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Material for Exam 2

by: America Seach

Material for Exam 2 BIOL

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These are all of the notes from lecture and from the quiz for exam 2.
Evolutionary Biology
Study Guide
evolution, Biology, Clemson, genetic, variation, hardy-weinberg, mutations, alleles, frequency, Genome, duplications, muller's ratchet, recombination, reproduction, population, disequilibrium, linkage, allele, heterozygote, homozygote, selectio
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This 24 page Study Guide was uploaded by America Seach on Saturday February 27, 2016. The Study Guide belongs to BIOL at Clemson University taught by Sears in Spring 2016. Since its upload, it has received 112 views.


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Date Created: 02/27/16
Evolution Notes Exam 2: 2/4/16 - Variation Among Individuals- it is the raw material for evolution o Plants, animals, humans all vary in appearance - Cells are distinguished by the proteins they make: o Red blood cells: hemoglobin to transport oxygen o Goblet cells: digestion o Rod cells: in eye o DNA can have different folding patterns - Vp = Vg + Ve + Vg*e o Phenotypic variation = genotypic variation + environmental variation + gene by environment interaction o Genotype variation: different alleles o Environment: depends on food they eat o Gene by environment: can have the same gene but may have different environment - Genetic Variation: there are different alleles for each gene o Taste receptors: PTC- bitter flavor; PAV allele fits into receptor and taste bitterness; AVI allele doesn’t fit into receptor so do not taste bitterness; PAV/PAV= very bitter; PAV/AVI = not too bitter; AVI/AVI= not bitter o Genetic variation consists of differences among individuals that are encoded in the genome and transmitted from parents to offspring - Environmental Variation: occur by changes in the environment o Consists of differences among individuals due to exposure to different environments; one way environments can influence phenotypes is by altering gene expression o Daphnia: if exposed to predator, it grows a horn; if it is not exposed to a predator, it does not grow a horn; phenotypic plasticity - Epigenetics: o “Linnaeus would be proud”- being able to pass changes specifically because of the environmental exposure § toadflax shows variation - Gene by environment interaction o Leopard gecko: experience temperature dependent sex determination- temperature experience during birth affects the gender of the gecko; more males produced at moderate temperatures, females at extremes § Climate change could cause all male or all female populations § Some are sensitive/insensitive to temperature change o Happens in people: have different genotypes for serotonin transporter gene; chances of depressive episodes are more likely if you have ss genotype o Caterpillars: most exhibit the black gene, but with heat shock (42 degrees), they start showing more green o What happens if you breed heat shock? o Because of their heritable component, genetic variation and genotype- by-environment interaction are raw material for evolution by natural selection - How do we know what is responsible for phenotypic variation: o Common garden: bringing them to the same temperature; if it is only genetic, it should remain the same size regardless of the change in environment o Reciprocal transplant: swapping location/temperature; maintain the same body size means its genetic only o Common garden ENVIRO ONLY: change location to same one, they line up o Reciprocal transplant: ENVIRO ONLY parallel lines o Common garden and reciprocal transplant (intermediate- gene by environment): don’t align and do not stay the same o Example not in textbook: rufous-collared sparrows: took animals from low and high environments to see what happens; some of the proteins were different but when they group up together to be similar o Can the thermal environment explain geographic patterns of body size? Depending on where you are, the body size changes; more active season creates a larger body size; when you look at the ones in nature- the body sizes were very different (~50%), but grew to normal size after juvenile years § Differences were only environmental; variation in body size is not genetic due to the common environment not causing changes in body size - Where new alleles come from: o Arise from alterations to existing alleles o DNA makes copies of itself by complementary base pairing o Sometimes there are spontaneous deamination: methylated cytosines can react with a water to become thymines; mutation that can be passed on throughout generations o Misalignment: the template and nascent DNA strand can slip out of register at repeat sites, resulting in duplications and deletions; hard to come back from o Survival of mice: normal mice live longest, deficient mice do not last as long; and doubly deficient mice live only about 3 months - How mutations alter protein function: o Depends on where mutation is o Point mutation: sometimes just changing the third codon does not affect the amino acid; but changing either first or second can drastically change the amino acid (maybe from polar to nonpolar; acid to base, etc); can affect how it folds o Transversion: purine to pyrimidine o Transition: purine to purine; - Where new genes come from? o Gene duplication: done by unequal crossing over o Duplication by retroposition: introns spliced out then reverse transcription happens, then integration, and final product is new gene o Phylogeny from RNASE1 genes: douc langer is a vegetarian monkey; may have better digestive abilities because of RNASE1B (might have occurred because of unequal crossing over) o Corgis have short legs: comes from DD alleles found in short legged dogs (retropositions- lack introns) o Occurs when genes are formed from scratch because of a change from a stop codon to not a stop codon so have long strand of dna compared to what was intended - Gene duplication is an important category of mutation for evolution. An increase in copy number may itself be adaptive. Duplication followed by divergence in function generates gene families. 2/9/16 - Chromosome Mutations: - Point mutations: single mutation where base pair switches - Chromosome inversions: they suppress crossing over, resulting in ‘super genes’; both ends of the chromosomes break and then are bound back together, but sometimes there are mistakes where they bind to the wrong side of the chromosome; linkage changes- either linked physically or by function- two genes that are closer together are more likely to be inherited together than two that are on opposite ends o Recombination: when they cross over and a chunk from each chromosome goes to the opposite side o Linkage in these areas go up if crossing over doesn’t occur- large portions of chromosomes inherited together - Are they important in evolution? o Flies: we know so much about these flies and they exist out in nature; notice that there’s specific mutations/duplication in certain locations; can tack genomes as they track latitudes (typically associated with climate); same inversions in North America as South America; by linking genes close together and inheriting them together, they might be favored by certain environments—evolve to fit this environment: CLINES o Selection might favor chromosomal inversions to help maintain combinations of alleles across nearby loci - Genome duplications: o Duplications of the entire genome are an important mechanism of speciation—particularly in plants o EX: Diploid parent produces diploid gametes because they can self- fertilize and “back-crosses” to parent; forms an incompatible species and can create a whole new species o Can isolate themselves from a population - Genome duplication as a mechanism of adaption o Changes in ploidy can alter phenotypes in a way that makes individuals better adapted to new environments o Hexads do good in dry environment; neohex did better than tetraploids o Can act on entire genome mutation - Genome duplication can occur in animals too: 1. Female doesn’t incorporate any male genetic material 2. Female incorporates male genes, but increases ploidy levels 3. Female replaces some of her genetic material - rates and fitness effects of mutations: o mutation accumulation experiments demonstrate that mutation rate evolves (putting in a controlled environment) o gene duplication can be more common that mutations o a lot of variation in mutation rates- high mutation rates in viruses o mutation itself is a trait that can evolve - everyone is a mutant: we inherit up to 100 mutations from our parents o in US: males are the ones who cause most mutations o in Nigeria: the egg carries a majority of the mutations - variation between gender, population, location - the distribution of fitness effects of new mutations: site-directed mutagenesis and accumulation o mutated genes randomly and looked at frequency of their mutations and correlations with fitness § 20% were lethal, ~half were neutral § have ones that are lethal, neutral, beneficial, and somewhat damaging o many of the mutations accumulate lines carried beneficial mutations - mutations come in four kinds: lethal, deleterious, neutral (MOST COMMON), and beneficial o lethal and deleterious mutations outnumber beneficial mutations - the balance between mutation and natural selection o it is the action of natural selection, culling damaging mutations and preserving the advantageous ones, that saves population from inexorable decline o while mutation is random, natural selection acts on these to make more advantageous individuals - Population Genetics: integrates evolution by Darwinian evolution with Mendelian genetics o From a population geneticist’s perspective, evolution can be defined as change across generations in the frequencies of alleles (a copy of a gene). - Frequency of TRYP1 G allele: this G allele decreases drastically - The lifecycle of an idealized population: o We want to know whether particular alleles or genotypes become more common or less common across generations and why o Adults produce gene pool of gametes that are fertilized to zygotes to create a population of juveniles that will grow into adults. (no genetic drift, no mating preference) o Adults choose their mates at random: gene pool with a frequencies of 0.6 for Allele A and 0.4 for allele a - Closing your eyes and picking random alleles o Calculating allele frequency o If not all get to reproduce, the population has to evolve due to “blind luck” - A Numerical Calculation: random mating in the gene pool produces zygotes with these proportions if they are heterozygous: 36% AA, 48% Aa, and 16% aa for 100% total - When chances play no role, the allele frequencies do not change from one generation to the next so no evolution occurs o MAKE SURE IT ALWAYS ADDS TO ONE - Yule vs Punnett: o Yule: when half are A and half are a, then the population is stable o Punnett: the frequency of one allele + the frequency of another allele totals 1. - Hardy-Weinberg Equilibrium Principle: Each person has a p+q so you do 2 (p+q) =1 because it involves diploid; o Conclusion 1: the allele frequencies in a population will not change, generation after generation o Conclusion 2: if the allele frequencies in a population are given by p and q, the genotype frequencies will be given by p , 2pq, and q 2 § ASSUME: No selection, no mutation, no migration, no chance events, individuals choose mates at random and population is BIG - if your population is not at equilibrium, one of the assumptions is affecting the population. - A case study: o MM: 1787 o MN: 3039 o NN:1303 § Add them all up and divide the individual numbers by the total for the population - What are the gene frequencies? o M à p= [1787 + (0.5* ) divided by the total population o Nà q= - Square p for MM, multiply 2pq for MN, and square q for NN. 2/11/16 - Assumptions of Hardy-Weinberg equilibrium: 1. there is no selection 2. there is no mutation (increases variation in population) 3. there is no migration (brings in new variations to change allelic frequencies) 4. there are no chance events (populations are infinitely large) 5. individuals choose their mates at random - Conclusions of H-W equilibrium o P + 2pq + q = 1 o Conclusion 1: the allele frequencies in a population will not change, generation after generation o Conclusion 2: if the allele frequencies in a population are given by p and q, the genotype frequencies will be given by p , 2pq, and q 2 - Mechanisms of Evolution: o By providing a set of explicit conditions under which evolution does not happen, the hardy-weinberg analysis identifies the mechanisms that can cause evolution in real populations o Genetic drift (founders effect): small population size causes this o Selection: forces evolution; o Migration: new people come in from another population o Mutation: switching from dominant to recessive alleles or vice versa but are rare - How do we know when a population is not in H-W equilibrium? o Use a statistical test known as CHI-SQUARED - Chi-squared test: o Need a test statistic: take the sum of all phenotype calculations for this formula [(observed-expected) ] / expected o Degrees of freedom (how many choices you have before you have no more meaningful choices): df = k-1-m (m is alleles) o Cutoff for statistical significance for 1 degree of freedom is 3.841. o EXAMPLE: § Need to go to observed frequencies to expected (find values for p and q) § P= .62 Q= .38; p =0.384, 2pq= 0.47, q = 0.14 § AA= 36.6 (p *N(total population)à 0.384*95) § Aa= 44.7 (0.47*95) § Aa= 13.3 (0.14*95) § Chi-squared: take the (observed- expected)^2 divided by the expected for each genotype; add them together • = 0.44 • since it is less than 3.841, you can assume its in h-w equilibrium o p value greater or less than 0.05 - Selection: happens when individuals with particular phenotypes survive to sexual maturity at higher rates than those with other phenotypes, or when individuals with particular phenotypes produce more offspring during reproduction than those with other phenotypes - Calculating gene frequencies under selection: incorporating fitness of genotypes o Fitness is denoted as w o First have to average the fitness for the population (add each fitness up after multiplying by the frequency for each fitness) o For finding genotypic frequencies: take the fitness multiplied by the frequency and divide by the average for the population o For new allelic frequencies: you take p w +pqw di11ded by12he average to get A1; q w +pq22divided12 the average to get A2 - Allelic frequency change by Selection: o Flies attracted to alcohol, but it is deadly to them o Flies that grow up in ethanol, changes the frequency of having the fast allele over generations - Selection can change genotype frequencies so that they cannot be calculated by multiplying the allele frequencies. This is an example of OVER- DOMINANT; heterozygote have an advantage over homozygotes - Can human populations evolve in response to HIV? 2/16/16 - Effects of lethal recessive alleles: hard to get rid of within a population because it hides in the heterozygotes - Selection on Recessive alleles: this formula says that as long as it is in the population, it will never disappear; will not reach zero - Selection on Dominant Alleles: if selection is one, it becomes zero- so it is easy to get rid of in one round of breeding - Recessive hard to get rid of, dominant easy to get rid of - Selection favoring heterozygotes: overdominance; reach and equilibrium showing some sort of optimum in the genes; - - selection for homozygotes: have higher fitness than heterozygotes - frequency dependent selection: elder flower orchids o fitness is based on how many of you are present; if there are more yellows in the population, it is more likely that a bee will land on the yellow flower than the red flower o equation for relative frequency of success is in the book but do not need to know this one - Mutation: typically too small to affect measurable evolutionary change; mutation rate formula: - mutation creates base for future evolution - salt tolerance in flies: flies that survived exposure to salt evolved to be more beneficial to survival - What is the relative importance of selection vs mutation for evolution? - Selection-mutation balance for a deleterious recessive allele - selection-mutation balance for a deleterious dominant allele: much more simple than it is for recessive alleles - Know examples of Medea - Know example of CF and typhoid in humans - Migration: immigration from a large area to a small area which changes the genetic frequencies; also different types of selection could be acting on both - If too many come from the main land, all of the species would start to look the same - Migration example: knocks out hardy-weinberg - Nerodia in Lake Eerie: have a crytic plain form is more beneficial for survival compared to other areas in the lake; and sometimes it is maintained even if it isn’t favored - One island model: come to equilibrium at some point - Island model specific to Nerodia: predicting allelic frequencies in the population - Effects of Genetic Drift: if you have a small population, the genetic frequency that occur in the founding population; if it was for a larger population, the genetic frequency will be more symmetrical - The further away from founding area, the more you loose genetic diversity - Effects of genetic drift: - If you draw a small population from a larger one, they fixate quickly to homozygosity; heterozygosity disappears quickly - If you draw a larger population, allelic frequencies and heterozygosity remain stable over time but still lose some genetic diversity over time. 2/18/16 - Drift is a problem of sampling - If genetic drift is the only evolutionary process at work, eventually one allele will drift to a frequency of 1 and all other alleles will be lost - Fixation of a population is (x/2N) - Genetic drift leads to a loss of heterozygosity - how to determine loss of heterozygosity over generations - the smaller the population, the faster loss of heterozygosity - over a long enough time, it will fix on one allele or the other (really happens fast in small, isolated populations) - Just because you can count 16 flies in the population, doesn’t mean that they are all breeding- why the prediction matched a population of 9, not 16 - Effective population size drives drift: uneven ratios of males and females causes population skewness - Random fixation and loss of heterozygosity in natural populations: lots of small populations might be isolated and produces fixation - Imbreeding depression leads to disease in a population - Genetic polymorphism: the fraction of loci within the genome that have at least two alleles with frequencies higher than 0.01, increased with population size in nature; so did the number of alleles per locus - As you increase population size, allelic richness and polymorphism increases - What is the rate of evolution if only genetic drift is at work? - The rate of evolution is the rate at which new alleles created by mutation are substituted for other alleles already present o Loss of original allele that is replaced with a new allele is called substitution - The rate of evolution is equivalent to the mutation rate: - Selection versus neutral processes: o When mutation, genetic drift, and selection interact, three processes occur: 1. deleterious alleles appear and are eliminated by selection 2. neutral mutations appear and are fixed or lost by chance 3. advantageous alleles appear and are swept to fixation by selection (starts to appear more often) - the relative importance of 2 and 3 in determining the overall substitution rate is a mater of debate - when populations are subject to both selection and genetic drift, smaller populations follow more diverse evolutionary paths - just because an allele is favored by selection, if it is in a small population, it can still be lost - 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? - - as population becomes larger, the effects of drift become smaller - synonymous mutation: same amino acid replaces the same amino acid - nonsynonymous mutation: a different amino acid replaces the intended amino acid - Neutral Theory as a null idea: - the neutralist-selectionist controversy is a debate about the relative importance of drift and positive selection in explaining molecular evolution. - Nonrandom mating: either like breed with like OR the reverse; “selfing”- prefer mating with identical species - Selfing loses heterozygosity, but enriches homozygotes - Even though you’re changing the genotypic frequencies, evolution hasn’t occurred---- different from genetic drift because evolution does occur - F: the probability that the two alleles in an individual are identical by descent (meaning that both alleles came from the same ancestor allele in some previous generation) - How to calculate; will simplify to the HW formula if no inbreeding occurs: - - inbreeding depression negatively affects offspring, likely due to increased numbers of homozygous recessive: higher mortality rates among children produced from first cousins 2/23/16 - Evolution of Multiple Loci: linkage and sex o Not all animals reproduce through sexual contact - Where do new alleles come from and how are they maintained in a population? o Adaptive significance of sexual reproduction - Evolution at Two loci o Two loci that are physically linked next to each other on the same chromosome (or are mechanistically connected) o Goal: track allele frequencies and chromosome frequencies - 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? (hope for no or independent assortment isn’t at play) - Populations can have identical allele frequencies but different chromosome frequency o Gene frequencies can be equal between two populations but one can be at hardy Weinberg and the other isn’t - Calculate the frequency of B on chromosomes carrying a and A allele. If in equilibrium the frequencies should be equal - Two loci in a population are in linkage equilibrium when the genotype of a chromosome at one locus is independent of its genotype at other locus. - Two loci are in linkage disequilibrium when there is a nonrandom association between a chromosome’s genotype at one locus and its genotype at the other locus. - - hardy-weinberg analysis for two loci: 10 possible zygote genotype frequencies: - - recombination rates must be incorporated - As recombination increases, the gamete percentage decreases - If you’re in equilibrium, frequencies should not change from one generation to the next - Selection on multilocus genotype can create linkage disequilibrium: o To see this, calculate the frequency of allele a and allele b and use criterion 2 - Freq a= frequencies with little a /total frequencies à (0.47*1/2)/0.6528 à 0.24 - If they’re heterozygotes, you have to multiply by ½ - Genetic drift and selection can cause linkage disequilibrium - Genetic drift is the mechanism because disequilibrium occurs only in a finite population - Population admixture can create linkage disequilibrium: combination of populations with different alleles and chromosome frequencies created a new population with an excess of AB and ab chromosomes - With sexual reproduction and random mating, linkages disequilibrium falls over time - The rate of decline in linkage disequilibrium between a pair of loci is proportional to the rate of recombination between them - The bad news about linkage disequilibrium: single-locus population genetics model looking only at locus B will make inaccurate predictions about evolution o Hardy Weinberg equilibrium values will be incorrect - Elevated concentrations of ergothioneine may contribute to Crohn’s disease: the apparent connection between the two is a spurious result of linkage disequilibrium - Good news: 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 - On human chromosome 22, most pairs of loci are in linkage equilibrium: o Situated near enough to each other on the same chromosome that crossing over between them is rare. o Far apart= low disequilibrium value—more equilibrium - Practical reasons to study linkage disequilibrium: o the rate of crossing over between the loci to estimate the rate at which the disequilibrium is decaying o depending on the recombination rate, one can determine the mechanism of evolution - glucose-6 phosphate dehydrogenase deficiency: a locus in linkage disequilibrium with nearby markers may be young and if common under positive selection; high disequilibrium value - The signature of recent positive selection: neutral alleles evolving by drift can have a high frequency, or a high linkage disequilibrium, but not both - Sexual reproduction is complicated, costly, and dangerous: o Offspring develop from unfertilized eggs is called parthenogenesis - Which reproduction mode is better? o A 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 (no selection) - Can reproduce quicker when reproducing asexually, but it doesn’t happen often - 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, to a population geneticist, means allelic segregation and genetic recombination - In a population genetics analysis, sexy only does two things: restores hardy- weinberg equilibrium, and it restores linkage equilibrium - Elevated mutation rate selects for outcrossing in C. elegans: o Outcrossing is (partly) an adaptation for maintaining fitness in the face of deleterious mutations o A higher mutation rate selected for more frequent outcrossing, and thus more males - Muller’s ratchet: asexual populations accumulate deleterious mutations through drift - The genetic load carried by the asexual population becomes so high that the population goes extinct - Sex breaks muller’s ratchet: asexual species accumulated far more nonsynonymous, deleterious mutations - Pathogens select for outcrossing in C. elegans o Sex is adaptive because it recreates these missing genotypes through segregation and recombination - A host parasite arms race can make sex beneficial - Genes for sex ride to high frequency In the currently more fit genotypes they help create - The frequency of sexual individuals in snail populations: males are more frequent in populations where more snails are infected - We have learned that by reducing disequilibrium, sex both helps maintain fitness despite deleterious mutation and facilitates evolution in response to selection o Recreates favorable multilocus genotypes that were recently eliminated by selection. 2/25/16 Exam is up until chapter 8: - if you are in disequilibrium, you are not in hardy- Weinberg; need recombination to get back to hardy-weinberg - closer together = higher disequilibrium; - add mixture: combining gene pools together - closer to zero, the less disequilibrium Chapter 5: - Variations that occur within individuals: genetic variation, environmental variation, and genotype-by environment variation - An organism that develops different phenotypes in different environments has phenotypic plasticity. - Daphnia grows protective armor when it senses chemicals through the protections process known as inducible defense. - The pattern of phenotypes a person can develop when exposed to different environments is known as reaction norm. - Genetic variation of humans based off of taste using PTC- humans experience a bitter taste when they put PTC on their tongue - Substituting a purine with a purine or a pyrimidine with a pyrimidine is known as transition. - Substituting a purine for a pyrimidine or vise versa is known as a transversion. - A mutation that occurs in a DNA sequence but leaves the resulting amino acid unchanged is known as synonymous or silent mutation - A mutation that changes the amino acid specified is known as nonsynonymous or replacement substitution. - Smallest possible mutation in DNA involving only one base is a point mutation. - The genetic code is redundant because some amino acids are coded for by more than one codon. - Genes duplicated within a genome and later their functions diverge (RNASE1 in the douc langer monkeys) are known as paralogous genes. - The RNASE1 gene in douc langer monkeys and in humans are derived from a sequence of a common ancestor and separated due to speciation is known as orthologous genes. - A hypothetical population has two alleles for a gene: A and a. In a random sample of 50 individuals, 20 are homozygous for a, 20 are homozygous for A, and 10 are heterozygous. What is the frequency of A? ----50% - Genes can be duplicated when a processed messenger RNA, from which introns have been spliced out, is reverse-transcribed to form a double- stranded DNA segment that is reintegrated into the main chromosome. What is the name for this process that may form nonfunctional pseudogenes? --- Retroposition or retroduplication - Chromosome inversions that begin with radiation and is a multistep process causes two double-stranded breaks in a chromosome. - Polyploidy organisms have more than two chromosome sets. - Frequencies of inversions and/or allele frequencies often vary regularly when examined over a geographic area changing in either latitude or climate. This type of regular change is called a cline. - Mutations that are observed in most organisms: deleterious, lethal, neutral, and beneficial. - The haploid genome contains 3.2 billion base pairs, and a person inherits 36 mutations from each of the gametes that united to the zygote - Loss of function mutation: a mutation that destroys the function of the resulting gene product - Chromosomal Inversion: reversal of the orientation of a large stretch of DNA - Reasons why analyses of loss-of-function mutations underestimate actual mutation rates: and silent site mutations produce no change in amino acid sequences, so they are uncounted; not because large-scale phenotypic changes cant be caused by point mutations - High mutation rates are advantageous in novel environment - Most mutations are neutral or slightly deleterious - The most important source of new genes is probably gene duplication caused by unequal crossing over - Evidence that human hemoglobin evolved via gene duplication: The globin gene family shows all the classic traits of a gene family that has arisen through gene duplication. These include similar position of exons and introns, sequence similarity in exons and introns, similarity in function, pseudogenes, and physical clustering on the same chromosome. - Chromosome inversions prevent specific groups of alleles from being separated by crossing-over, allowing them to be inherited together as single “supergenes” - For polyploidy to result in a new species after one generation, Self- fertilization with diploid gametes allows the first tetraploid individual to arise. The tetraploid individual must then be able to produce more tetraploid individuals (through more self-fertilization, or mating with a parent or sibling). Finally, to form a distinct species, the tetraploid population must be reproductively isolated from the parent species; this typically occurs because of the infertility of triploid offspring. - Polyploidy (genome duplication) can create new species immediately and creates large numbers of extra copies of all genes - Gene duplication: creates small numbers of extra copies of a few genes - Point mutation: creates new alleles - Classically, genetic diversity was expected to be low in most populations, but this was proven to be incorrect - Researchers have identified varying mutation rates in bacteriophages, E. coli, and other organisms showing that individuals vary within populations - Specific mutations have been identified that change the efficiency of DNA synthesis and repair enzymes: variation among individuals are passed from parent to offspring - E. coli cells with high mutation rates had higher fitness than normal cells when grown in novel environments showing that survival and reproduction are nonrandom Chapter 6: - If a population is in hardy-weinberg equilibrium, allele frequencies will not change from one generation to the next - Genetic drift: random changes in allele frequencies that occur due to chance - Selection: nonrandom changes in allele frequencies that occur due to differing reproductive success 2 - Hardy-Weinberg equilibrium: genotypic frequencies are given by p , 2pq, and q . - Gene pool: the total of all copies of all genes in a population - Overdominance: selection that favors heterozygotes - Underdominance: Selection that favors homozygotes - Over the long term, selection favoring the rare phenotype in a polymorphic population will maintain genetic diversity in the population. - Allele frequencies may initially hover at an unstable equilibrium, but will eventually change; allele frequencies tend to move towards fixation or loss. - When selection acts against a recessive allele that is initially at high frequency in a population, the frequency of the allele will decline rapidly, and then stabilize at a very low frequency - When selection favors heterozygotes over homozygotes, it is known as overdominance and it can maintain deleterious alleles in populations; may explain why natural populations have a high genetic diversity - When selection favors homozygotes over heterozygotes, the most common allele will be fixed (will increase to a frequency of 1) in the population. - If selection is strong and mutation rate is low, the equilibrium frequency of a deleterious allele will be low. - When selection is weak and the mutation rate is high, the frequency of an allele will be relatively high. - Selection of one phenotype over another does not include having the phenotypes affected by the environment. Chapter 8: - Haplotype: multilocus genotype of a chromosome or gamete - Linkage disequilibrium is reduced by sexual reproduction and increased by any random sampling error that happens to create or destroy certain chromosome genotypes but not others. - When two loci are in linkage disequilibrium, the allele carried on a chromosome at one locus is independent of the allele carried on the chromosome at another locus. In this case, the frequency of each haplotype can be calculated by multiplying the frequency of its two alleles. - Selection on multilocus genotypes in random-mating populations leads to linkage disequilibrium when some allele combinations confer greater fitness than others. - By breaking up overrepresented haplotypes and creating new ones, crossing over/sexual reproduction/genetic recombination/meiosis reduce linkage disequilibrium. - Haplotype: all of the alleles present on a single chromosome or in a single haploid gamete - Linkage disequilibrium: a state in which the probability of an allele being present at one locus is independent of the allele present at another locus on the same chromosome. - Genetic load: the fitness burden caused by the accumulation of deleterious mutation in a population - Genetic recombination (crossing over): creation of new combinations of alleles during sexual reproduction - Population admixture: the blending of gene pools that occurs when two different populations meet. - The genetic signature of recent positive selection on a locus is high frequency and high linkage disequilibrium. - The CCR5-delta32 allele was probably driven to its current frequency in European populations by selection. - Muller’s ratchet model for the selective advantage of sexual reproduction is characterized by o Drift establishing linkage disequilibrium because multilocus genotypes with few mutation are eliminated by chance events o In populations without sexual reproduction, deleterious muations accumulate, eventually imposing such a burden that the population goes extinct o Sex is favored selectively because it recreates the zero-mutation genotypes lost due to drift - Sexual reproduction is advantageous in changing environments but disadvantageous in constant environments when compared to asexual reproduction; produces only half as many grand-offspring per female compared to asexual reproduction; causes genetic recombination via crossing-over (combining genotypes from different parents) - For Muller’s ratchet, changing environment isn’t a rapid process - Sexual reproduction can gain immediate advantage if the environment changes


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