardyPredicted Genotypic frequencies in the next generation? Since p = f(A1) = 0.6, and q = f(A2) = 0.4 f(A 0.6, f(A 0.6 of the sperm will carry A1 and 0.6 of the eggs will carry A1 0.4 of the sperm will carry A2, and 0.4 of the eggs will carry A2 We'll make an assumption of random mating, that 1 randomly drawn sperm We' mating, fertilizes 1 randomly drawn egg Predicted genotype frequencies: A1 egg; p = 0.6 A1 sperm; p = 0.6 SPERM A2 sperm; q = 0.4 .36, .48, .16 Population Genetics The Hardy-Weinberg Equilibrium Hardy- Genotypic frequencies in the next generation after that? Once again, we use the parental genotypes from the previous generation to calculate the allele frequencies for the gametes: p (A1) = ___________________ q (A2) = ___________________ p + q = ___________________ EGGS A2 egg; q = 0.4 So allele frequencies did not change...Thus no evolution change...Thus Now let's calculate predicted genotype frequencies from these allele let' frequencies: A1A1 = _____________________ A1A2 = _____________________ A2A2 = _____________________ f(A1A1) = ______ (compare to 0.30 in the original gene pool) f(A1A2) = 0.24 + 0.24 = 0.48 (compare to 0.60 in the original sample) f(A2A2) = ______ (compare to 0.10 in the original gene pool) Now genotype frequencies stopped changing, too! Population Genetics The Hardy-Weinberg Equilibrium Hardy- Population Genetics The Hardy-Weinberg Equilibrium Hardy- YOU COULD REPEAT THIS HUNDREDS OF GENERATIONS & YOU'D YOU' KEEP GETTING THE SAME RESULT. Neither the allelic, nor the genotypic ratios will change after the 1st round of random mating (we began with a population slightly out of equilibrium genotype frequencies) G. H. Hardy & W. Weinberg recognized this simultaneously at the beginning of the 20th century, proposing the HARDY WEINBERG EQUILIBRIUM The Hardy-Weinberg Theorem: In diploid organisms, allele frequencies & Hardygenotypic ratios in large biparental populations reach an equilibrium in one equilibrium generation, and remain constant thereafter, unless disturbed by... by... 1. 2. 3. 4. 5. 1. Mutations 2. Gene flow from other populations 3. Genetic drift/chance 4. Nonrandom mating 5. Natural selection H-W equilibrium expectations (predicted genotypic frequency): (predicted p2 = freq(A1A1); 2pq = freq(A1A2); q2 = freq(A2A2) 5 Population Genetics The Hardy-Weinberg Equilibrium HardyThings that follow from the H-W equilibrium: H1. At H-W equilibrium, genotypic frequencies will be determined Hsolely by allelic frequencies 2. Note that when there are 2 alleles, and p = q = 0.5, the expected ratio of homozygotes to heterozygotes is 1:2:1, as it was for Mendelian inheritance 3. Mendelian inheritance is just a special case of the general principle of H-W equilibrium -- a single Mendelian cross using Ha Punnett square gives predicted genotype frequencies in a gene pool with both alleles at a frequency of 0.5 4. The equation we use here is for 2 alleles at a locus. Similar (but more complicated) equations can be derived for any number of alleles (e.g. 6 alleles in our M&M population). But for >3-4 alleles, it's easier to use quantitative genetics... >3it' Population Genetics The Hardy-Weinberg Equilibrium HardyAn example from the textbook... p = _________________ q = _________________ Mix into giant bag (gene pool)... Text Fig 22.7 Population Genetics The Hardy-Weinberg Equilibrium HardyGeneration II Population Genetics The Hardy-Weinberg Equilibrium HardyNow, we could compare the expected genotype frequencies (which we just calculated) to the observed genotype frequencies (from counting genotypes) to see if the population is in H-W equilibrium H- H-W Equilibrium: the fundamental theorem of population genetics The H-W theorem makes a set of null predictions about expected allelic and Hgenotypic frequencies If the observed values of genotypic frequencies do not match those expected those at H-W equilibrium, THEN SOME EVOLUTIONARY PROCESSES MUST BE HACTING ON THE GENE POOL AA =___________ Aa = ___________ p = 0.55 q = 0.45 0.55(2) = 0.3025; 2*.45*.55 = 0.495; 0.45(2) = 0.2025 Text Fig 22.7 Aa = ___________ Next up: What are those processes & what effects do they have on allelic & genotypic frequencies? From Transmission (Mendelian) to Population Genetics Transmission genetics explains how traits are transmitted from parents to offspring 1. 2. Transmission genetics concerns individual organisms & their alleles and genotypes. Remember that segregation, independent assortment, recombination, and syngamy (the formation of a diploid zygote from haploid gametes) destroy parental genotypes and form novel ones So, genotypes are not transmitted from parent to offspring, only alleles. 3. Population genetics concerns... concerns... 1. populations of organisms that are members of the same species 2. 3. 4. the origin and maintenance of genetic variation within populations patterns and organization of genetic variation within populations the mechanisms that cause changes in allelic & genotypic frequencies from generation-to-generation within populations review 6 ...
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