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Unformatted text preview: Lecture 12-13: Population Genetics Genetics I. From Transmission Genetics to Population Genetics I.
Natural Selection requires variation among individuals. Where does this variation come from, and how is it maintained? this
1. ALL new genetic variation comes from _mutations__: ALL _mutations__ • But Darwin knew that mutation was rare and couldn’t explain all variation • He also knew that most mutations were bad for the organisms 1. MENDEL, SEX, & MEIOSIS:
• Principle of Segregation: if there are 2 different alleles on each homolog, each will be allocated at random to 1N gametes(all of our gametes are haploid, we are diploid, babies form from two haploid cells); so at fertilization, new allelic combinations (genotypes) will be formed that differ from those present in the combinations parents parents • ___Independent Assortment___: Genes for different traits on non-homologous chromosomes will be allocated at random to each gamete (trait combinations can get shuffled around, ie hair or eye color) get • Recombination: Through crossing over (main way of talking about recomb.), novel combinations of alleles arise on the same homolog novel • Sexual reproduction: individual’s get 1/2 their genes from their mom and 1/2 from their dad (mixing of two things, get new genotype combination in next popul. I. From Transmission Genetics to Population Genetics
_Transmission genetics_ explains how traits are transmitted from parents to offspring (includes Mendelian genetics) from
1. 2. Transmission genetics concerns individual organisms & their Transmission alleles and genotypes alleles Remember that genotypes are not transmitted from parent to Remember offspring, only alleles offspring, • Segregation, independent assortment, recombination and Segregation, sexual reproduction deconstruct the parental genotype and form a new genotype with the old pieces and 3. Mutation adds new cards to the deck; Segregation, independent Mutation assortment, recombination and sexual reproduction reshuffles the deck the I. From Transmission Genetics to Population Genetics I.
Now we’ll shift our focus to __population genetics_, which Now __population which concerns: concerns:
1. 2. 3. 4. Populations of organisms that are members of the same species The origin and maintenance of genetic variation within populations Patterns and organization of genetic variation within populations Patterns (genetic structuring) (genetic The mechanisms that cause changes in allelic & genotypic The frequencies from generation-to-generation within populations (i.e. evolution) (i.e. _population genetics__ = the study of genetic variation and its causes _population in a population, and how this genetic variation changes over time (i.e. evolution) (i.e. II. Population Genetics II. A. Population Genetics and Evolution
Organic Evolution (a.k.a. Biological Evolution) = changes in the heritable properties of a population over the course of heritable population generations generations 1. What is meant by population? What population 2. What is meant by heritable properties? What heritable II. Population Genetics II. A. Pop Gen and Evolution, 1. What is a Population?
A population is a group of individuals of the same species that population lives & interbreeds in a particular place lives REMEMBER:
• Individual organisms do NOT evolve, __populations & species evolve_ Individual __populations • We’re stuck with the genes we have...we cannot evolve. But the number of We’re offspring that each and every one of us have (and whether they survive and reproduce), can cause evolutionary change in our population our • Natural selection is only one of the processes that can cause evolution in Natural only populations...there are others (e.g. drift, gene flow, etc) populations...there • But NS is the only process that can cause adaptation (the process by But only which a beneficial trait spreads in a population) other processes can cause allele and genotipic frequencies but NS is the only things causing adaptation, II. Population Genetics A. Pop Gen and Evolution, 2. What are allele frequencies?
Evolution = changes in the heritable properties of populations heritable populations over the course of generations over • heritable properties includes allele frequency and genotype allele frequency frequency •_allele frequency___: the frequencies of particular alleles in
the population (the # of a given allele / the total # of alleles) the •_genotype frequency__: the frequencies of particular
genotypes in the population (the # of a given genotype / the total # of individuals/genotypes) of
Why don’t we focus on phenotypic differences? We look at alleles and genotypic differences. The relationship between genotype and We phenotype is very complex, cannot just study phenotype, need to know what is happening at level of genes is II. Population Genetics A. Pop Gen and Evolution, 3. What are heritable properties?
Because the relationship between phenotype and Because genotype is very complex, due to... genotype
1. _interactions_ between alleles at the same 1. locus (e.g. dominance vs. recessiveness, effects locus of multiple alleles, and pleiotropy) and interactions between alleles at different loci at (Epistasis: diff genes interacting with each other to cause one effect ie labs on the pic to right, non additive interaction between two (one gene controlled the activation or silencing of another gene)) another Plyotrophy: one gene multiple effects, additive Plyotrophy: one gene interaction: iie siamese cats, proteing to e gene coloration and eye crossing coloration 1. _environmental effects____: the phenotype the produced by a given genotype may vary according to the environment in which the genes are expressed (two species change to their environment, there is phenotypic change in popul, nut no evolution (muscle making) popul, II. Population Genetics A. Pop Gen and Evolution, 4. Levels of Analysis
The process of evolution is studied at 2 different scales: The Microevolution is the study of changes that occur within a population Evolution = changes in the heritable properties of populations over the Evolution course of generations course •This is what we’ll be talking about for the next few lectures... Macroevolution is the study of changes between populations that can/may or may not lead to speciation can/may • Populations may be come subdivided, into subpopulations Populations • If different changes occur in the subpopulations, they may diverge and eventually become distinct species (speciation) and •Macroevol. Is caused by microevol. Macroevol. • We’ll talk about speciation later in the quarter... We’ll II. Population Genetics B. Populations as gene pools
__population___: A group of individuals of the same species that __population___ lives & interbreeds in a particular place lives
• Most species consist of multiple populations • From an evolutionary perspective, we need to study populations From because we are interested how alleles increase or decrease in frequency relative to other alleles in a group of interbreeding frequency organisms, because this is where the “struggle for existence” plays organisms because out out To understand evolution, it makes no sense to compare the To reproductive success/fitness of organisms that cannot exchange genes (like fruit flies vs. humans) genes __gene pool_: The collection of all copies of all alleles at all loci (or for some focal loci) in a population (or
• Evolutionary change involves changes in allele (and genotypic) Evolutionary frequencies through time in a gene pool frequencies II. Population Genetics B. Populations as gene pools
Last week that we calculated the predicted offspring genotypes from a given cross using a offspring Punnett square Punnett I used the analogy of a bag of pollen from the used male and a bag of ovules from a female and choosing one of each at random... choosing NOW, we’re predicting the offspring genotypes NOW, for the _entire population___, not just a _entire not particular cross between individuals particular So instead of a bag of pollen from one So 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 population Each reproductive event draws one pollen and Each one egg at from this bag of gametes, which is the ____gene pool______ ____gene II. Population Genetics B. Populations as gene pools, 1. Gene pools as M&Ms
Package Package 1 Breeding rules for M&M’s Breeding
1. Each color represents an allele (n = 6 alleles) for 1 locus 2. Frequencies (f) of each color/allele range from 0 to 1 of to 3. We make a 2N (diploid) zygote by combining two 1N (haploid) gametes • There are 21 unique genotypes! 4. All gametes are randomly picked 5. A package represents a gene pool package • Gametes can only be picked from the same package (gene pool) • Picking gametes from different packets would be like gene flow Package Package 2 Predicting GENOTYPE frequencies: HOMOZYGOUS GENOTYPES 1. freq(RedRed) = freq(red)*freq(red)=freq(red)^2 (probab. multipl. rule) 2. f(GrnGrn) = = freq(green)*freq(green )=freq(green)^2 freq(green)*freq(green 3. Same rule for all other homozygotes 3. HETEROZYGOUS GENOTYPES 1. f(RedGrn) = [[freq(red)*freq(green)]+ [freq(green)*freq(red)]]= =2[freq(red)*freq(green)] 2. f(RedBlu) = [[freq(red)*freq(blue)]+ [freq(blue)*freq(red)]]= =2[freq(red)*freq(blue)] addition [[freq(red)*freq(blue)]+ rule rule 3. Same rule for all other heterozygotes II. Population Genetics B. Populations as gene pools, 1. Gene pools as M&Ms
COLOR COLOR Red Green Yellow Blue Orange Brown TOTAL (n) Package 1 21 (0.123) 33 (0.193) 25 (0.146) 30 (0.175) 33 (0.193) 29 (0.170) 171 171 Package 2 14 (0.081) 47 (0.273) 25 (0.145) 37 (0.215) 24 (0.139) 15 (0.087) 172 Package 1 Package
1. 2. 1. 2. f(RedRed) = f(GrnGrn) = (0.123)^2 Package 2 Package
(0.081)^2 f(RedGrn) =freq red +freq green *2 f(RedBlu) = II. Population Genetics C. The Hardy-Weinberg Equilibrium
The M&M example is to illustrate the concept of the __gene pool_ __gene But a population is not a bowl of gametes; it is a group of individuals But population individuals of the same species that lives & interbreeds in a particular place of So now we want to create a general model that will allow us to So predict allele frequencies and/or genotypes of individuals in a population gene pool...this is the ___hardy weinberg equation__ ___hardy We’ll use a simpler population with 1 focal locus and just 2 We’ll alleles (the population genetics of the M&M population with 6 alleles for 1 locus is more complicated than we’ll tackle in this class) for II. Population Genetics C. The Hardy-Weinberg Equilibrium
N = 50 individuals
A2A2 A1A2 A1A2 A1 A1 A1A1 A1 A2 A1A1 A2 A2 A1 A2 A1A2 A1A2 A1A1 A1 A1 A1A2 A1A2 A1A2 A1 A2 A1A2 A1 A2 A1A1 A2A2 A1A1 A1A1 A1A2 A1A2 A1 A2 A1 A2 A1 A2 A1A2 A2 A2 A1 A2 A1 A2 A1A2 A1 A1 A1 A1 A1A2 A1A2 A1A2 A1 A2 A1 A2 A1A1 A2 A2 A1A2 A1A2 A1 A1 A1 A2 A1 A1 A1A2 A1A1 At locus A, there are 2 alleles (A1 & A2) in this gene pool (A Let p = freq(A ) Let A1A1 II. Population Genetics C. The Hardy-Weinberg Equilibrium Predicted Genotypic frequencies in the next generation? Predicted
Since p = f(A ) = 0.6, and q = f(A ) = 0.4 Since 0.6 0.4 We’ll make an assumption of random mating, that 1 randomly drawn sperm We’ll random that fertilizes 1 randomly drawn egg Predicted genotype frequencies: Predicted
A1 egg; p = 0.6 0.6 A1 sperm; p = 0.6 0.6 SPERM A2 sperm; q = 0.4 0.4 EGGS Draw a Prout square:
A2 egg; q = 0.4 0.4 0.36 0.36 0.24 0.24 0.16 f(A1A1) = 0.36 (compare to 0.30 in the original gene pool) f(A1A2) = ___0.48___ (compare to 0.60 in the original sample) f(A2A2) = 0.16 (compare to 0.10 in the original gene pool) II. Population Genetics C. The Hardy-Weinberg Equilibrium Genotypic frequencies in the next generation after that?
Once again, we use the parental genotypes (offspring from the previous Once generation) to calculate the allele frequencies for the gametes: generation) p (A ) = _____________0.6___________ Now let’s calculate predicted genotype frequencies from these allele Now predicted frequencies: frequencies: • A1A1 = 0.6*0.6=__0.36_________________ • A1A2 = _2*(0.6*0.4)=____0.48______________ • A2A2 = _0.4*0.4__0.16________________ Now genotype frequencies stopped changing, too! II. Population Genetics C. The Hardy-Weinberg Equilibrium
YOU COULD REPEAT THIS HUNDREDS OF GENERATIONS & YOU’D KEEP GETTING _the same result_____________________, blah, blah, blah: blah: • Neither the allelic, nor the genotypic ratios will change after the 1st round of _random mating, as long as they continue randomly mating_ (we began with a population slightly out of equilibrium mating_ genotype frequencies) genotype • G. H. Hardy & W. Weinberg recognized this simultaneously at the G. beginning of the 20th century, proposing the HARDY-WEINBERG beginning EQUILBRIUM EQUILBRIUM II. Population Genetics C. The Hardy-Weinberg Equilibrium The Hardy-Weinberg Theorem: In diploid organisms, allele frequencies & genotypic ratios in large biparental populations reach an equilibrium in one generation, and remain constant thereafter, unless disturbed by… generation, 1. mutations __if none of 2. gene flow from other populations 3. genetic drift/chance 4. nonrandom mating 5. natural selection
__if none of these are happening then no Evolution. H-W equilibrium expectations (predicted genotypic frequency): p2 = freq(A1A1); 2pq = freq(A1A2); q2 = freq(A2A2) II. Population Genetics C. The Hardy-Weinberg Equilibrium
Things that follow from the H-W equilibrium: Things 1. At H-W equilibrium, genotypic frequencies will be determined At solely by allelic frequencies solely 2. Note that when there are 2 alleles, and p = q = 0.5, the Note expected ratio of homozygotes to heterozygotes is 1:2:1, as it was for Mendelian inheritance was 3. Mendelian inheritance is just a special case of the general Mendelian principle of H-W equilibrium -- a single Mendelian cross using a Punnett square gives predicted genotype frequencies in a gene pool with both alleles at a frequency of 0.5 gene 4. The equation we use here is for 2 alleles at a locus. Similar The (but more complicated) equations can be derived for any number of alleles (e.g. 6 alleles in our M&M population). number II. Population Genetics II. C. The Hardy-Weinberg Equilibrium
An example from An the textbook... the Mix into giant bag (gene pool)... Ver8 =Text Fig 22.7, Ver9= 21.7 II. Population Genetics II. C. The Hardy-Weinberg Equilibrium
Generation II To calculate the predicted To (expected) genotype frequencies... We use the H-W equilibrium equation H-W (no need to draw a Prout no square to solve these...this is just for illustration) is AA = __________ Aa = ___________ Aa =___________ II. Population Genetics C. The Hardy-Weinberg Equilibrium
Now, we could compare the expected genotype frequencies (which we just Now, expected calculated) to the observed genotype frequencies (from counting genotypes) to see if the population is in H-W equilibrium see If not, then at least one of the assumptions is not met that can knock it out of HW If equilibrium, and something interesting may be happening... equilibrium, H-W Equilibrium: the fundamental null hypothesis of population genetics population
Null hypothesis (no change, no relationship between two factors) = the default position, no relationship between two or more measured phenomena, or no treatment effect. ****Represents what would happen if everything is _due to chance._ It is presumed to be true until statistical evidence nullifies it for an alternative hypothesis. What is the null hypothesis for a clicker question? II. Population Genetics C. The Hardy-Weinberg Equilibrium
H-W Equilibrium: the fundamental null hypothesis of population genetics genetics • The H-W theorem makes a set of null predictions about expected The allelic and genotypic frequencies _assuming no evolution_ _assuming • If the observed values of genotypic frequencies do not match those If expected at H-W equilibrium, ___then some evolutionary processes must be acting on the gene pool processes • In order to study evolutionary processes, we need a null hypothesis. In The H-W equilibrium provides that. The Next up: What are those processes & what effects do they have Next on allelic & genotypic frequencies? on ...
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