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Unformatted text preview: Problem of the day
Imagine a locus with three alleles (A1,A2,A3). The frequency of alleles are summarized by p, q, and r, respectively (i.e., the frequency of allele A1 is p). Feb 9 Problem of the day The expected frequency of A1A3 heterozygotes is (at Hardy Weinberg equilibrium):
A) (p2 * r2) / 2pr B) 2*p*r C) 2*p*q*r D) 2*p*q E) We are not able to figure that out given the information provided A population is at Hardy Weinberg equilibrium for two traits, each with two alleles. For the first trait (A/a), p = 0.9, q=0.1. For the second trait (B/b), p = 0.4, q=0.6 The traits sort independently. What is the frequency of individuals that are homozygous recessive for both traits (aabb)? 1) 0.1, 2) 0.01, 3) 0.36, 4) 0.036, 5) 0.0036 6) There is not sufficient information to figure this out
Breaking the problem down: A) the probability of aa is q^2 = 0.01. B) The probability of bb is q^2 = 0.36. C) The probability of both events happening is 0.01 * 0.36 = 0.0036 Feb 9: Natural Selection 1 Causes of Evolution
Mutation Gene flow Genetic drift Non-random mating Non- Natural Selection
Types of natural selection, including... 1. stabilizing selection 2. directional selection 3. disruptive selection 4. balancing selection 5. frequency-dependent selection frequency6. sexual selection 7. kin selection (and the evolution of cooperation) Causes of Evolution, Terminology REVIEW
1. ______________: The differential contribution of offspring ______________ to the next generation by various genetic types belonging to a population 2. Natural selection acts on __________, 3. ________ is the relative reproductive contribution of a phenotype to subsequent generations 4. Changes in the ___________ success of different HERITABLE aspects of phenotypes in a population leads to changes in the frequencies of the alleles that contribute to a phenotype (i.e. evolution by natural selection) The Consequence
Natural selection increases the frequency, across generations, of individuals with more advantageous alleles (or genotypes) "Phenotypes" fits where? Phenotypes"
Evolution, Phenotypes (or individuals), Fitness, Relative alleles or genotypes relative to individuals with less advantageous Lecture 20, Natural Selection 1 1 Causes of Evolution, E. Natural Selection
Studying Natural Selection: If the trait favored by selection is discrete and controlled by one or a few alleles--like flower color or seed color in peas--then we can alleles-- peas-- examine evolution by studying the change in ________________ over time But many traits are ____________, and controlled by many genes ____________, (i.e. ___________) and also affected by the environment ___________) Here we look at the change in the phenotypic distribution of the population over time
Phenotype Frequency Causes of Evolution, Natural Selection Human height as a heuristic
Human height is a polygenic and quantitative character 0.16 Mean = 5.6
0.12 0.08 A Histogram showing a normal distribution of height We will now examine the types of natural selection, and how they act on quantitative traits 0.04 0 5.42 5.50 5.58 5.83 5.92 6.00 6.08 6.25 6.33 6.33 5.25 5.33 5.67 5.75 5.00 5.08 5.17 6.17 6.42 Allele frequencies, quantitative, polygenic Height (feet) II. Causes of Evolution, E. Natural Selection II. Causes of Evolution, E. Natural Selection 0.16 0.16 Phenotype Frequency 0.12 0.08 What if natural selection got rid of everyone over 6' and 6' everyone under 5.3'? 5.3' Phenotype Frequency 0.12 0.08 What if natural selection got rid of everyone over 5.75'? 5.75' 0.04 0.04 0 5.42 5.50 5.58 5.83 5.92 6.00 6.08 6.25 6.33 6.42 5.25 5.33 5.67 5.75 6.17 5.00 5.08 5.17 0 5.42 5.50 5.58 5.83 5.92 6.00 6.08 6.25 5.25 5.33 5.67 5.75 5.00 5.08 5.17 6.17 6.42 Height (feet) Height (feet) II. Causes of Evolution, E. Natural Selection 0.16 0.12 0.08 0.04 1. Stabilizing selection
5.25 5.33 5.42 5.50 5.58 5.67 5.75 5.83 6.08 6.25 6.25 6.25 6.33 6.33 6.33 5.08 5.17 5.92 6.00 5.00 6.17 6.42 Phenotype Frequency 0 0.16 0.12 0.08 0.04 0.16 2. Directional selection
5.42 5.50 5.58 5.67 5.75 5.83 5.92 6.00 6.08 6.17 5.00 5.08 5.17 5.25 5.33 6.42 Phenotype Frequency 0.12 0.08 0.04 What if natural selection got rid of the middle--everyone middle-- over 5.42' and under 5.42' 5.83'? 5.83'
5.42 5.50 5.58 5.83 5.92 6.00 6.08 6.25 6.33 5.25 5.33 5.67 5.75 5.00 5.08 5.17 6.17 6.42 0 0.16 0.12 0.08 0.04 0 3. Disruptive selection Diversifying selection
5.42 5.50 6.00 5.25 5.33 5.58 5.67 5.75 5.83 5.92 6.08 5.00 5.08 5.17 Height (feet) Height (feet) Lecture 20, Natural Selection 1 6.17 6.42 0 2 Causes of Evolution, 3 common types of Natural Selection based on directionality with quantitative traits
___________ __________ ___________ favors average phenotype favors individuals that are EITHER above OR below the average phenotype favors individuals that are BOTH above AND below the average Causes of Evolution, Natural Selection Stabilizing Selection
Stabilizing selection: selection: 1. favors individuals with the average phenotype 2. reduces phenotypic variance for that trait
FITNESS FUNCTION Relative Fitness frequency RESPONSE FUNCTION
before selection after selection Phenotypic trait (z) Phenotypic trait (z) Stabilizing Selection does not significantly change the mean; it reduces the phenotypic variance Causes of Evolution, Natural Selection Stabilizing Selection
CASE STUDY: Stabilizing selection on human birth weight
Infants pre-mature pre- Causes of Evolution, Natural Selection Directional Selection
Directional selection: selection: 1. shifts the mean value of a trait 2. usually reduces phenotypic variance for that trait
FITNESS FUNCTION RESPONSE FUNCTION
after after selection before selection Infants can't can' get out! "Many obstetricians and some midwives recommend inducing labor if you are near or at full-term, and they fullthink the baby is larger than average -- macrosomia, literally, "big body." Typically, they use an estimation macrosomia, body." that the baby weighs or will soon weigh 4,000 grams (8 lbs. 13 oz.) as the threshold." oz.) threshold."
from parenting.ivillage.com Directional Selection favors more _______________ individuals (e.g. largest or smallest) and leads to a change in mean Lecture 20, Natural Selection 1 3 Causes of Evolution, Natural Selection Directional Selection
CASE STUDY Directional selection in the peppered moth, Biston betularia H.B.D. Kettlewell Causes of Evolution, Natural Selection Directional Selection
Directional selection in peppered moths: as soot declines so does the dark (carbonaria) morphs (carbonaria)
100 % Melanic Moths 80 60 40 "typica" form typica" "carbonaria" form carbonaria" amount of soot
20 Directional selection acting over many generations can lead to major evolutionary change 0 1959 1963 1967 1971 1975 1979 1983 1987 1991 1995 Figure 22.12 Natural Selection Can Operate on Quantitative Variation in Several Ways Disruptive/diversifying selection favors individuals at the extremes of a phenotypic distribution.
If individuals at both extremes have higher fitness... ...variation in the population is increased, and a bimodal pattern may result. Disruptive selection: individuals at either extreme are more successful than average individuals. CASE Study: Disruptive selection in black-bellied seed crackers black- Frequency Fitness BEFORE AFTER Phenotypic trait (z) Phenotypic trait (z) Disruptive/diversifying selection ... 1. has little effect on the mean value of a trait 2. usually INCREASES phenotypic variance for that trait 3. maintains genetic variation in a population (it is a form of BALANCING SELECTION). East Africa Large, hard seeds Soft, small seeds Smith 1993 Disruptive selection results in a bimodal phenotypic distribution & maintains genetic variation.
Fitness function Magalhaes IS, Mwaiko S, Schneider MV, et al. 2009. Divergent selection and phenotypic plasticity during incipient speciation in Lake Victoria cichlid fish Journal Of Evolutionary Biology 22: 260-274. Lecture 20, Natural Selection 1 4 Dayan & Simberloff `94 Character displacement in mustelids Mustellids
appear to have communities structured by competition. The diameter of their upper canine predicts a more regular distribution than expected by chance Hendry AP, Huber SK, De Leon LF, et al. 2009. Disruptive selection in a bimodal population of Darwin's finches. Proceedings Of The Royal Society Bbiological Sciences 276: 753 759 Published: FEB 22 2009 Balancing Selection 2: Heterozygote Advantage/Heterosis 2: Advantage/Heterosis Warfarin resistance in Norway rats Vitamin K complexes with coagulants in the blood to stop bleeding. Warfarin is an anticoagulant/blood thinner that prevents vitamin K from complexing with coagulants in the blood. Non-resistant rats that eat warfarin Nonbleed to death. In 1959, warfarin-resistant rats warfarinappeared in rat populations in the United Kingdom Warfarin resistance conferred by Q: Why didn't the warfarin resistance allele (Wr) go to fixation? didn' (W
100 % RESISTANT RATS + warfarin - warfarin 100 80 60 40 20 0 % RESISTANT RATS + warfarin - warfarin 80 60 40 20 0 a single mutation at the W-locus: W- Ws Wr WsWs homozygotes susceptible WsWr heterozygotes resistant WrWr homozygotes resistant 1950 1959 1966 1980 1959 1966 1980 1950 A: WrWs heterozygotes have higher fitness than either homozygote. homozygote. Figure 22.12 Natural Selection Can Operate on Quantitative Variation in Several Ways A: WrWs heterozygotes have higher fitness than either homozygote. Here's why WrWs heterozygotes have higher fitness than either Here' homozygote. 1. Rats need vitamin K in their food, and vitamin K is almost always in short dietary supply. 2. The allele that confers warfarin resistace (Wr) also makes it more difficult to absorb dietary vitamin K. 3. So, individuals carrying the Wr allele need LOTS more individuals vitamin K in their diets than individuals with the Ws allele.
Genotype Resistance to warfarin Vitamin K requirement Heterozygote advantage & warfarin resistance in Norway rats: the data please... please...
Observed f(Ws) = 0.339 Observed f(Wr) = 0.661 WsWs H-W Expected Frequencies Observed Frequencies 0.115 0.054 WsWr WrWr 0.437 0.378 TOTAL 1.000 1.000 0.448 0.568 WsWs WsWr WrWr susceptible resistant resistant 1x 2-3x 20x There are 12% more heterozygotes than expected at H-W equilibrium. H- Lecture 20, Natural Selection 1 5 Frequency-dependent selection in scale-eating cichlids FrequencyscalePerissodus microlepis Positive versus negative frequency dependence Positive frequency dependence The more common a particular trait, the more the trait is favored Right-mouthed P. Rightmicrolepis attack left flank of prey Left-mouthed P. Leftmicrolepis attack right flank of prey leftFrequency left -mouthed fish Negative frequency dependence The less common a particular trait, the more the trait is favored. Hori (1993) Science 260: 216 Sample Year Negative Frequency Dependent Selection
Gamoetophytic self-incompatibility genes self- An agricultural problem Gametophytic self-incompatibility allows individuals to avoid selfing and maintains high genetic variability. S-RNase allelic diversity can be high (7-15 different alleles). With many clones of the same tree, even if it grows well, it will not produce almonds because of gametophytic self-incompatibility. Now, imagine a wild population. If one genotype has the highest fitness, then it may spread. However, fitness can be reduced by increasing the frequency of inbreeding and self-incompatibility genes being expressed. This fosters the maintenance of variability. Almonds (and many, many other plants) Positive Frequency Dependent Selection Snail chirality
Speciation and gene flow between snails of opposite chirality. Davison et al. PLoS chirality. Biology 2005. Japanese Land Snails, Euhadra (not pictured). Snails of opposite chirality cannot interbreed. Positive frequency dependent selection could drive one or the other extinct by initial chance events. A word about Heritability Heritability is mentioned in your lab manual. The proportion of phenotypic variability that is attributable to genetic variation. As an equation: Phenotype (P) = Genotype (G) + Environment (E). Var(P) = Var(G) + Var(E) + 2 Cov(G,E). Lecture 20, Natural Selection 1 6 1. Population ecology and population genetics from the perspective of Epidemiology
Pest and pathogen outbreaks in the natural world.
Strange Pilgrims 100 (million) Years of Solitude Ia. Strange Pilgrims (1993)
Various geographic regions of the world are currently besieged by a series of invasive pests and pathogens that wreaking havoc on native communities Ballast water Agro/ forestry systems Horticultural industry Pet trade 2. 3. 4. 5. The population biology of epidemics
Chronicle of a Death Foretold The evolution of virulence
Love in the Time of Cholera Evolution of treatment resistance
The Autumn of the Patriarch Ecosystem complexity and transmission
The General in His Labyrinth Python in the everglades Ib. 100 (million) years of solitude Insects
Naive and novel hosts: historic isolation => susceptibility to pest and pathogen outbreaks Natural pest and pathogen outbreaks. Pathogens = disease causing organisms -- Often host - specific -- Can devastate host populations Asian longhorn beetle Gypsy moths -hardwoods Emerald Ash borer Hemlock wooly adelgid...... Diseases White pine blister rust Dogwood wilt....
How do we manage to maintain forests with the current onslaught of epidemic pests and disease? American Chestnut 1. Cryphonectria parasitica. An ascomycete fungus. Introduced from Asia circa 1900. By 1940 chestnuts throughout eastern North America were dead or dying Exponential expansion of novel diseases to hosts with no resistance American Chestnut and the "Chestnut Blight" Lecture 20, Natural Selection 1 7 http://kellylab.berkeley.edu/SODmonitoring/SODmovie.htm Sudden Oak Death Phytophthora ramora a generalist pathogen Horticultural introduction Emerald Ash Borer (EAB) EAB introduced in the 2002 in Detroit on pallets. Since 2002 EAB has killed an estimated 25 million ash trees in the upper Midwest. II. Chronicle of a Death Foretold
Human Disease Examples: same pattern Smallpox, Typhoid, Measles Bubonic plague, Influenza, Diptheria --- Diseases that were unknown to North America prior to European settlement. ---Very low immune response to these novel diseases among native North Americans. Syphilis, malaria, yellow fever, ... other examples Guns, Germs and Steel, J. Diamond II. Chronicle of a Death Foretold Population Biology of Epidemics
Measles in London in the 1900's What happened? Antibiotic treatment; vaccinations SIR's Model of disease epidemics
Birth, Immigration Susceptible B Death Infected R Recovered The epidemic stops when the number of susceptible individuals drops. B = P (contact) x P(transmission) R = Recovery rate D = Death rate N Time Lecture 20, Natural Selection 1 8 ...
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This note was uploaded on 10/08/2009 for the course BIS 2 taught by Professor Schwartzandkeen during the Spring '09 term at UC Davis.
- Spring '09