Evolutionary Bio Exam 2
Consider a population containing the following genotypes: Aa, Aa, AA, aA, aa, Aa, aa, aA, aa, Aa. What is the frequency of the genotype aa? Allele A?,Allele a? can you tell which of the genotypes is most advantageous? Can you tell whether Aa resembles AA or aa? Why or Why not?
(2x 3) + 6/ (2x10) = 12/20 = 0.6 f (A) = 0.4 Since we only have 10 individuals (genotypes) in the population, we cannot make good conclusions about the advantageous genotypes. If we had a larger sample, in the similar ratios: 6Aa: 3aa: 1AA, we could say that heterozygotes are the most advantageous. If we use symbols A and a, we are indicating that allele A is dominant over a. Thus we have two phenotypes in our population of 10 individuals, where dominant phenotype A/- is represented with 7 individuals, while recessive phenotype aa is represented with 3 individuals.
Population Genetics
-Forces causing changes in the allele frequency within population (Natural Section) -Factors influencing the maintenance and loss of genetic variation Evolutionary forces are: NS. Genetic Drift, Gene flow, mutation
dN=? ds=? 1) If dN/ds <1, then ? 2) If dN/ds =1 then ? 3) if dN/ds> then ?
1) If replacements are deleterious (purifying selection) 2)Neutral 3) If replacements are advantageous =positive selection
Give examples of each: Genetic Variation Environmental Variation Genotype by environment interaction
1-differences in skin color (newborns) 2-tanning due to sun exposure 3-variation among individuals in the amount of tanning when exposed to the same sunlight
HW cont.
1. Allele frequencies will not change across generations 2. We can predict genotype frequencies from allele frequencies
Interaction between genetic drift, selection, and mutation:
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 The relative importance of (2) and (3) in determining the overall substitution rate is a matter of debate
Ways to test adaptive hypotheses:
1. Experiments (can have control/manipulate/garter snake) 2. Observational studies (observation in nature) 3. The comparative method (looking at variation and relationships of phylogeny)
Sequences are now available for both the humankind the chimpanzee genomes. Outline how you would analyze homologous genes in the two species to determine which of the observed sequence differences result from drift and which result from selection.
A classic approach is to calculate the ratio of replacement, or non-synonomous, substitutions to silent, or synonymous, substitutions. A ratio greater than 1.0 indicates that selection has acted on that site. However, this is a conservative test. A more sensitive approach is possible with the McDonald-Kreitman test, which compares the same ratio within versus among species. (The M-K test is not concerned with whether a given ratio is greater or less than 1.0, but rather with whether one ratio is greater than another ratio.) An M-K test would require numerous sequences from individual humans and chimpanzees. The ratio (replacement substitutions / silent-site substitutions) would be calculated both for human-human comparisons, chimp-chimp comparisons, and finally, human-chimp comparisons. A higher ratio for the human-chimp comparison than for the within-species comparisons would indicate that positive selection had occurred
Do question 6 and 7 on page 366.
A) Heritability (h2) is approximately 0.045, the slope of the best-fit line of a scatterplot of midoffspring speed (y-axis) as a function of midparent speed (x-axis). B) No. A heritability of 0.045 is quite low; only 4.5% of the variation in running speed can be attributed to genetic variation. One generation of selection is unlikely to cause a large change in running speed. C) The breeder should concentrate on environmental factors, which apparently explain 95% of the variation in running speed. Some obvious factors include behavioral training, physical conditioning, racing experience, and diet. Other possible factors include fetal and neonatal effects such as diet of the mother and litter size. A) The selection differential is 4.82 m/s, the difference between mean speed of breeders (13.3 m/s) and mean speed of nonbreeders (8.5 m/s). The selection gradient is 0.32, the slope of the best-fit line of midparent speed vs. relative fitness, where relative fitness is 3 for breeders and 0 for nonbreeders. B) The predicted response to selection is 0.22 m/s (selection differential of 4.8 m/s multiplied by heritability of 0.045). Predicted average running speed of the next generation is 10.30 m/s, the sum of the average speed of the parental generation (10.09 m/s) plus the response to selection (0.22 m/s). (Numbers have been rounded.) C) The actual running speed of the offspring of the breeding families is only 8.95 m/s, lower than predicted. This is because of the high scatter in the data: that is, in the scatterplot of midparent versus midoffspring values, data points do not fall exactly on the best-fit line. In particular, in this data set average running speed of all puppies is lower than average running speed of all adults. This unexpected result is almost certainly due to low sample size, which increases probability of genetic drift (e.g. puppies may just happened to have inherited low-speed alleles rather than high-speed alleles from heterozygous loci of their parents), and of variation in environmental effects (e.g., puppies might not have been trained optimally). In a much larger data set of thousands of dog families, we would expect to see closer correspondence of predicted and actual response to selection.
A. Name the phenomenon being described in each of these hypothetical examples, and describe how it is likely to affect allele frequencies in succeeding generations. a. A beetle species is introduced to an island covered with dark basaltic rock. On this dark background, dark beetles TT or Tt, are much more resistant to predation than are light-colored-beetles tt. The dark beetles have a large selective advantage, both alleles are relatively common in the group of beetles related on the new island. b. Another belt population this time consisting of mostly light beetles and just a few dark beetles is introduced onto a different island with a mixed substrate of light sand, vegetation and black basalt. On this island, dark beetles have only a small selective advantage. d. In a tropical plant, CC and Cc plants have red flowers and cc plants have yellow flowers. However, Cc plants have a defective flower development and produce very few flowers. E. IN a species of bird, individuals with genotype MM are susceptible to avian malaria. Mm birds are resistant to avian malaria, but mm birds are also vulnerable to avian pox.
A) Migration followed by natural selection. The frequency of the T allele is likely to increase rapidly. B) Migration followed by natural selection. The frequency of the T allele may increase, but only slowly, and perhaps not at all, due to the rarity of the T allele and the weakness of selection D) Frequency-dependent selection. The frequency of small males is likely to gravitate toward a stable equilibrium frequency, at which small and large males have identical fitness. E. Heterozygote superiority, or overdominance. The frequency of the m allele is likely to gravitate toward a stable equilibrium frequency.
Describe in your own words, the three major modes of selection and their general effects on population means and on population variation.
A) Stabilizing selection occurs when individuals with average values of a trait have highest fitness. This tends to trim the tails off of the population distribution, reducing variation, but not changing the population mean. B) Directional selection occurs when a value to one side of the population average (higher or lower, but not both) has highest fitness. This trims one tail off the population distribution and expands the other tail, shifting the population mean. Variation tends to reduce (because one tail is trimmed off) but not very much (because the other tail tends to lengthen, depending on available genetic variation). c) Disruptive selection results when high and low values have greater fitness than the average value. This tends to split the population into two morphs (forms) and reduce frequencies of individuals with trait values near the center of the distribution, increasing variation but not changing the mean.
What is the relationship between natural selection and adaptation?
Adaptationism is not a null hypothesis. need evidence for adaptation to claim that trait is adaptive.
What is an evolutionary constraint? Why do they occur? Give two examples. How does the occurrence of trade-offs illuminate the general question of whether all traits are adaptive?
An evolutionary constraint is an obstacle that prevents a taxon from evolving a certain trait, often due to developmental pathways, or some other competing process of physiology or ecology. Examples include pigs' failure to evolve wings (due to a developmental program that does not allow multiple pairs of forelimbs), the retention of flowers on Kotukutuku trees for several days after fertilization (possibly due to the physiological constraint of slow growth of pollen tubes), and the lack of host shifts in body feather lice of birds (possibly due to an ecological constraint of limited dispersal opportunities). The occurrence of evolutionary constraints demonstrates that not all traits are perfectly adaptive.
Black color in horses is a governed primarily by a recessive allele at the A locus. AA and Aa horse are nonblack colors such as bay, while aa horses are black all over. ( other loci can override the effect of the A locus, but we will ignore that complication.) In an online conversation, one person asked why there are relatively few black horses of the arabian breed. One response was, " Black is a rare color because it is recessive. More Arabians are bay or gray because those colors are dominant." Discuss the merits and or problems with this argument. ( Assume that A and a allele are in Hardy-Weinberg equilibrium, which was probably true at the time of this discussion.) Generally, what does the Hardy-Weinberg model show us about the impact that an allele's dominance or recessiveness has on its frequency?
An important lesson of Hardy-Weinberg equilibrium is that recessiveness and dominance, by themselves, cannot cause allele frequencies to change. Intuitively, many people expect that dominant alleles will tend to become more common, simply because of their dominance, but this is not so. In horses, some other breeds are entirely black (e.g., Friesians), demonstrating that recessiveness alone should not prevent black from being a common coat color. Black color has been historically rare in Arabians, perhaps originally because of natural selection against dark (hot) coat colors in this ancient desert-adapted breed and later because the color was not selected by Arabian breeders. In the last two decades, black Arabians have become more common in the United States because Arabian breeders began selecting for this color after the movie The Black Stallionmade black Arabians fashionable. Thus, selection by horse breeders has begun to reverse the effects of a much older period of natural selection in a desert environment.
What is the adaptionist program?
Analysis of traits part by part rather than a whole- Dissecting organisms into adaptive traits without evidence of adaptation
As we have seen, inbreeding can reduce offspring fitness by exposing deleterious recessive alleles. However, some animal breeders practice generations of careful inbreeding within a family or line breeding. and surprisingly many of the line-bred animals, from champion dogs to prize cows have normal health and fertility. How can it be possible to continue inbreeding for many generations without experiencing inbreeding depression due to recessive alleles? Generally, if a small population continues to inbreed for many generations what will happen to the frequency of the deleterious recessive alleles over time?
Animal breeders have an advantage over natural selection-they can assess the likely future consequences of their actions, and can alter their selection plans accordingly. "Line breeding" is usually successful only when careful animal breeders deliberately avoid breeding any individuals suspected to carry deleterious recessive traits or reduced fertility. In addition, line-bred animals typically have good veterinary care, which may reduce effects of inbreeding depression due to reduced heterozygosity (i.e., reduced resistance to new diseases). In general, if an inbred population can survive the first several generations of inbreeding (when deleterious alleles are first exposed), the frequency of deleterious alleles will eventually decline as natural selection weeds them out. (Deleterious alleles are not the only problem of inbreeding, however. A longer-lasting problem may be the reduction in allelic diversity.)
Neutral theory cont.
But the neutral theory of molecular evolution suggests that most of the genetic variation in populations is the result of mutation and genetic drift and not selection.
In the mid-1980s, conservation biologists reluctantly recommended that zoos should not try to preserve captive populations of all the endangered species of large cats. For example, some biologist recommended ceasing effort tot breed the extremely rare Asian lion. In the place of the Asian lion, the biologist recommended increasing the captive populations of other endangered cats, such as the sibarian tiger and Amur leopard. By reducing the number of species kept in captivity, the biologist hoped to increase the captive population size of each species to several hundred, preferably at least 500. Why did the conservation biologist think that this was so important as to be worth the risk for losing the asian Lion forever?
Conservation biologists were hoping to keep the captive population size (for each species) high enough to avoid loss of allelic diversity and inbreeding depression. Ultimately they were trying to minimize the risk of extinction of the captive populations, over a time scale of up to several centuries into the future. As of a 2009 report , the Felid Taxon Advisory Group of North American Zoos is now attempting to manage 16 species of large cat, almost all of them endangered, in an estimated 2,100 available zoo living spaces. The Asian lion was indeed phased out, partly due to the fact that the entire captive population was discovered to be descended from hybrid Asian-African lions.
Conservation managers often try to purchase corridors of undeveloped habitat so that larger preserves are linked into networks. Why? What genetic goals do you think the conservation managers are aiming to accomplish?
Corridors can potentially link small isolated populations together, causing increased gene flow among them, and reducing the effects of genetic drift. The intended genetic goals are the preservation of allelic diversity and increased heterozygosity.
Consider the nucleotide sequence TGACTAACGGCT. Transcribe this sequence into mRNA. Use the genetic code to translate it into a string of amino acids. Give an example of point mutation , an insertion, deletion, frameshift mutation and a synonymous substitution, as well as a non synonymous substitution.. Then a nonsense mutation. Which of your examples seem likely to dramatically influence protein function. Which seem to have little effect? Why?
DNA: TGACTAACGGCT RNA: ACUGAUUGCCGA Polypeptide: Threonine-Aspartic Acid-Cysteine-Arginine A point mutation, such as T to G in the DNA strand, gives CCU for the first codon and that would replace amino acid threonine with proline. An insertion or a deletion would cause a frame-shift. For example, a deletion in DNA: TGACTAACGGCT, leaves mRNA sequence as: ACGAUUGCCGA and the polypeptide would be: Threonine-Isoleucine-Cysteine. Duplication/insertion of a single base also causes a frameshift, since each codon has three bases. This also affects the rest of the sequence. If the polypeptide change remains the same due to a change where DNA has one base-pair change, yet same amino acid remains in its place, we use the term synonymous substitution. For example ACU codes for Threonine, but if there is a silent substitution of ACU to ACC, ACG or ACA, the amino acid will remain in its place. The protein will function the same, with such mutation. A silent site mutation does not change the amino acid specified by a codon; a replacement mutation does. If there is a substitution of one amino acid to another, due to the base-pair change in DNA and RNA, we use the term non-synonymous substitution. A nonsense mutation will bring a stop codon, instead of an amino acid. Example is UUA for Leucine, might become a stop codon with one base change (UGA). Nonsense mutations probably affect the carrier most dramatically, because they do not allow polypeptide chain to grow.
Allele Polymorphism
Different versions of the same gene- Specific variant in a gene. More than one allele present in a population variation within a population is genetic or phenotypic (environment)(
What are the three modes of selection?
Directional Selection-fitness consistently increases or decreases with the value of a trait. Reduces the variation in a population, bot dramatically but often Stabilizing Selection-individuals with intermediate values of a trait have highest fitness. Stabilizing selection on a continuous trait does not alter the average value of the train in the population. it does reduce the number of individuals in the tails of the traits distribution, reducing variation. Disruptive Selection- extreme values of a trait have highest fitness. on a continuous trait, does not alter the average value of the trait in the population. Disruptive selection does trim off the top of the traits distribution thereby increasing variance.
Bodmer and McKie (1995) review several cases, similar to chromatopsia and the Pingelapese, in which genetic diseases occur at usually high frequency in populations that are, or once were, relatively isolated. An enzyme deficiency called hereditary tyrosinemia, for example occurs at an unusually high rate in the chicoutimi region north of Quebec City in Canada. A condition called porphyria is unusually common in South Africans of dutch descent. Why are genetic diseases so common in isolated populations? What else do these populations have in common?
Genetic diseases are common in isolated populations due to founder effects and subsequent genetic drift. These random effects can, just by chance, override the effects of selection, sometimes resulting in deleterious alleles becoming quite common. These effects are much more pronounced in small populations; the three populations mentioned here are all quite small.
What is the difference between genetic variation, environmental variation, and genotype-by-environment interaction? give examples of each
Genetic variation is based on differences in alleles (versions of a gene) and ultimately the entire genomes, among the individuals. Genetic variation is necessary for evolution, since these differences are encoded and transmitted from one generation to the next. For example, genetic variation in a blood type gene in humans, results in four different phenotypes. In this case, three different alleles of one gene are: I A, I B, i (where I A and IB are codominant, while allele i is recessive to either one). Different combinations of these alleles produce four possible phenotypes: A, B, AB and O blood types, with different frequencies in different parts of the world. Environmental variation is based on the differences produced when same genotypes are exposed to different environments. This usually happens because certain environments might alter gene expression. For example one genotype in a species of plants, often produces different sizes of mature plants, when grown in the different altitudes or with different soil nutrients. Similarly, dark pigmentation on the tips of ears and paws of Siamese cats develops in certain latitudes with colder temperatures. Many additional examples of traits that could vary a great deal under environmental changes are found in quantitative traits. Genotype by environment variation is based on both differences in the genomes and ways that environment affects the phenotypes. When one genotype develops different phenotypes in different environments, we could say that this genotype exhibits phenotypic plasticity. For example, a change from asexual to sexual reproduction, based on the amount of nutrients, predation or parasitism. Phenotypic plasticity can also evolve.
Suppose you are telling your roommate that you learned in biology class that within any given human population, height is highly heritable. Your roommate who is studying nutrition says, " that doesnt makes sense, because just a few centuries ago most people were shorter than they are now, clearly because of diet. If most variation in human right is due to genes, how could diet make such a big difference? Your roommate is obviously correct that poor diet can dramatically affect height. How do you explain this apparent paradox to your roommate?
High heritability within a population does not mean that variation between populations is due to genetic differences. If the populations differ in an environmental factor, the variation between populations can be due entirely to environment. In this case, your roommate is comparing height between two populations (a medieval population versus a modern population) that differ in dietary environment.
How many redheads live in a village of 250 people, where the frequency of red hair is .18?
If there are 250 people in the village and 18% of them have red hair, there are 45 red heads in the village.
If you were a manager charged with conserving the collared lizards of the Ozarks, one of your tasks might be to reintroduce the lizards into glades in which they have gone extinct. When reintroducing lizards to a glad, you will have a choice between using only individuals from a single extant glade population or from several extant glade populations. What would be the evolutionary consequences of each choice, for both the donor and the recipient populations? Which strategy will you follow, and why?
Introductions from a single population will reduce the population size of the donor population. The resulting recipient population is likely to have low allelic diversity and low heterozygosity (at most equal to, but most likely lower than, the source population). However, this strategy might also preserve unique genotypes of the source population. Introductions from several donor populations will have a lower impact on the size of each donor population, and the resulting recipient population will likely have greater allelic diversity and higher heterozygosity than any of the source populations. However, this strategy may result in loss of unique genotypes and loss of any adaptations that the various donor populations had evolved to their particular environments. The choice of strategy is up to the reader.
Because you are studying different subjects, the diversity of knowledge among you and your classmates is larger now than it was at the beginning of the school year. What kind of variation is this? could the diversity of knowledge serve as raw material for evolution of the campus ? why or why not?
Learning / gaining knowledge is a phenotypic change, caused by the environment. This cannot be a material for evolution in biological sense, because this variation is not going to be passed on from generation to generation. We could only talk about cultural evolution, which in fact represents the shared knowledge through tradition and education.
You are an orange farmer trying to increase the juiciness of your fruit. The average orange produces 200 ml of juice. Previous work by your fruit-‐‐juice colleagues has shown that additive genetic and phenotypic variances in fruit-‐‐juiciness are: VA = 50, VP = 100. a) What is the heritability of the fruit-‐‐juice trait? b) Being a goal-‐‐driven individual, you want to increase the juiciness of your fruit to 250 ml of juice per orange in one generation! How do you go about doing this?
Look at notes Day17
Recessive advantage
Lose variation
Recessive Disadvantage
Lose variation graph plateaus
Heterozygote Advantage
Maintains genetic variation only selection is occurring
As a review, list all the reasons you think of that may cause a given trait not to be adaptive despite the action of positive natural selection on the trait.
Many answers are possible. Traits may not be adaptive, or not fully adaptive, due to: trade-offs with other traits; evolutionary constraints (developmental, physiological, ecological, etc.); insufficient time for natural selection to have operated; insufficient genetic variation; and opposing selection at other levels (e.g., selection at the level of the cell).
In-breeding:
Mating among genetic relatives ->decreases frequencies of heterozygotes -> increases frequencies of homozygotes can expose deleterious recessives inbreeding depression: reduced mean fitness in a population resulting from increased frequency of individuals who are homozygous for deleterious recessiveness
Gene Flow
Migration-moving to new population
How do new alleles rise?
Mutation 1)point mutation -cause of single change in nucleotide sequence-> Single nucleotide Polymorphism (SNPs) -Isertion/ deletions "indels" (shift reading frame) Central Dogma = DNA RNA Amino Acid Protien Codon= 3 nucleotide base pairs code for amino acids
_____ ______ is the most important evolutionary process
Natural Selection
The view that natural selection was the predominant evolutionary force made an important prediction: Selection did not agree with the fruit fly heterozygosity experiment
Natural selection is a force that decreases genetic variation (polymorphisms) within populations and within species • Beneficial new mutations will be fixed by positive selection • Fixation of alleles = loss of genetic diversity This means that through the continued action of natural selection over thousands of years, natural populations should harbor little genetic variation
Part I: Referring to the information about Eastern grey squirrels, calculate the percentage of black squirrels in each year. Have phenotype frequencies changed over time in this population, and if so, can you tell why? Can you determine if the population is in, or close to, Hardy-Weinberg equilibrium? Part II: Referring again to the information about Eastern grey squirrels, assuming the population is in Hardy-Weinberg equilibrium, calculate the frequencies of the black and grey alleles in each year.
Part I: Referring to the information about Eastern grey squirrels, calculate the percentage of black squirrels in each year. Have phenotype frequencies changed over time in this population, and if so, can you tell why? Can you determine if the population is in, or close to, Hardy-Weinberg equilibrium? Part II: Referring again to the information about Eastern grey squirrels, assuming the population is in Hardy-Weinberg equilibrium, calculate the frequencies of the black and grey alleles in each year. Part I: The observed frequency of black squirrels was 16% in 1986, 26% in 1987, and 17% in 1994. The data show fluctuation in black squirrel frequency, but it is unclear whether this fluctuation is "real" - it may be due to small sample size or observational technique, and if real, there is not enough information to tell whether drift, selection, or migration, or nonrandom mating are the causes. (Mutation is unlikely to produce allele frequency changes this rapidly.) Since black squirrels may be homozygotes or heterozygotes, we cannot determine actual genotype frequencies, and thus we cannot determine if the population is in Hardy-Weinberg equilibrium. Part II: If the population is in Hardy-Weinberg equilibrium, genotype frequencies can be calculated by knowing that the frequency of grey squirrels will equal q2, solving for q, and then calculating p = 1-q. Frequencies for the grey allele and black allele were: Black coat color in squirrels is theorized to be advantageous in cold climates due to greater absorption of solar radiation, but disadvantageous where natural predators are numerous due to the conspicuousness of black squirrels. This may explain the greater frequency of the black color morph in northeastern city parks, which have cold winters but few natural predators. http://wps.aw.com/wps/media/objects/15335/15703573/img/06_q07fdbk.jpg
List the types of mutations that can occur
Point mutation • Gene duplications • Chromosomal inversions • Whole genome duplication
Predicting the evolutionary response to selection:
Predicting the evolutionary response to selection: R = h2S If we know heritability and the selection differential, we can predict the response to selection Responses : Stabilize, directional, disruptive
QTL
Quantitative trait loci- potions of the genome that influence quantitative traits. -given QTL may contain one or more genes.
Genetic Drift
Random chance
What are reaction norms and why do they matter? Draw your own reaction norm for mood as a function of the temperature outside. What kind of variation allows reaction norms to evolve?
Reaction norm is a pattern of phenotypes one individual might develop when exposed to varying environments. Different genotypes would show different mood change/reaction to changing temperatures. Draw your own, similar to Figure 5.11
HIV epidemic is unlikely to lead to and increase in the CCR5 delta-32 allele over short term because:
Selection will eventually cause an advantageous allele to become more common, but it's a slow process. For selection to cause a rapid increase in an allele's frequency, the selection must be strong and the allele must already be somewhat common. The delta-32 allele of CCR5 is most common in European populations, but HIV infection is low there. Selection due to HIV is strongest in Africa, but the delta-32 allele is very rare there.
State how the following processes tend to vary in speed and effects in small versus large populations. Selection Migration Genetic Drift Inbreeding New mutations per individual New mutations per generation in the whole population Substitution of a new mutation for an old allele. Fixation of a new mutation
Selection: Lesser effects in small populations, due to the greater impact of genetic drift Migration: Greater effects in small populations, because each new migrant represents a greater proportion of total population size Genetic drift: Greater effects in small populations Inbreeding: Greater effects in small populations New mutations per individual: Similar in populations of all sizes New mutations per generation in the whole population: Fewer in small populations New mutations per year in the whole population: Fewer in small populations Probability that a new mutation will be effectively neutral: Similar in populations of all sizes Neutral mutation rate: Similar in populations of all sizes
When researchers compare a gene in closely related species why is it logical to infer that positive natural selection has taken place if replacement substitutions outnumber silent substitutions
Silent substitutions accumulate at a rate determined largely by mutation rate and genetic drift. If replacement substitutions accumulate at a faster rate than silent substitutions, some other process must be driving new alleles to fixation faster than genetic drift could do alone. This process is likely to be natural selection: There are other processes that could affect fixation rate, but they are unlikely to vary between replacement sites and silent sites.
On a graph, what is evolutionary rate?
Slope.
Small Populations vs. Large Populations ----INCREASED OR DECREASE evolutionary rate due to drift? ----INCREASED OR DECREASED fixation of slightly deleterious mutations ---INCREASE OR DECREASE number generation/time ---INCREASE OR DECREASE of fixation of slightly deleterious mutations?
Small= Increased, Increased, Decreased, increased Large=Decreased Decreased, increased, decrease
Drift is _______ in small populations
Strong
What is a spandrel:
Structure that exists as a byproduct of development or evolutionary history.
How do new alleles arise? From mutation to altered proteins ex. Synonymous mutations Non synonymous mutations Nonsense mutations Indwells
Synonymous mutations do not alter the amino acid Nonsynonymous mutationschange the amino acid Nonsense mutations alter the amino acid to a stop codon Insertions and deletions (indels) shift the reading frame and thus alter codons
Selection
Systematic violations of Hardy- Weinberg assumptions: 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. Differential reproductive success.
What are the Hardy Weinberg assumptions? Why is it useful to know the conditions that prevent evolution? For each condition, specify whether violation of that assumption results in changes in genotype frequencies, allele frequencies or both.
The five conditions are: no selection, no mutation, no migration, no chance events (also can be stated as infinite population size, or no genetic drift), and random mating. Violation of selection, mutation, migration, and/or chance events will result in changes in allele frequencies and genotype frequencies in the population. Violation of random mating—but not the others—will result in changes in genotype frequencies but not in allele frequencies.
Consider three facts: 1. loss of heterozygosity may be especially detrimental at MHC loci, because allelic variability at these loci enhances disease resistance; 2) Microsatellite loci show that the gray wolves on Isle Royale, Michigan are highly inbred.; 3) This wolf population crashed during an outbreak of canine parvovirus during the 1980's. How might these facts be linked? What other hypotheses could explain the data? How could you test your ideas?
The population crash of the Isle Royale wolves may have been related to low heterozygosity at MHC loci, and consequently lowered disease resistance, in the small population. Another possible explanation is that parvovirus could have caused a massive crash in any population of wolves, regardless of their MHC heterozygosity. (Canine parvovirus appeared suddenly in 1978, apparently derived from a mutant feline distemper virus, and spread worldwide in just a few months. Mortality rates exceeded 80% in many canid populations.) The two hypotheses could be tested by comparing MHC heterozygosity and parvovirus resistance of this wolf population to other, more outbred, wolf populations. If parvovirus mortality rate is related to MHC heterozygosity, wolf populations that are more outbred should have showed lower mortality than the Isle Royale wolves during the parvovirus outbreak.
We used figure 6.14 as an example of how the frequency of an allele in fruit flies does not change in unselected control populations but does change in response to selection. However, look agains at the unselected control lines in figure 6.14. The frequency of the allele in the tow control populations did change a little, moving up and down over time. Which assumption of the Hardy-Weinberg model is most probably being violated? If this experiment were repeated, what change in experimental design would reduce this deviation from Hardy-Weinberg equilibrium?
These small changes are likely due to genetic drift caused by chance events. The easiest way to reduce this effect is to use a larger population size.
If we know the variance due to genetics (VG) and the variance due to the environment (VE), then we can partition the total phenotypic variance (VP) into these parts.
VA = variation among individuals due to the additive effects of genes VD = variation among individuals due to gene interactions (such as dominance) narrow-sense heritability = h2 = VA/VP The selection differential (S) is the difference between the mean of the selected individuals and the mean of the entire population
Substitution
When mutations become dominant in a population.
We noted on the first page of the chapter that humans vary considerably in height. State a hypothesis about whether this reflects genetic variation, environmental variation or genotype by environment interaction. What kinds of evidence might settle the question? Are there experiments that, at least in principle, would decide the matter? Would it be easier to do them with another species, such as mice?
You can propose any of the above hypotheses and make predictions. For example, if height is solely determined by the environment, you would expect that same genotypes show different results in different environments. On the other hand, if human height is purely result of genetic variation, you would expect same height for the same genotype in different environments. It would be very difficult to test this in humans, but you could use identical twin studies. Mice would be a better experimental model system to compare the phenotypic variation in body size, for example. However, when it comes to human height, we are looking at the quantitative trait (polygenic and highly impacted by the environment).
Nearly Neutral Mutations
[[[[Tomoko Ohta (1973) proposed a modification to the neutral theory which accounts for mutations that are slightly deleterious (or slightly advantageous).]]]] {{{{[What if alleles are influenced by both selection and drift? • In small populations, drift will predominate • In large populations, selection will predominate • Most new mutations are deleterious...but • They will behave as neutral in small populations • They will be selected against in large populations.]}}}} The nearly neutral theory Cont. But, population size is usually inversely proportional to generation time • We expect faster rates of neutral evolution in small populations (where drift predominates), but long generation times slows down the effective rate of evolution • In large populations with short generation times, we expect relatively slow rates of evolution due to selection against deleterious new mutations, but because generation times are fast there are many more opportunities for fixation of new mutations Wikipedia not all mutations are either so deleterious such that they can be ignored, or else neutral. Slightly deleterious mutations are reliably purged only when their selection coefficient is greater than one divided by the effective population size. In larger populations, a higher proportion of mutations exceed this threshold for which genetic drift cannot overpower selection, leading to fewer fixation events and so slower molecular evolution. The nearly neutral theory was proposed by Tomoko Ohta in 1973.[1] The population-size-dependent threshold for purging mutations has been called the "drift barrier" by Michael Lynch, and used to explain differences in genomic architecture among species.
Three Genotypes AA Aa aa Beginning of season 100 132 15 End of season 25 95 7 a) calculate % survival of each genotype: b) setting the fitness of the best genotype to calculate that relative fitness of the other two genotypes: c) What form of selection is the butterfly experiencing? What are the long-term evolutionary consequences of this form of selection for the alleles A and a?
a. AA=25% Aa=71% aa-46% b. AA= .25/.71 Aa= 1 aa= .466/.71 C. Heterozygous advantage. The genotype Aa will stabilize and become more frequent. Genetic variation will be maintained.
Qualitative Traits
can assign individuals to categories just by looking at them. Flower is purple or yellow
QTL mapping-
collective name for a suite of related techniques that employ marker loci to scan chromosomes and identify regions containing genes that contribute to a quantitative a quantitative trait. For each F2 individual, the researchers measure the phenotype for the quantitative trait of interest and the genotype at the marker loci distributed across the genome. Examining entire F2 population, researchers compare individuals with different genotypes at each marker locus. If phenotypes diver among individuals with different genotypes at a particular marker, we can infer that the parker sits near a locus that contributes the the quantitative trait.
phenotypic plasticity
different phenotypes emerge from the same genetic background in different environments —> plasticity itself can evolve It is the variation in the phenotype associated with a single genotype... example: height in malnourished vs non malnourished humans.
Mutation
drives evolution change in allele frequencies
Deleterious mutations are elected against therefore
evolutionary rates decrease
Over dominance = Under dominance=
heterozygote advantage heterozygote disadvantage
The probability of fixation of a new allele is equal to what
its frequency in the population example: 1/2N = frequency in the population so, (2Nμ)*(1/2N)= μ [2N cancels out] Kimura
Selection is relatively stronger in ___________ populations
larger -- Strength of selection also depends on relative fitness of different alleles.
Heterozygote disadvantage
loss and fixation occurs, unstable equilibrium, genetic variation is lost.
Using population genetics we can ...?
make specific conclusions about relative fitness of different genotypes, and the population response to selection
neutral theory of molecular evolution (Kimura)
most evolutionary changes and most of the variation within and between species is not caused by natural selection but by genetic drift of mutant alleles that are neutral. A neutral mutation is one that does not affect an organism's ability to survive and reproduce. The neutral theory allows for the possibility that most mutations are deleterious, but holds that because these are rapidly purged by natural selection, they do not make significant contributions to variation within and between species at the molecular level. Mutations that are not deleterious are assumed to be mostly neutral rather than beneficial. In addition to assuming the primacy of neutral mutations, the theory also assumes that the fate of neutral mutations is determined by the sampling processes described by specific models of random genetic drift. Wiki.
Rate of evolution under drift alone is equal to?
mutation rate
2nμ
number of alleles created by mutation each generation μ=mutation rate.
Quantitative Genetics
the branch of evolutionary biology that provides too for analyzing the evolution of multi locus traits. ex. continuous variation such as height, athletic ability, intelligence. they are determined by combined influence of the genotype and many different loci, and the environment.
reaction norm:
the pattern of phenotypes an individual may develop upon exposer to different environments.
Adaptation: How do we know when its taking place?
trait benefitting and increasing fitness (Survive and reproduce) "A trait that increases the ability of an individual to survive or reproduce compared with individuals without the trait." 1. determine what the trait is for 2. show that individuals possessing the trait contribute more genes to future generations than individuals lacking it
Adaptationism
what is adaptationism? Viewing traits as adaptations without rigorous testing of alternative hypotheses.
A few key ideas of the synthesis:
• Mendelian genetics, Darwinian evolution (i.e. natural selection as the mechanism for change) and gradual evolution are fully compatible ideas • Evolution occurs through gradual change • Microevolution and macroevolution occur as results of the same set of processes • Natural selection is the most important mechanism of change
