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Week 6 and 7 Bundle

by: Kennedy Deaver

Week 6 and 7 Bundle 12050 - BIOL 3350 - 001

Kennedy Deaver
GPA 4.0
Evolutionary Biology
Dr. Michael Sears

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These notes cover lecture material from the sixth and seventh weeks of class.
Evolutionary Biology
Dr. Michael Sears
Evolutionary Biology
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This 0 page Bundle was uploaded by Kennedy Deaver on Friday February 26, 2016. The Bundle belongs to 12050 - BIOL 3350 - 001 at Clemson University taught by Dr. Michael Sears in Fall 2016. Since its upload, it has received 33 views. For similar materials see Evolutionary Biology in Biological Sciences at Clemson University.


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Date Created: 02/26/16
BIOL 3350 Week 6 Chapter 6 0 Selection 0 Nature acting on some phenotype might lower reproductive success of one phenotype less survive or less offspring with particular phenotype are produced during reproduction 0 Evolution occurs when it causes a change in the overall genotypes different frequencies than what you started with Calculating gene frequencies under selection 0 w tness subscript alleles 0 Have to know average tness of entire population 0 Selective process gets you out of HWE 0 Strong selection allele is xed quickly 0 Weak selection takes longer to x allele 0 Fruit y 0 Raise them on media without alcohol over time not much change in frequency 0 Bred on media with alcohol Adh fast allele increased in frequency 0 Effect of lethal recessive alleles 0 Hard to get it out of population because heterozygotes survive 0 Two lethal alleles come together lethal 0 Lethal allele levels off but never completely gone because heterozygote form 0 In some environments there is selection for lethal allele in heterozygote Selection on recessive alleles o S selection S 1 then everyone died 0 W bar from the avg tness of the population 0 Frequency can get really small but never goes away completely 0 Selection on dominant alleles 0 Same selection on heterozygotes 0 Selection is one then they all die easy to get rid of dominant allele 0 Even in heterozygous form it will die 0 Selection Graphs 0 Can plug in values and determine frequency of alleles over time 0 Selection favoring heterozygotes 0 Fitness of heterozygote higher than dominant and recessive is completely lethal 0 Intermediate is favored o Overdominanace heterozygote superiority Selection for homozygotes 0 Go to xation Frequency dependent selection 0 Fitness changes based off how many others in your population have your phenotype or not o If there are a lot of yellow owers bees more likely to pollinate yellows o More of you there are then more t Mutation o Creates new information that can be selected on o How much effect does it have Mutation typically too small to affect measurable evolutionary change Doesn t create that much change in the population Won t cause much change on its own because it happens so rarely Salt tolerance in ies 0 High concentration of salt kills off ies o In unstressed lines few survive o In stressed lines more surviving offspring What is the relative importance of selection vs mutation for evolution 0 Selection mutation balance for a deleterious recessive allele lf selection rate is small then have large mutation rate lf selection is higher then low mutation rates 0 Selectionmutation balance for a deleterious dominant allele After selection equilibrium value is 1 Cystic brosis allele is recessive but still in population Why 0 Maintained in heterozygotes high percent of carriers 0 Cannot be explained by mutations could not maintain the percentage of carriers by itself 0 Carriers of CF could be less susceptible to typhoid fever because they have less copies of CFTR protein used by typhoid bacteria as a point of entry 0 Heterozygotes have advantage superior tness during typhoid epidemic o Medea Maternal Effect Dominant Embryonic Arrest 0 Trying to make mosquitos resistant to malaria so they don t infect humans 0 Medea had 2 instructions mothers infuse eggs with poison or embryos make an antidote 0 Mother and baby carry gene baby lives 0 Mother carries gene but baby does not baby dies 0 Ones that die all lack Medea selective advantage to having gene 0 Medea should rise in frequency Chapter 7 0 Migration 0 Small population receives immigrants from large population Signi cant input into that system Changes allelic frequencies on the island Immigrants can offset selection More migration look more alike 0 Populations out of HWE Nerodia example 0 Have different forms solid vs checkered Checkered pattern could cause a bird to see you on a rock Solid could blend better into rock On mainland see checkered and on islands see plain form 2 different optima On islands there is some mix Maintain those alleles even though they aren t favored because migration migrants bring alleles with them and breedcontribute to the gene pool 0 Genetic Drift o Is purely random 0 If you have a small population or a small amount of animals are founding a population allelic frequencies could be quite different from where they came 0 Further away from founding events losing genetic diversity 0 Effects of Genetic Drift 1 Because of the uctuations in allele frequency from one generation to the next are caused by random sampling error every population follows a unique evolutionary path 2 Drift has a more rapid and dramatic effect on allele frequencies in small populations than in large populations 3 Given sufficient time genetic drift can produce substantial changes in allele frequencies even in populations that are fairly large 0 Three different scenarios 0 Small populations xate very quickly 0 Increase population size still start to see populations xate but it takes much longer 0 Increase the population further maintain genetic diversity 0 In lab have to have large enough population size to know that selection is operating not just drift 0 No coalescence 0 Probability of xation 0 Through time likely to see some alleles become xed 0 Can calculate the probability of xation of allele OOOOOO 0 Genetic drift leads to a loss of heterozygosity 0 Due to drift you re always losing heterozygosity o Drift in 107 populations of 16 ies 0 Start with equal numbers of p and q alleles then let the populations breed 0 After one generation still got roughly the same mean but with every generation you lose heterozygosity 0 Over long enough time any small population will x on one or the other allele 0 Heterozygosity maximized when p and q are equal 0 Effective population size population needs equal amount of males and females 0 Uneven ratios will cause populations to be smaller than expected 0 Effective population size drives drift 0 lnbreds reduce population size also 0 Random xation and loss of heterozygosity in natural populations Hzards o Glades are remnants of old dessert and animals have held on and are scattered throughout the mountains 0 Used to have res but now people have allowed growth of brush 0 Lizards become separated and have small isolated populations May cause xation of genes 0 Most of the populations have xated on one form of the genotype lsolation is causing xation o Losing genetic diversity could cause problems for the lizards harder to adapt to change 0 Random xation and loss of heterozygosity In plants 0 polymorphisms increase with population size 0 As you increase population size allelic richness goes up 0 What is the rate of evolution if only genetic drift is at work 0 Substitution lose original allele lose yellow for green 0 The rate of evolution is equivalent to the mutation rate 2Nv x 12N v Selections vs neutral processes 1 Deleterious alleles appear and are eliminated by selection 2 Neutral mutations appear and are xed or lost by chance 3 Advantageous alleles appear and are swept to xation by selection 0 Red ower beetles 0 Set up populations with equal amounts of alleles for color 0 In both populations the mean value went up selective advantage for darker coat color Just how large an advantage or liability must an allele carry in a population of a given size for selection to overcome drift and play a role in determining the allele s fate o X scale is 2 times population size times selection Can have synonymous and nonsynonymous mutations 0 Selection acts to prevent nonsynon mutations Neutral theory as a null model o If replacements are neutral substitution for nonsyn to syn are equal Nonrandom mating 0 Could be assortive mating or negative assortive mating o Sel ng prefer yourself losing heterozygosity and enriching homozygotes 0 Negative assortive enhance heterozygotes o Allelic frequencies stay the same even though genotypic frequencies change evolution has not occurred F the probability that two alleles in an individual are identical by descent meaning that both alleles came from the same ancestor allele in some previous generation 0 Inbreeding decreases heterozygosity in population Calculating F o Halfsib vs fullsib parents Inbreeding depression 0 Higher mortality rates because combinations of homozygous recessives that you wouldn t normally have 0 Greater for traits expressed later in life Week 7 Chapter 8 Where do new alleles come from and how are they maintained in a population Evolution at 2 Loci 0 Either loci have 2 alleles Two loci that are physically linked 0 Can be linked physically and mechanistically Does selection at the A locus interfere with our ability to use the models of earlier chapters to make predictions about evolution at the B locus 0 Compare 2 gene pools population 1 and population 2 0 Calculate allelic frequencies and chromosome frequencies 0 Gene frequencies between 2 populations can be identical and 1 can be in HWE while the other isn t 0 Calculate the frequency of B on chromosomes carrying a and A allele If in equilibrium frequencies should be equal 0 Population 1 Frequency of B on a 810 08 Frequency of B on A 1215 08 0 Population 2 Freq of B on a 910 09 0 Big B is clinging onto a linkage Freq of B on A 1115 073 The coefficient of linkage disequilibrium D o Ranges between 025 and 025 gAagab 39 gAbgaa D Linkage equilibrium when the genotype of a chromosome at one locus is independent of its genotype Linkage disequilibrium when there is a nonrandom association between a chromosome s genotype at one locus and its genotype at the other locus Two loci are in linkage equilibrium if 0 1 The frequency of B on chromosomes carrying allele A is equal to the frequency of B on chromosomes carrying allele a o 2 The frequency of any chromosome haplotype can be calculated by multiplying the frequencies of the constituent alleles freq of AB chromosomes can be calculated by multiplying freq of allele A and freq of allele B Haplotype two loci referring to one chromosome 0 3 The quantity D is equal to 0 10 possible zygote genotype frequencies 0 product of individual frequencies for gamete genotypes Recombination rates must be incorporated If you re in equilibrium genotype frequencies should be constant from one generation to the next If in disequilibrium every generation should get closer to linkage equilibrium Selection on multilocus genotypes can create linkage disequilibrium o Freq of a 01536 0153606528 047 x 05 024 06528 total of all values multiply by 05 because only half contain little a o Freq of b 00576 0057606528 017 x 05 008 o Freq of ab 024 x 008 0021 Genetic drift can create linkage disequilibrium 0 Has to be a nite population Population admixture can create linkage disequilibrium 0 Combination of populations with different allele frequencies Recombination can reduce linkage disequilibrium Linkage disequilibrium falls over time 0 Both populations gradually got closer to equilibrium in ies o Alleles weren t sticking together Bad news about linkage disequilibrium o HWE predictions will be wrong Crohn s disease 0 Gene for ergothioneine near crohn s disease locus o It was closely linked to other genes that had to do with autoimmune disorders Good news about linkage disequilibrium o If locus A and locus B are in linkage equilibrium then selection on locus A has no effect whatsoever on allele frequencies at locus B Human chromosome 22 0 Close together high disequilibrium values 0 Far apart low disequilibrium values Practical reasons to study linkage disequilibrium 0 Can calculate how many generations it took to reduce disequilibrium 0 Can determine the mechanism of evolution Glucose 6phosphate dehydrogenase de ciency 0 High prevalence of malaria largest frequency of de ciency alleles o In linkage disequilibrium because under positive selection Young has high disequilibrium value 0 Takes time to fall into equilibrium with other genes around it Common The signature of recent positive selection 0 Not a neutral allele 0 High frequency and high disequilibrium Sexual reproduction is complicated costly and dangerous 0 Copy themselves develop young from unfertilized eggs parthenogenesis Which reproductive mode is better 0 Reproduce quicker if asexual o Null Model 1 A female s reproductive mode does not affect how many offspring she makes 2 A female s reproductive mode does not affect the probability that her offspring will survive aka no selection Asexuals reproduce much faster than sexuals Everything should be asexual based on model Males can persist in a population of facultatively sexual females if they have sufficiently high fertilization success if they produce offspring that survive at a sufficiently elevated rate or both Sex allelic segregation and genetic recombination o Restores HWE and restores linkage equilibrium 0 C elegans 0 Calculated a tness value and compared to experimental treatments Some don t breed at all outcrossing rate 0 All reproduce rate 1 Some reproducing somewhere between Highest tness for ones using sex all the time As sexual reproduction increases maintain tness at original value 0 Outcrossing reproducing sexually is adaptation for maintaining tness in face of bad mutations Muller s ratchet asexual populations accumulate deleterious mutations through drift 0 Cloud represents random chance event where individuals got knocked out because so few of them 0 Eventually populations go extinct Sex breaks Muller s ratchet o Asexuals have higher rates of nonsynonymous mutations Pathogens select for outcrossing o Constant rates of outcrossing 0 Evolution treatment select individuals that survive pathogen arti cial selection for organisms that live 0 Spike in outcrossing then slowly starts to decrease o Coevolution selected individuals that survived and selected pathogens that killed c elegans evolutionary arms race c elegans had to continue to outcross to reduce deleterious mutations in order to bode well with pathogen 0 Genes for sex ride to high frequency in the currently more t genotypes they help to create 0 Frequency of sexual individuals in snail populations 0 Areas with high infection rates higher number of males 0 Reducing disequilibrium OOOOO Review for Exam 2 o How do you break linkage disequilibrium 0 Lose disequilibrium every generation due to recombination 0 Things close together higher disequilibrium 0 Higher recombination rate means you ll get to HWE faster 0 Things that push population to linkage disequilibrium 0 Selection genetic drift and admixture Closer to zero less disequilibrium 025 025 Know how to calculate D coefficient of linkage disequilibrium and come up with allele frequencies Know what each equation is used for HWE selection for and againstoverdominanceunderdominance mutation tness chi square Asexually reproducing organism that is AA at one locus if it gets a mutation then its progeny will have that mutation 0 So in small population size mutations accumulate o If you have sexual reproduction then you can have organisms without the mutation in the population More likely to reproduce sexually in stress environment need more variation to survive In a stable environment usually species are asexual Small population size reduces genetic variation 0 Drift more effective on small populations


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