Mid 2 Evolution Mechanisms PDF

END OF CHAPTER 6: Mechanisms of Evolution - The first 4 are technically the mechanisms, the 5th one is an honourary mention bc it creates conditions where selection occurs - Nonrandom mating doesn’t create evolution Selection selection happens when individuals with particular phenotypes survive to reproductive age at higher rates than individuals with other phenotypes or when individuals with certain phenotypes produce more offspring than others with different phenotypes both are differential RS (selection) selection only leads to evolution when the phenotypes have a genetic basis Selection = natural and sexual selection MID 2 Always compare individuals to the average of the population In evolution you wanna be above the average Both survival and reproductive success combine to give reproductive success (RS) sexual + natural selection combined is the biggest mechanisms that determine fitness If the trait has no genetic basis, you cant have natural or sexual selection acting on it If the trait is highly heritable (trait value is close to 1) it can be selected within a population more rapidly. Itll move through the population quicker and help them survive and reproduce If a trait has low heritability 0.1 heritability or hertitability closer to 0, it'll move through the population but might take more generations to popn genetics often assumes that phenotypes are determined strictly by genotypes. e.g. pea plants (Tall - TT, short - tt) accurate for some traits (but not all) if phenotypes are discrete classes, we can think of selection acting directly on genotypes “popn genetics often assumes that phenotypes are determined strictly by genotypes.” this is not true most of the time but we use it to teach at a lower level This phenotype to genotype linkage is accurate for simpler traits (like size) but not all phenotypes are coded for by 2 alleles on one locus Selection acts on the genotype here bc its so simply coded for This wouldn’t be true for human height bc many genes contribute so selection doesn’t act on the genotype bc theyre are so many genes. in reality = most phenotypic traits are not determined by a genotype. Ends up being many loci that contribute e.g. TT pea plants - vary in height due to genetic variation at other loci & environment more about this in Chapter 9. Quantitative genetics Adding selection to H/W selection can change allele frequencies locus that affects survival probability single locus with 2 alleles: B1 & B2 3 possible diploids: B1B1, B1B2, B2B2 B1 frequency = 0.6 B2 frequency = 0.4 Simplified example of selection Selection can change allele freq Locus often affects survival or reproductive success, sometimes even both Here we will look at survival Single locus w two alleles that are Codominant after random mating: B1B1, = 0.36 B1B2, = 0.48 B2B2 = 0.16 lets assume there are 100 zygotes thus 36 (B1B1), 48 (B1B2), 16 (B2B2) After All individuals random mate - Selection against B2 and for the B1, so some B1B2 and B2B2 killed off - In the end up with more B1 and less B2 - Is this difference big enough to be significant? - YES, not in HW and reject null - Evolution occurred - Selection for an allele and against another - Looking at the 60/40 split: the next generation in theory with no evolution would be 60/40 again - Not the case here bc not all zygotes survive equally - Selection pressures at the juvenile stage - B1B2 75% survive and 25% die - B2B2 only 50% lived - Having the B2 allele is a bad thing here - B2 is the “bad gene” - Selection against B2 - B1 gets selected - End result: B1 0.675 and B2 0.325 - B1 went up in proportion and B2 went down in proportion. Still have to add up to 100 - The change from 60% to 67.5% is very significant. Big jump in one generation - If the selection pressure didn’t change over time, B2 would eventually disappear and go to 0 - B1 would be 100, reached FIXATION - In a case of recessive/dominant, the bad gene can stay in heterozygotes bc it gets masked by the dominant allele but here its co-dominant - A big jump isn’t so common,, its usually small changes - Whats good now, may not be good in a few years impose selection: genotypes differ in their rates of survival all B1B1 survive 75 % of B1B2 survive 50% of B2B2 survive result (n=80): 36 (B1B1), 36 (B1B2), 8 (B2B2) Gamete contributions - 36 B1B1 donating 10 gametes: 10 x 36 = 360 games, all B1 - 36 B1B2: make 360 gametes but alleles will be split 50/50 by B1 and B2 - B2B2: 8x10 = 80 - This is how we got the end result from the figure Evolution has occurred frequency of B1 has risen by 7.5% frequency of B2 has dropped by 7.5% violation of the no selection assumption has occurred thus, population has evolved in response to selection usually, not such strong selection in one generation small changes over a long time have large effect Here it was related to survival Selection pressure over a long time can drastically alter phenotype. This is how we get changes at the species level, bc species end up not recognizing eachother in order to mate and end up isolated Persistent selection can produce large changes initial frequency of B1 = 0.001, frequency of B2 = 0.99 red line: 100% for B1B1, 90% for B1B2, 80% for B2B2 Right hand side: different levels of selection Strongest selection: red line Weakest selection: yellow line Selection is favouring B1 The stronger the selection for B1, leads to higher loss of B2 When freq of B1 is 100% = fixation Yellow is whats more normal in wild In lab we can get alleles going to fixation quicker if we impose selection Climate change is a relatively rapid adaptation with strong selection, closer to red line Polar icecaps melting has massive selection pressure on polar bears bc they cant find food (need seals on ice to eat) now theyre eating duck eggs. So now there is selection for the bears to eat duck eggs, environmental pressure on a behavioural phenotype Rapid evolution happens just isn’t as common Fruitflies: Drosophila melanogaster - 50 generations Cavener & Clegg (1981) - change in allele frequencies over many generations model system = Drosophila melanogaster (fruitflies) make an enzyme that breaks down alcohol (poison) alcohol dehydrogenase (ADH) 2 alleles at the ADH locus (AdhF & AdhS) F = fast, S = slow (with respect to gel electropheresis) ADH is produced by flies to break down alcohol Spiking their food with bad chemicals to see how they respond The alleles are called F and S with respect to how they migrate in gel F has lower molecular weight and S has higher molecular weight 2 experimental populations on food spiked with ethanol 2 control populations on normal (nonspiked) food picked breeder for each generation at random natural selection expt: different environments but, they did not themselves directly manipulate the survival or RS of individual flies 2 populations with alc and 2 polulations as control Go into jar and take a female and let it be the breeder as random every several generations Cavener & Clegg took a random sample of flies from each population calculated the allele frequencies what did they find? - From textbook - Y axis: frequency of F allele of locus - If the allele isn’t an F it has to be an S - Y acis is percent that have the F allele - If 40% had F then 60% had S - - Did this for 50 generations - Starting w the control population - Stochastic fluctuation. Random movement around an average - The line is not significantly different from the start point - Breakdown of F or S allele did not change significantly in the control population - Ethanol: - Over time, went upto almost 100% F allele - F allele is very good for them to process alcohol compared to the S allele - - Cant assume all animals have the genes to adapt (they’ll go extinct) control popn: no large/significant change in allele frequencies expt popn: rapid increase in AdhF (decrease in AdhS) H/W holds true in control, but not experiment populations likely due to “no selection” assumption violation AdhF homozygotes break down alcohol 2X better Section 6.4 Mutation Read pages 216-224 (6.4 - Mutation) don’t worry about page “Computation consequences” case study regarding cystic fibrosis Cystic fibrosis is among the most common serious genetic diseases among people of European ancestry affecting approximately 1 newborn in 2,500. Cystic fibrosis is inherited as an autosomal recessive trait.. Affected individuals suffer chronic infections with the bacterium Pseudomonas aeruginosa and ultimately sustain severe lung damage most individuals with cystic fibrosis live into their thirties or forties, but until recently few survived to reproductive age. Although cystic fibrosis was lethal for most of human history, in some populations as many as 4% of individuals are carriers How can alleles that cause a lethal genetic disease remain this common? new disease alleles are constantly introduced into populations by mutation Second on the list of assumptions for the Hardy–Weinberg equilibrium principle was that there are no mutations. We now explore what happens to allele frequencies when this assumption is violated. Mutation by itself is generally not a rapid mechanism of evolution. Mutation is a weak mechanism of evolution In a single generation in our model population, mutation produces virtually no change in allele and genotype frequencies. Hardy–Weinberg analysis shows that mutation is a weak mechanism of evolution. Almost no effect is not the same as exactly no effect. After 1,000 generations, the frequency of allele A in our model population will be about 0.81. Mutation can cause substantial change in allele frequencies, but it does so slowly. Mutation and selection: t fruit fly populations with virtually no initial genetic variation accumulate novel alleles quickly enough to allow rapid adaptive evolution. all flies in the inbred stock were essentially genetically identical. The researchers next reared larvae from their inbred stock on food spiked with table salt (NaCl) at concentrations ranging from 1% to 6%. At least a few larvae survived to adulthood at concentrations up to 4%, but all the larvae died at 5%. used flies from the inbred stock as founders for six experimental populations, which they maintained for 30 generations. They kept the population sizes large, establishing each generation with 200 pairs of randomly chosen adults from the previous generation. kept two of the populations under benign conditions, and four on food spiked with salt. They distributed the salty food in patches with different concentrations, but all of it was stressful for the flies. sThe conditions of the experiment allowed the populations to evolve by natural selection to adapt to their new environments, but the populations would do so only if they accrued genetic variation via mutation. The original inbred stock appears first, as a reminder that for the founding flies, 5% salt was 100% lethal. The unstressed lines appear next. Even though theses lines had evolved under benign conditions, both included a few individuals that could survive in 5% salt. This result demonstrates the accumulation of genetic variation by mutation in the absence of selection. The salt-stressed lines appear last. They contained higher proportions of individuals that could survive 5% salt. This result demonstrates adaptive evolution as a result of mutation and natural selection in combination. Further evidence that the stressed lines harbored alleles for salt tolerance at higher frequency than the unstressed lines came when Zhang and colleagues attempted to rear larvae on 6% salt. A few individuals from each of the salt-stressed lines survived, but all the flies from the unstressed lines died. Mutation-selection balance: Unlike the mutations that allowed the evolution of increased salt tolerance in Zhang et al.’s fruit fly populations, many mutations are at least mildly deleterious. Selection tends to eliminate such mutations from populations. Deleterious alleles persist, however, because they are continually created anew When the rate at which copies of a deleterious allele are being eliminated by selection is exactly equal to the rate at which new copies are being created by mutation, the frequency of the allele is at equilibrium. This situation is called mutation–selection balance Research by Brunhilde Wirth and colleagues (1997) on patients with spinal muscular atrophy provides an example Spinal muscular atrophy is a neurodegenerative disease characterized by weakness and wasting of the muscles that control voluntary movement. It is caused by deletions in a locus on chromosome 5 called the telomeric survival motor neuron gene (telSMN) In some cases, the disease may be exacerbated by additional mutations in a nearby gene. Spinal muscular atrophy is, after cystic fibrosis, the second most common lethal autosomal recessive disease in Caucasians Collectively, the loss-of-function alleles of telSMN have a frequency of about 0.01 in the Caucasian population. the selection coefficient is about 0.9. With such strong selection against them, we would expect that disease-causing alleles would slowly but inexorably disappear from the population. How, then, do they persist at a frequency of 1 in 100? At the same time selection removes deleterious alleles from a population, mutation constantly supplies new copies. In some cases, this balance between mutation and selection may explain the persistence of deleterious alleles in populations. Wirth and colleagues analyzed the chromosomes of 340 individuals with spinal muscular atrophy, and the chromosomes of their parents and other family members. They found that 7 of the 340 affected individuals carried a new mutation not present in either parent. These numbers allowed the scientists to estimate directly the mutation rate at the telSMN locus. Their estimate is 1.1 x 10^-4. Are the Alleles That Cause Cystic Fibrosis Maintained by a Balance between Mutation and Selection? Cystic fibrosis is caused by recessive loss-of-function mutations in a locus on chromosome 7 that encodes a protein called the cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is a cell-surface protein expressed in the mucous membrane lining the intestines and lungs. CFTR’s key functions is to enable cells of the lung lining to ingest and destroy Pseudomonas aeruginosa bacteria Selection against the alleles that cause cystic fibrosis appears to be strong. Until recently, few affected individuals survived to reproductive age; those that do survive are often infertile And yet the alleles that cause cystic fibrosis have a collective frequency of approximately 0.02 among people of European ancestry. Could cystic fibrosis alleles be maintained at a frequency of 0.02 by mutation– selection balance? the mutation rate creating new disease alleles would have to be 4 * 10^-4. The actual mutation rate for cystic fibrosis alleles appears to be considerably lower than that: approximately 6.7 * 10^-7 We can conclude that a steady supply of new mutations cannot, by itself, explain the maintenance of cystic fibrosis alleles at a frequency of 0.02. Perhaps the fitness cost suffered by cystic fibrosis alleles when they are in homozygotes is balanced by a fitness advantage they enjoy when they are in heterozygotes. In other cases, the frequency of a deleterious allele may be too high to explain by mutation– selection balance. This may be a clue that heterozygotes have superior fitness. hypothesized that cystic fibrosis heterozygotes might be resistant to typhoid fever and therefore have superior fitness. Typhoid fever is caused by Salmonella typhi bacteria (also known as Salmonella enterica serovar typhi). The bacteria initiate an infection by crossing the layer of epithelial cells that line the gut. suggested that S. typhi bacteria infiltrate the gut by exploiting the CFTR protein as a point of entry. If so, then heterozygotes, which have fewer copies of CFTR on the surface of their cells, should be less vulnerable to infiltration. tested their hypothesis by constructing mouse cells with three different CFTR genotypes: homozygous wild-type cells; heterozygotes with one functional CFTR allele and one allele containing the most common human cystic fibrosis mutation, a single-codon deletion called ∆F508; and homozygous ∆F508 cells. The researchers exposed these cells to S. typhi, then measured the number of bacteria that got inside cells of each genotype. As the researchers predicted, homozygous ∆F508 cells were almost totally resistant to infiltration by S. typhi, while homozygous wild-type cells were highly vulnerable. Heterozygous cells were partially resistant; theyT accumulated 86% fewer bacteria than did the wild-type cells. These results are consistent with the hypothesis that cystic fibrosis disease alleles are maintained in human populations because heterozygotes have superior fitness during typhoid fever epidemics. Also consistent with the hypothesis are two more recent discoveries by Pier and coworkers. First, Jeffrey Lyczak and Pier (2002) found that S. typhi bacteria manipulate the gut cells of their hosts, causing the cells to display more we CFTR protein on their membranes and easing the bacteria’s entry. This helps explain why cells that cannot make CFTR are resistant to invasion. Second, Lyczak, Carolyn Cannon, and Pier (2002), using data compiled from the literature, found an apparent association across 11 European countries between the severity of tyhoid fever outbreaks and the frequency a generation later, among CFTR mutations, of the ∆F508 allele (Figure 6.31b). Section 6.4 Mutation mutation is a weak mechanism of evolution mutation is weak bc mutations on average are uncommon Weak form of evolution but OCCASIONALLY a mutant can have high fitness Mutation is weak on average bc it takes many loci to contribute to the phenotype but if you had a phenotype only coded for by a couple alleles and a mutation allowed you to survive better, that mutation would get through the population very quickly if it was good for your survival Here, if you have a mutation event, going from 0.9 to 0.8999, still very high mutation rate and the outcome is still small In a single pop, a mutation might be 1 per 10 000 which is very high, usually its 1 per 100 000 or 200 000 High mutation rate gives a small outcome but given enough time, mutation can have a profound effect on the population through: 1. Small incremental changes 2. Or the odd mutation can be very good for survival so it lasts in the population over very long periods of time mutation can have an effect Multi generational standpoint Mutation can have an effect but takes thousands of generations Slow acting change CHAPTER 7 PT 1: MIGRATION, DRIFT, NON-RANDOM MATING: Mechanisms of Evolution Ch 6: - Selection - Mutation Ch 7: - Migration - Genetic drift - Nonrandom mating Migration migration: movement of alleles between populations not the same as seasonal movement of individuals gene flow: transfer of alleles from the gene pool of one populations to the gene pool of another population mechanisms of gene flow: occasional long-distance migration of juveniles, spores spread by wind, etc.. migration varies a lot depending on mobility of individuals and propagules Gene flow is the physical movement of the alleles through the sperm/egg of individuals Propagules: items that float through environment like seeds. Plants reproduce by sending their seeds off Why do trees shed into the wind: trying to avoid inbreeding so they send their seeds out to increase reproductive success Dropping seeds near yourself and self fertilize, less fit Dispersal of propagules is more fit Adding Migration to H/W one island model: simple model of migration 2 popns: continent & small island offshore island is small so any movement from island to continent does not affect allele or genotype frequencies Big arrow bc when seeds or alleles go from the continent to the island has a big effect bc diversity on the continent is larger than the diversity on the island bc it’s a small population Small arrow bc they’ll have a small impact since huge number of individuals on the continent migration (& gene flow) is one way from the continent to the island bc migration from island to continent is insignificant single locus with 2 alleles (A1 & A2) can migration from the continent to the island take the allele and genotype frequencies on the island away from H/W? before migration: A1 = 1.0 (fixed is the island population) thus, when gametes in the gene pool in which A1 is fixed, mixes at random to make zygotes, the genotype frequencies in the zygotes are: assume: fixed population size, so assume there are 800 zygotes which develop to juveniles and then adults assume: continental population is fixed for allele A2 assume: 200 individuals migrate over from continent to the island after migration: 80% (alleles from island) & 20% (continent) right: 100% A1 Then migration of 200 A2A2 Now allele frequencies are 80/20 Severe deviation from HWE When you see a change from 100/0 (fixation) to 80/20 or 70/30 or 60/40 this is usually due to gene flow Massive changes in one generation of allele frequencies, usually due to gene flow/migration Evolution is happening Reason: migration new genotype frequencies are: thus, when individuals reproduce on the island, their gene pool will have 0.8 for A1 and 0.2 for A2 migration has changed the allele frequencies on the island, violating an assumption of H/W after migration the allele frequency of A1 is 0.8 (before it was 1.0) island population has evolved as a result of migration Exam mc: Homozygotes go from 100% A1 to 80/20 and no heterozygotes, you had fixed individuals moving over from mainland after migration, there is an excess of homozygotes and a deficiency of heterozygotes note: a single bout of random mating will put the population back to H/W After migration, there's an excess of homozygotes and a deficiency in heterozygotes compared to what HWE predicts Signature pattern of geneflow/migration Note: if the mice migrate to the island, initially evolution has happened but if they interbreed randomly (HWE) then the next gen will have a mix of alleles and will go back to HWE Assuming they randomly mate Case study: Water Snakes individuals vary in appearance strongly banded to unbanded determined by a single locus with 2 alleles banded allele is dominant over unbanded allele Using phenotype to demonstrate migration but we can do it genetically Phenotype is indicator of genotype bc banding is genetic mainland = banded, island = unbanded likely due to natural selection (predation) unbanded snakes on islands were more cryptic unbanded snakes on islands had higher survival thus, we would expect all island snakes to be unbanded, but this is not the case why?: because mainland snakes move over On the island, lots of beaches and the unbanded camouflaged better NS was the reasoning for banded vs unbanded If selection was the only thing effecting evolution, wed expect banded in one place and unbanded in the other But we don’t see that Bc mainland snakes move over to the island to breed if there aren’t enough breeders for them on the mainland migrant snakes bring copies of banded alleles to gene pool migration is acting against natural selection (fixed for banded) Likewise in reverse No good to survive if your reproduction is 0 Trade off between natural and sexual selection Blends more common on islands bc mainland has so many snakes so migration only has a small effect on them but island had less individuals so migration effects them more Genetic drift populations genetics tells us that NS is not the only mechanism of evolution non-selective mechanism does not lead to adaptation but does lead to changes in alleles frequencies random process drift results from violation of the infinite popn size assumption Genetic drift is quite random and doesn’t select for a specific trait NS is not random but drift is Adding Genetic Drift to H/W Small population Drift has larger effect on small population vs larger ones How does this happen? we did not pick the exact 0.6 (A1) & 0.4 (A2) the ratio was richer in A1 and poorer in A2 this was due to sampling error: random discrepancy between theoretical expectations and actual results thus, genetic drift is: sampling error in the production of zygotes from a gene pool because it is an accumulation of random events (blind luck), genetic drift cannot produce adaptation If you only pick a few sperm and egg randomly, if you only pick a few individuals, by chance you might deviate from the 60/40 split You could choose more A2 eggs by chance bc small population Larger pop gives you larger chance of being at the same probability you started with Drift is small population and certain individuals breeding more than others Know definition of sampling error Possible outcomes for 10 mice 100-18= 82 percent chance of the time drift is going to occur in this small population Probability of getting less than the original 0.6 is 40.5 In this small population Odds of change were 40.5+41.5= roughly 80% The chance of getting the exact ratio of 60/40 from the start is only 18% Simulation drawing alleles from gene pool instead of drawing sperm/eggs to make 10 zygotes, lets make 250 zygotes as computer draws each gamete, it gave a running report of frequency of A1 early on frequency of A1 fluctuates a lot as cumulative number of zygotes made increases, gradually approaches the expected 0.6 frequency sampling error diminishes as sample size increases (large popn) When you get to 100% for one allele its called fixation In small population drift has a large effect on allele freq As you get more zygotes, its closer to 0.6 in A1 (equilibrium) More fluctuation when there are less individuals Sampling error & evolution = founder effect observing drift in nature - small populations often small populations are founded by a few indvs allele frequencies are likely different from the older (previous generation), large population due to chance (= founder effect) direct result of sampling error very important in conservation biology Drift itself does not create an adaptation Drift is a result of sampling error, having a small population = founder effect Small number of founder parents gives founder effect where you might lose some alleles Small populations tend to be endangered populations Banff example: Major highway that bisects the park in half This separated the animals and they couldn’t cross the road Genetic drift started impacting the population bc theyre split into smaller populations What did they do? Create corridors that go over the highway so that animals would cross over Allows alleles to move back and forth This helps by allowing gene flow which keeps drift at a minimal Drift is bad bc it keeps alleles from moving back and forth causes loss of genetic variation on both sides of the highway Molecular evidence of founder effect Tinghitella et al. (2011) - crickets & founder effect Polyneisan field crickets – native to northern Australia and New Guinea also found on islands across the Pacific (Hawaii) How did crickets cross the ocean?? short distance = fly or float on vegetation longer distance = need boats (i.e. stowaways) Study on crickets and founder effect Chain of islands that had the same crickets Did they fly in on vegetation? Stowaways: hid with vegetation on boats for sales of goods if crickets dispersed across Pacific, by hopping from island to island aboard boats then each islands population would have been founded by a few indvs these founders would have carried a subset of the genetic variants present on the islands they came from unless there is ongoing migration after the invasion of new islands, cricket popns should have fewer alleles with greater distance from Australian continent Jump from big island (Australia and new guinea) to other smaller islands = island hoping These would contain a subset of alleles from the island they came from, these change depending on the island they come form Everytime they hop, youll lose alleles each time = founder effect Founder effect is a sub category of drift (one type of drift) Founder effect at each island causing losing alleles each time researchers determined genotypes of 394 crickets from 19 popns at 7 microsat loci founder effect prediction: each new population will have a randomly chosen subset of alleles present from the original population (founders) predict: as crickets went from island to island, allele variation should decrease along the route Looked at diversity of alleles at each island Founder effect : Totri 9a locus for crickets From textbook Yellow/orange is mainland Bar graphs are distribution charts of alleles. Amount of bars= number of alleles, height of bar is how many individuals have it Intermediate islands in purple Further away islands in green (hawaian islands) Decrease in allelic richness Australian (orange) populations have numerous alleles at low frequencies Oceanic populations (purple, Fiji, Samoa, etc) have fewer alleles, some at high frequency Hawaiin populations (green, remotest) have just 2 or 3 alleles each (one in high frequency) same pattern for ALL 7 loci (not just this one) Hawaii < Oceanic < Australia (boat dispersal & genetic drift in the form of founder effect) A loci has multiple alleles This was true for all locus Founder effect: Pingelapese people atoll is 2700 miles SW of Hawaii 20 survivors of typhoon & starvation (1775) high degree of color blindness 20 ppl stranded on the island Did not represent allelic freq of mainland island 180 years later they found them Problems w inbreeding High amount of colourblindness, due to founder effect of everyone having this allele Genetic Drift Genetic drift can have large effect over time (even on larger populations) READ pages 246-274 (remainder of genetic drift section) Three patterns are evident: 1. Because the fluctuations in allele frequency from one generation to the next are caused by random sampling error, every population follows a unique evolutionary path. 2. Genetic 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. Note that if genetic drift is the only evolutionary mechanism at work in a population—if there is no selection, no mutation, and no migration—then sampling error causes allele frequencies to wander between 0 and 1. The wandering of allele frequencies produces two important and related effects: (1) Eventually alleles drift to fixation or loss, and (2) the frequency of heterozygotes declines. As any allele drifts between frequencies of 0 and 1.0, sooner or later it will meet an inevitable fate: Its frequency will hit one boundary or the other. If the allele’s frequency hits 0, then the allele is lost forever (unless it is reintroduced by mutation or migration). If the allele’s frequency hits 1, then the allele is said to be fixed, also forever As some alleles drift to fixation and others to loss, the allelic diversity in a population falls. Now imagine a finite population where several alleles are present at a particular locus: A1 , A2 , A3 , A4 , and so on. If genetic drift is the only evolutionary mechanism at work, then eventually one of the alleles will drift to fixation. At the same moment one allele becomes fixed, the last of the others will be lost. Sewall Wright (1931) proved that the probability that any given allele in a population will be the one that drifts to fixation is equal to that allele’s initial frequency If, for example, we start with a finite population in which A1 is at a frequency of 0.73, and A2 is at a frequency of 0.27, there is a 73% chance that the allele that drifts to fixation will be A1 and a 27% chance that it will be A2. As allele frequencies in a finite population drift toward fixation or loss, the frequency of heterozygotes decreases Fixation index (Fst) formula: HT is the expected heterozygosity under Hardy–Weinberg equilibirum in a total population created by combining all of our separate populations HS is the average across separate populations (also known as subpopulations) in their expected heterozygosities. At the start of the simulation depicted in graph (a), FST is zero, because both HT and HS are 0.5. By the end, FST is 1, because—with all subpopulations fixed—HS is 0. Peter Buri (1956) studied these phenomena empirically, in laboratory population of 16 fruit fly Drosophila melanogaster. established 107 populations of flies, each with eight females and eight males. All the founders were heterozygotes for an eye-color gene called brown. They all had the genotype bw75/bw. Thus, in all 107 populations, the initial frequency of the bw75 allele was 0.5. tained these populations for 19 generations. For every population in every generation, Buri kept the population size at 16 by picking eight females and eight males at random to be the breeders for the next generation. What results would we predict? If neither allele bw75 nor allele bw confers a selective advantage, we expect the frequency of allele bw75 to wander at random by genetic drift in every population Because allele bw75 has an initial frequency of 0.5, we expect it to be lost about as often as it becomes fixed. As bw75 is drifting toward fixation or loss in each population, we expect the average heterozygosity across all populations to decline. After one generation of genetic drift, most populations still had an allele frequency near 0.5, although one had an allele frequency as low as 0.22 and another had an allele frequency as high as 0.69. In generation four, the frequency of bw75 hit 1 in a population for the first time. In generation six, the frequency of bw75 hit 0 in a population for the first time. As the allele frequency reached 0 or 1 in ever more populations, the distribution of frequencies became U-shaped. By the end of the experiment, bw75 had been lost in 30 populations and had become fixed in 28. The 30:28 ratio of losses to fixations is very close to the 1:1 ratio we would predict under genetic drift. the average frequency of heterozygotes steadily declined. the effective population size in Buri’s experiment was 9: see figure The solid gray curve shows the predicted decline for a population size of 9; it fits the data well. Buri’s populations lost heterozygosity as though they contained only 9 individuals instead of 16. Among the explanations are that some of the flies in each population may have died due to accidents before reproducing, or some males may have been rejected as mates by the females. Random Fixation and Loss of Heterozygosity in Natural Populations collared lizards In 1990, Alan Templeton and colleagues investigated genetic drift in collared lizards in Missouri’s Ozark Mountains, which were once part of a desert extending from the American Southwest during a hot, dry period from 8,000 to 4,000 years ago. As the climate cooled, the Ozarks became overgrown with savannas and forests, leaving desert-like glades as isolated habitats for the relict populations of collared lizards. Periodic wildfires previously maintained these savannas, but fire suppression by European settlers in the 1950s allowed oak-hickory forests and invasive eastern red cedars to encroach on the glades. This habitat change severely isolated the lizard populations, restricting their movement and gene flow between glades. As a result, many populations became genetically isolated, with some groups consisting of only a few dozen lizards. Because of the small size and genetic isolation of the glade populations, Templeton and colleagues (1990) predicted that Ozark collared lizards would bear a strong imprint of genetic drift. Within each population, most loci should be fixed for a single allele, and genetic variation should be very low Empirical data from a natural experiment confirm that due to drift, small isolated populations lose their genetic diversity. The researchers screened lizards for their genotypes at a variety of enzyme loci, for their ribosomal DNA genotypes, and for their mitochondrial DNA genotypes. They identified among the lizards seven distinct multilocus genotypes the nearly complete loss of genetic diversity in the glade populations had doomed the Ozark collared lizards to extinction. This extinction would happen one glade at a time and have any of a number of proximate causes. If a pathogen appeared that could infect and kill one of the lizards in a glade, it could infect and kill all lizards in the glade—because they were virtually identical. As the biological and physical environment changed, the lizard populations would be unable to evolve in response—because genetic variation is the raw material for adaptive evolution. If Templeton and colleagues were right, simple measures could save the Ozark collared lizards. One is the relocation of lizards to repopulate the empty glades. on, Templeton and colleagues established three new populations in the Stegall Mountain Natural Area, a former ranch with many glades but no lizards. The lizards in the new populations thrived but did not migrate, neither from population to population nor to any of the empty glades. As long as the oak–hickory forest was in the way, the populations would remain isolated and suffer the longterm consequences of genetic drift. the Missouri Department of Conservation and the United States Forest Service began using controlled burns to clear the oak–hickory forest at Stegall Mountain. The lizards responded almost immediately, moving among populations and colonizing many of the empty glades. This behavior should restore the genetic diversity of the glade populations The Rate of Evolution by Genetic Drift the rate of evolution when genetic drift is the only process at work. Mutation versus substitution Mutation is the creation of a new allele; substitution is the fixation of the new allele, with or without additional mutational change. This graph shows the 10 alleles present in each of 20 successive generations in a hypothetical population of five individuals. During the time covered, the dark green allele was substituted for the light green allele. The blue allele may ultimately be substituted for the dark green allele, or it may be lost. The figure follows a gene pool of 10 alleles for 20 generations. Initially, all of the alleles are identical (light green dots). In the fourth generation, a new allele appears(dark green dot), created by a mutation in one of the original alleles. Over several generations, this allele drifts to high frequency. In generation 15, a second new allele appears (blue dot), created by a mutation—at a different nucleotide site—in a descendant of the first dark green allele. In generation 19, the last copy of the original allele is lost. At this point, we can say that the dark green allele has been substituted for the light green allele. Thus, by evolutionary substitution, we mean the fixation of a new mutation, with or without additional mutational change When genetic drift is the only mechanism of evolution at work, the rate of substitution is equal to the mutation rate true regardless of the population size, because two effects associated with population size cancel each other out: More mutations occur in a larger population, but in a large population each new mutation has a smaller chance of drifting to fixation. Under genetic drift, large populations generate and maintain more genetic variation than small populations, but populations of all sizes accumulate substitutions at the same rate. 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; and (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. Neutralists predict that for most genes in most populations, the rate of evolution will be equal to the neutral mutation rate. advantageous mutations are exceedingly rare and that most alleles of most genes are selectively neutral selectionist theory: advantageous mutations are common enough that they cannot be ignored. Selectionists predict that for many genes in most populations, the rate of substitution will reflect the action of natural selection on advantageous mutations. Genetic Drift versus Natural Selection In an ideal population of infinite size, natural selection favoring one allele over others will inexorably carry the favored allele to fixation. If the same beneficial allele occurs in a finite population, however, sampling error will cause the allele’s frequency to fluctuate at random around the trajectory it would have taken in a population of infinite size. Sometimes the allele’s frequency will rise, and sometimes it will fall. The allele may even go extinct. Likewise, in an infinitely large population, selection favoring heterozygotes will maintain multiple alleles at equilibrium frequencies indefinitely In a finite population, genetic drift may cause one allele to become fixed and the other to be lost. Whether drift or selection plays the predominant role in determining the evolutionary outcome will depend on both the size of the population and the strength of selection. red flour beetle red flour beetles are typically red. But not always. Rich and colleagues took advantage of genetic variation for color at the b locus. The wild-type allele is called b +. A mutant allele that can be maintained in lab populations is called b. Beetles with genotype b+\ b+ are red beetles with genotype b+ \b are brown and beetles with genotype bb are black. set up 24 populations of flour beetles in which the initial frequencies of allele b + and allele b were both 0.5. They started 12 populations with 50 males and 50 females and 12 with 5 males and 5 females. They maintained the populations at these sizes for 20 generations, each generation choosing adults at random to serve as breeders for the next generation. Every generation, they examined 240 randomly chosen individuals from each population to assess the frequencies of the two alleles. When populations are subject to both selection and genetic drift, smaller populations follow more diverse evolutionary paths.. In these populations, drift was predominant. In the large populations, however, selection was predominant. If twice the effective population size multiplied by the selection coefficient is less than –1 or greater than 1, then selection substantially alters an allele’s chances of loss or fixation. early data on molecular evolution did not match expectations derived from the notion that most evolutionary change was due to natural selection. But if natural selection does not explain evolution at the molecular level, then what process is responsible for rapid, clocklike sequence change? Many researchers believe the answer is genetic drift. neutral theory The neutral theory models the fate of new alleles that were created by mutation and whose frequencies change by genetic drift. It claims to explain most evolutionary change at the level of nucleotide sequences. the neutral theory of molecular evolution to explain the observed patterns of amino acid sequence divergence Mutations that are deleterious tend to be eliminated by natural selection and thus contribute little to molecular evolution. Mutations that are neutral (or nearly so—more on that later) rise and fall in frequency as a result of genetic drift. Many are lost, but some become fixed. Mutations that are beneficial are often lost to drift while still at low frequency, but otherwise tend to rise to fixation as a result of natural selection. Kimura’s neutral theory holds that effectively neutral mutations that rise to fixation by drift vastly outnumber beneficial mutations that rise to fixation by natural selection. Genetic drift, not natural selection, is thus the mechanism responsible for most molecular evolution. Kimura postulated that the rate of molecular evolution is, to a good approximation, equal to the mutation rate. Although Kimura’s theory appeared to explain why the amino acid sequences of hemoglobin, cytochrome c, and other proteins change steadily over time, the theory was inspired by limited amounts of data. How did the neutral theory hold up, once large volumes of DNA sequence data became available? Pseudogenes are functionless stretches of DNA that result from gene duplications Because they do not encode proteins, mutations in pseudogenes should be neutral with respect to fitness. When such mutations achieve fixation in populations, it should happen solely as a result of drift. The evolution of pseudogenes conforms to the assumptions and predictions of the neutral theory Molecular evolution in influenza viruses is consistent with the neutral theory Because the genetic code is redundant DNA sequence changes that do not result in amino acid changes are called silent-site (or synonymous) mutations; sequence changes that do result in an amino acid change are called replacement (or nonsynonymous) mutations. The neutral theory predicts that both will accumulate by drift, but synonymous substitutions will accumulate faster. Silent changes are not exposed to natural selection on protein function, because they do not alter the amino acid sequence. New alleles created by silent mutations should thus increase or decrease in frequency largely as a result of drift. Replacement mutations, in contrast, change the amino acid sequences of proteins. If most of these alterations are deleterious, then most of them should be eliminated by natural selection without ever becoming common enough to be detected. This type of natural selection is called negative or purifying selection, as opposed to positive selection on beneficial mutations. Natural selection against deleterious mutations is called negative selection. Natural selection favoring beneficial mutations is called positive selection. In most coding sequences, substitution rates are higher at silent sites than at replacement sites. This result is consistent with the notion that molecular evolution is dominated by drift and negative selection. genes responsible for the most vital cellular functions appear to have the lowest rates of replacement substitutions. Like histones. In contrast, genes less vital to the cell, and thus under less stringent functional constraints, show more rapid rates of replacement substitutions. similar straiture When researchers compare homologous DNA sequences among individuals and want to explain the differences they observe, they routinely use the neutral theory as a null hypothesis. The neutral theory specifies the rates and patterns of sequence change that occur in the absence of natural selection. If the changes that are actually observed are significantly different from the predictions made by the neutral theory, and if a researcher can defend the proposition that the sequences in question have functional significance for the organism, then there is convincing evidence that natural selection has caused 1 molecular evolution I When sequences evolve by drift and negative selection, synonymous substitutions outnumber replacement substitutions. When sequences evolve by drift and positive selection, replacement substitutions outnumber synonymous substitutions. In many examples, replacement substitutions outnumber synonymous substitutions—a signature of positive selection positive selection causes replacement changes to spread through the population much more quickly than neutral alleles can spread by chance. Comparing Silent and Replacement Changes within and between Species BRCA1, a gene associated with breast cancer, provides another example. BRCA1 encodes a protein that participates in the repair of damaged DNA. Positive selection on the BRCA1 gene in humans and chimpanzees A polymorphism is a locus at which different individuals in a population carry different alleles. analyze the alcohol dehydrogenase (Adh) gene in three species of fruit flies. This gene was particularly interesting because it helps the flies detoxify ethanol from rotting fruit, a primary food source for them. Since different fruits vary in ethanol content, researchers speculated that the Adh gene might experience selective pressure as populations adapt to different fruit types They found that among fixed differences between species, 29% involved amino acid replacements (replacement substitutions), while only 5% of within-species polymorphisms did. This sixfold difference (statistically significant, p = 0.0062) provided strong evidence against the neutral model, which predicts similar rates of replacement substitutions in both categories. these replacement mutations likely provided adaptive advantages, helping species to rapidly adapt to new environments after diverging. Which Loci Are under Strong Positive Selection? Positive selection seems to be particularly common in genes involved in biological conflict. Replacement substitutions appear to be particularly abundant in loci involved in arms races between pathogens and their hosts, in loci with a role in reproductive conflicts such as sperm competition and egg–sperm interactions Positive selection has also been detected in genes involved in sex determination, gametogenesis, sensory perception, interactions between symbionts, tumor suppression, and programmed cell death as well as in genes that code for certain enzymes or regulatory proteins. Selection on “Silent” Mutations silent mutation was coined to reflect two aspects of base changes at certain positions of codons: They do not result in a change in the amino acid sequence of the protein product, and they are not exposed to natural selection Direct Selection on Synonymous Mutations: Codon Bias and Other Factors. Codon bias refers to the nonrandom usage of synonymous codons—different codons that encode the same amino acid. While synonymous codon changes do not alter the amino acid sequence in proteins, and are often assumed neutral regarding fitness, this is not strictly accurate. If these changes were truly neutral, codon usage within a species would appear random, with each codon for a given amino acid appearing in proportions that match the species’ overall genomic G+C content. However, sequencing studies have shown that certain synonymous codons are used more frequently than others, indicating that factors like translational efficiency or cellular resource availability may influence codon preference, creating codon bias. Codon bias is strongest in highly expressed genes—such as those for the proteins found in ribosomes—and weak to nonexistent in rarely expressed genes. In addition, the suite of codons that are used most frequently correlates strongly with the most abundant species of tRNA in the cell Codon bias suggests that some synonymous mutations are not selectively neutral. Indirect Effects on Synonymous Mutations: Hitchhiking and Background Selection. Another phenomenon that affects the rate and pattern of change at silent sites is referred to as hitchhiking, or a selective sweep Hitchhiking can occur when strong positive selection acts on a particular amino acid change. As a favorable mutation increases in frequency, neutral or even slightly deleterious mutations closely linked to the favored site will increase in frequency along with the beneficial locus. These linked mutations are swept along by selection and may even ride to fixation. Note that this process occurs when only recombination fails to break up the linkage between the hitchhiking sites and the site under selection. example of hitchhiking happened on the fourth chromosome of fruit flies. The Drosophila fourth chromosome is unusual because it shows no recombination. The entire chromosome is inherited like a single gene. selective sweeps cleaned out all or most of the variation on the fourth chromosome in each species. Has hitchhiking produced all of these regions of reduced polymorphism? Probably not. Another process, called background selection, can produce a similar pattern Background selection results from negative selection against deleterious mutations, rather than positive selection for advantageous mutations. Like hitchhiking, it occurs in regions of reduced recombination. The idea here is that selection against deleterious mutations removes closely linked neutral mutations and yields a reduced level of polymorphism. Hitchhiking results in dramatic reductions in polymorphism as an occasional advantageous mutation quickly sweeps through a population. Background selection causes a slow, steady decrease in polymorphism as frequent deleterious mutations remove individuals from the population. Status of the Neutral Theory As a null hypothesis for detecting positive selection in molecular evolution, the neutral theory has been highly successful. Data are now accumulating that will allow researchers to evaluate the neutral theory’s claim that most molecular evolution is dominated by negative selection and drift. For now, the issue is undecided. the study of coalescence: Here we consider coalescence as a tool for estimating effective population size, although it has a great variety of other applications. If we could run the movie of molecular evolution backward, we would see alleles become less divergent and eventually merge into their common ancestral sequence. This process is called coalescence. The merging of genealogical lineages as we trace allele copies backward in time is called coalescence Mathematical model only requires population size The result is an evolutionary tree of genes—a gene tree or gene genealogy Mathematical descriptions of coalescence provide an efficient means of simulating evolution by genetic drift. Coalescence models can be fit to data, yielding estimates for parameters such as population size. END OF TEXTBOOK INFO Adding nonrandom mating to H/W H/W assumes mating is random most common type of nonrandom mating is inbreeding effect = increases the frequency of homozygotes compared to what is expected by H/W most extreme example: self-fertilization (selfing) in plants Selection, mutation , migration, drift are mechanisms mechanisms of evolution (direct) 5 DOES NOT cause evolution but causes conditions for evolution to occur (non random mating) (indirect) Inbreeding: Mating w someone more genetically similar to you compared to how related you are to the general population Creating more homozygous recessive in population, which have low fitness and get selected out of the population Inbreeding alters genotype frequencies although inbreeding causes genotype frequencies to change from generation to generation it does NOT cause allele frequencies to change thus, inbreeding by itself is not a mechanism of evolution BUT, inbreeding can have important evolutionary consequences (research lecture – mate choice and genetic quality, next lecture) Exam: Honourary bc created changes in genotype freq but not in allele freq Evolution: change in allele freq in extreme cases of inbreeding when same genotypes mate to make next generation % of heterozygotes will decline by 50% each generation, whereas homozygotes will increase 25% each generation BUT, from one generation to the next allele frequency does not change The heterozygotes end up becoming AA and aa In one generation: allele freq does not change Inbreeding depression Inbreeding does not cause evolution because allele freq not changing Inbreeding simply affects how genotypes are “packaged” into diploid zygotes Inbreeding does NOT change proportion of alleles in popn, simply moves them from heterozygote to homozygote genotypes This can lead to inbreeding depression (decrease in average fitness of inbred individuals) Know inbreeding vs inbreeding depression Inbreeding: mating w someone w genes similar to you Inbreeding depression: reduction in fitness of individuals that are a result of parents that mated and are similar Inbreeding DOESN’T equal inbreeding depression Purging: if a pop has been inbreeding for a while and bad alleles get wiped out Google definition: Genetic purging is the increased pressure of natural selection against deleterious alleles prompted by inbreeding Inbreeding doesn’t always lead to inbreeding depression Sea otter because inbreeding produces an excess of homozygotes, H/W analysis can be used to detect inbreeding in nature sea otters were nearly wiped out due to fur trade down to as few as 50 individuals (now: popn is 1500) If HWE says you should have 20% homozygous recessive and your pop has 40%, there is prob inbreeding investigated whether the reduced population size and density led to inbreeding determined the genotypes for 31 allozyme loci e.g. PAP locus (2 alleles: S (slow) & F (fast)) examined 33 individuals: SS = 16, SF = 7, FF = 10 more homozygotes and fewer heteros than expected authors also examined otters from Alaska (less of a bottleneck) no evidence of missing heterozygotes (n.b. small sample size) Homozygous FF is recessive Inbreeding depression General Analysis of Inbreeding inbreeding also occurs at more distant relatives inbreeding also reduces heteros but at a slower rate coefficient of inbreeding (F): probability that 2 alleles in an individual are identical by descent both alleles come from the same ancestor allele in some previous generation Can be inbreeding accidentally bc youre more related to individuals than you think The higher the inbreeding, the quicker heterozygotes go away check equations by using F = 0 gives original H/W equation or use F = 0.5, which gives the selfing values F= descendants If you sub in 0 for F, you get HWE Bc HW assumes you mate randomly Ways to find F: 1. Use microsatellites, neutral markers that scan genome. Can give an F value. 2. We do whole genome scans now not just a few microsatellites 3. If you don’t have whole genome. You can reintroduce animals and check their genotypes first. Using a pedigree How to calculate F directly: requires a pedigree (read page 280-282) Stud book for all endangered animals over the wold Zoos trade animals to avoid inbreeding ZIMS: stud book for all zoos over the world Keep track of all parents for all animals, genotyping them KNOW HOW DO FIND F AND DO THE MULTIPLICATION Figure 7.36a shows a pedigree leading to a focal female who is the daughter of half-siblings. She is inbred because her parents share a common ancestor in her grandmother. For the focal female to have gene copies that are identical by descent, the following would have to have happened (reading clockwise from the focal female): The female’s mother passed to her, via the egg, a copy of the same gene copy the mother received from the grandmother (an event with probability ½) ; the father received from the grandmother a copy of the same gene copy the mother received from the grandmother (probability ½ ) ; the focal female received from her father, via the sperm, a copy of the same gene copy the father received from the grandmother (probability ½ ) F is the probability of all three events happening together, or (½ )^3 = ⅛. Figure 7.36b shows that for an offspring of full sibs, there are two loops passing through a common ancestor, each with three internal links. F in this case is thus 1/8 + 1/8 = 1/4. Anytime F is greater than 0, the frequency of heterozygotes is lower in an inbred population than it is in a random mating population. Inbreeding depression usually results from the exposure of deleterious recessive alleles to selection To see how this works, consider the extreme case illustrated by loss-of-function mutations. These alleles are often recessive, because a single wild-type allele can still generate enough functional protein, in most instances, to produce a normal phenotype. Even though they may have no fitness consequences at all in heterozygotes, loss-of-function mutations can be lethal in homozygotes First, inbreeding effects are often easiest to detect when plants undergo some sort of environmental stress. Second, inbreeding effects are more likely to show up later in the life cycle —not, for example, during the germination or seedling stage. Third, inbreeding depression varies among family lineages Inbreeding depression although inbreeding does not change allele frequencies, it can still affect evolution mostly due to: inbreeding depression decreased vigour in terms of growth, survival, or fertility following one or more generations of inbreeding usually results from the exposure of deleterious recessive alleles to selection most extreme = loss-of-function mutations Changes second generation Most extreme: like embryos not hatching in drosphilia Loss-of-function mutations & inbreeding these alleles are often recessive recessive b/c a single w/type allele can still generate enough protein to produce a normal phenotype no real fitness consequence in heterozygotes bc the dominant allele can mask the recessive one lethal in in homozygotes by increasing homo frequency, inbreeding increases the affect of recessives on phenotypes Inbreeding depression in humans Humans are not immune to inbreeding Each dot is different societies If inbreeding wasn’t costly, the dots would fall right on the grey line Do the dots fall above or below the line on average? Here they fall above the line. Inbreeding depression is higher w individuals that are more related to eachother Inbreeding depression in Parus major A bird that mates in a certain area and tend to mate w relatives As F increases, chances of hatching decreases. More hatching failure as theyre inbred Even a small amount of inbreeding can be costly Inbreeding depression animals & plants evolve mechanisms to avoid inbreeding mate choice (research lecture), genetically controlled self-incompatibility, dispersal inbreeding unavoidable in some small populations common problem for rare & endangered species problem for captive breeding programs Florida Panther - case study FL have very low genetic diversity due to inbreeding Loss of heterozygosity Pumas and panthers are same species, just different subspecies. Can breed together FL panthers have lower genetic diversity bc they were at the tip of florida and trapped by cities and couldn’t move around, no gene flow either. In Idaho and south america there is more room for them to move around In FL panthers, their ability to reproduce was highly compromised. High inbreeding depression, loss of fitness. Dashed line: year where they introduced 9 female panthers from Texas in florida GENETIC RESCUE Heterozygosity went way up Right hand side: increase in survival of kids, from 80 percent to 90 percent survival Artificial gene flow Genie Simulation lecture Evolution by Genetic Drift: Patricia Voyer What is Genetic Drift? - A nonselective mechanism of evolution that leads to changes in allele frequencies Genetic drift has a more rapid and dramatic effect on allele frequencies in small populations than in large populations - This is a concern for conservation biologists Given enough time, genetic drift can produce substantial allele frequency changes, even in large populations With mutations (the introduction of a new allele), it can take longer for genetic drift to create a dramatic effect CH 7 PART 2: MATE CHOICE AND GENETIC QUALITY - Inbreeding is when you have individuals related more than average pop breeding - Inbreeding depression: effects fitness of offspring - Genetic quality is low when they are inbred - Genetic quality goes up in conservation Outline 1. What is genetic quality? 2. Mate choice & good genes 3. Mate choice & compatible genes - What is genetic quality? - Widow bird on left, the males have extravagant tails - The females are green without tails - Sexual dichromatism and sexual dimorphism - Sockeye salmon males are more red and have humps - Males are more ornamented in these examples - Dimorphism also occurs in humans, males are 20% taller Sexual Selection Selection on the phenotype through; 1. competition among members of one sex (usually males) for access to members of the other sex or 2. choice by one sex (usually females) of certain members of the other sex Intrasexual selection - Male-male competition Intersexual selection - Female choice t.fi choice o - Intra: within male sexual selection, could even be female-female - Causes evolution of weapons. Kyte in these animals have larger biting features to scare off other males - Intersexual: - Between the two sexes - Females chose more dramatically ornamented males - Painted buntings, females prefer more colourful males Genetic Quality - Females are getting good genes from the males. Additive genetic effects poration - Red circle represents how ornamentation they are - Larger circle means more ornamentation - Universal preference for the more ornamentation male - Each allele is a good genes bc every copy of the A/A allele from the males to the offspring is good - Ornamentation is often costly so they need good genes with it - - - Compatible genes: - Left is universal choice but right is based on relative preference of females - Theyre choosing based on their genotype relative to the males genotype - AA female avoids AA male bc she doesn’t want inbreeding to occur - - How do they know how related they are to the individuals? FACTORY QUES (pheromones) females have the ability to smell how related they are to males. Prefer males that smell different to them - That’s why there is no colour on the right hand side Genetic Quality good gene = allele that increases fitness independent of the architecture of the remaining genome compatible gene = allele that increases fitness when in a specific genotype Good genes: Helps kids to be better irrespective of the moms genes Current Controversy & Interest Even if there is a net gain for a male expressing a sexually selected trait (e.g. ↑ reproductive success) Why would a female prefer a male with an extravagant ornament? Ornamented males have better reproductive success House finches: females prefer males w more red plumage bc males w more red provide more parental care Sticklebacks: more red males gives more parental care Getting good care and good genes^ Peacocks (male) peahens (females), females assess quality of males tail, mate and produce kids then the female never sees the male again. So why does she care? GENETIC QUALITY Moor frogs: males turn blue during breeding. Females choose males that are more blue. Correlated with the males genetic quality In most systems there is no parental care at all Certain foods contain carotenoids sp that affects the males colour Sex f Top: traditional mate choice which is before they fertilize and copulatory Sperm utilization: where genetic benefits are coming from. Sometimes females get fertilized by 3 different males and she can internally choose with sperm is used to fertilize the eggs Differential: male dominates female and she cant stop the male. She will shed the eggs and starts over bc she knows the male is too related to her. Differentially invests less into the kids so they die. But if they were a good male then she would invest more into offspring All three mechanisms are trying to acquire balance of good and compatible genes Guppy Mating System 1. Do male phenotypes indicate good genes or compatible genes? 2. Can females bias paternity towards males with good or compatible genes? - Guppies are one of the most common model systems Male guppies differ in how much orange they have on them Males only give genes to the females, no parental care Females are much bigger than the males In circle: females give birth to 15-30 children every month Kids swim away Moms don’t give any parental care So kids are due to only genetic differences with mom and dad Model System female mate choice cues are well known multiple mating is common promiscuous non-resource based mating system females appear to gain little from males except sperm(alleles) Females prefer males w more orange on the body Orange Colour comes from carotenoids, hard to get in the wild. Cant fake them Females don’t care for black colour bc it can be faked by the males Mate choice for good genes females prefer males with larger areas of orange coloration survivorship, reproductive success Choosing males w more orange improves survivorship and reproductive success Showy: 30% of its body covered in orange Plain: 13% orange Offspring Performance: Good genes - Open circles vs white circles are just two diff studies - Positive relationship Trade-up Hypothesis Behavioral strategy to maximize genetic benefits: 1. Secure sperm supply 2. Re-mate for superior genes First hypothesis 1 and 2 are predictions of the hypothesis 1. Females are not chosy when they first reproduce just to make sure they can have some offspring (they have kids every month) 2. After the first reproductive cycle, they’ll look for males w more orange to better reproductive success - Took females that were close to being ready to sexually produce and raised them in tanks - - Exposed the females to a showy male on day one and some of the females get a plain male - day 2: take the females w showy male, half of those ones get a showy male again and the other half get a plain male - Showy-showy-female - Show-plain-female - Order matters On right: - Plan-showy-female - Plain-plain-female - On day 1 - Prediction: they shouldn't be very choosy - In wild females often die after first reproductive cycle so its important to secure a male Response to first male - Sigmoid: how the males show they colour off - Females approach males they prefer - And copulate a - High receptivity= she chose the male - Low receptivity = didn’t want the male - - No significant difference in female choice - So prediction 1 is correct Response to second male - Prediction 2 - Second day - Difference in female receptivity graphed - Positive= she really liked the second guy - Neg= she doesn’t care (wasnt super interested but not completely uninterested) - Really neg = doesn’t like second guy - Plain-plaine and showy-showy showed a slightly neg preference for the second guy. She doesn’t prefer them not reject them - Dashed line; average value between plane-plane and showy-showy taking into account the error bars - No big difference between plain-plain and showy-showy. Dont prefer them but dont not prefer them - Dashed line, cost of mating: average value between plain-plain and showy-showy. Taking into account error bars - Cost of mating bc when females see a showy guy on first day and showy guy on second day, they dont want to pay the cost of mating by going w the second male when there is no obvious benefit for them - Same goes for plain-plain - Cost is like predation, males injuring females, etc - If she already had a showy male, she wont want the plane male - If she started w a plane male, she should be more responsive to a second showy male - Don’t want to devalue the showy genes she got from the male in the first place - Showy-plane - Activity avoiding the plan male - Bc why dilute the good genes from showy male - - Plan-showy - Trading up - - Females avoid trading down Paternity Biasing - Paternity - Does behaviour turn into a difference in paternity - Can tell siblings based on where their colour pattern is - Females can use behaviour to bias who mates w them - Not the intensity of colour! But the colour pattern is heritable - Can use colour pattern of sons and determine paternity - Plane-showy - Showy male who goes second gets 80% of the kids - - Showy-plain - 50/50 split on who gets kids - Shes trying to fight off plain male to avoid diluting her genes - - Paternity from 0-100% - Plain-showy, the showy got majority of paternity - - Second male presidence: the second male to mate in the wild, often they have an advantage bc their fertilization is closer to the reproductive cycle in timing or they physically displace sperm from the other male - Trading up on the left and avoiding trading down on the right - Positive correlation - Males get more paternity when the female prefers you - Females use behaviour to bias more orange males to improve fitness of their kids - - Same data as last slide - Direct link between females preference and paternity. Higher female behaviour gives higher paternity, irrespective of if they're first or second Alternative Hypothesis - Difference in sperm quality? - Carotenoids in body are an ROS.i - The orange are from carotenoids from food. Carotenoids are good for you bc they quench(takeup/use) free radicals bc they cause cellular damage. Improving carotenoid levels, they have better sperm quality - - Reduces oxidative stress Sperm traits Number Motility Viability i I 7 Showy males have higher amount of sperm, motility and viability Better sperm Measures these 3 aspects - Orange males do have better sperm - And female behaviour also plays an aspect Inbreeding Depression Risk factors - Isolation - Siblings in tributaries - Trade up is about good genes - This is trade off between good and compatible genes - How do females avoid inbreeding depression? - Inbreeding depression: loss of fitness in offspring - Inbreeding: mating w someone close to you genetically - Sibling and tributaries: brothers and sisters are found in the same stream. - Become sexually mature in an isolated area, inbreeding chances increased - Happens when pools get smaller in the winter Compatible genes: Inbreeding “sibs in tribs” inbreeding depression? Pre-copulatory preference? Post-copulatory biasing? Is inbreeding depression occurring Do they do something Before or after they mate? This happens in every kind of animal All humans avoid breeding w relatives (and red head females mating w red head males bc they tend to be related) Inbreeding Depression How to assess whether there is inbreeding Put in tank and force them to breed Top: females Bottom: males Letters represent families - Males don’t care bc they don’t pay a huge cost and mate to w many individuals in one cycle - Greater cost for females bc they carry the children - Compare offspring - Inbreeding doesn’t always lead to inbreeding depression - Outbred produced more offspring - Inbred kids die in utero sometimes - Lower survival - - How many sperm did the kids that were inbred/outbred produce - Males that were outbred produced more sperm - Lower reproductive success - - How long did it take kids to be sexually mature - Outbred took less time to be sexually mature - Sexually maturing faster, gives reproductive advantage, can make kids earlier before you get killed by predators Avoiding Inbreeding Depression 1. Pre-copulatory mechanisms - Kin recognition 2. Post-copulatory mechanisms - Sperm choice - How do females avoid the cost? These are the two ways - Before mating : kin recognition.have a que to recognize if the individual is related to them or not. Done by smell (olfactory ques). When you sweat your smell it gives an indicators of your immune system - And after mating: sperm choice. Females can store sperm from males In their reproductive organs, can bias where they store sperm. Not the individual sperm. They could choose to mate w another male sooner, or leak out sperm from less dominant males - Pre copulatory - Had a tank - Let females choose amongst males - Didn’t allow them to mate - The dots are holes - Allow factory ques to go back and forth between males and females Pre-copulatory - Females at top - Males at bottom - Look at females receptivity based on smell - How receptive she is to the male based on his smell - There are dividers in the tank - Behavioural receptivity to a full sibling vs unrelated male - - - No Pre-copulatory mechanism - Percent of time females were interested - P=0.41, no statistical difference - No significance in female receptivity - Preferred them about the same Sigmoids: - The percent of time that males display to a female - Was the same if the female is a sibling or not - Males and females don’t care at pre-copulatary stage - No mechanism - Post-copulatory Polyandry mate withmany males Sperm choice ineach reproductivecycle Paternity bias - Guppies polyandrous: females mate w many males in each reproductive cycle - Sample of female reproductive tract, each black thing is a sperm head - Females had different folds In their ovaries g - Stored sperm from related males further away - Stored sperm from unrelated males closer to eggs - No choice: females have no choice but to mate w a certain kind of male - Choice: females can choose who they mate w - 1 2 3 4 5 sit sit non sib sib Prediction if females can multiply mate and bias paternity towards the unrelated male: Sib sib offpring number No choice but to make inbred offspring Females should produce less kids than non-sib|non-sib In choice tank: Non-sib|sib Should have similar number of kids as non sib|nonsib If female had 100% control, she would use non-related males so it should be similar to nonsib-nonsib Post-copulatory - Residual: how many kids they did they have for their body - Neg: less kids than expected for her body size - Pos: more kids produced than expected for her body size - Sib/sib : Less kids than expected, inbreeding depression - Nonsib-nonsib: more than expected - Wed expect pos number for nonsib-sib - Average of sib-sib and nonsib-nonsib - - If female has no control of relatedness, wed expect it to be on the dotted line for nonsib-sib - Random/ no difference Random warooq hill hypothesis - Significantly different than random - Females can reproductively bias towards non-sib - Can exclude sperm of siblings - Not perfect mechanism but is a fitness advantage - - Don’t have a pre-cop mechanism but they do have a post-cop mechanism - - If they weren’t polyandrous then they wouldn’t have a post-cop mechanism Guppy reproductive behaviour 1. Females trade up - Bias towards attractive males 2. Sperm competition - Quantity and quality of sperm 3. Females avoid inbreeding - Post-copulatory biasing CHAPTER 9: EVOLUTION AT MULTIPLE LOCI: QUANTITATIVE GENETICS - Quantitative genetics - In pop gen: one locus - Most traits this is too simple - Multiple loci: quant gen Japanese flounder - In the wild phenotypes don’t tend to be one or the other - Usually there is continuous variation - Phenotypes are continuous - Like human height - Intensity of colour - Normal distribution - Little bimodal - Continuous Quantitative Genetics chapters 6 & 7: how and why populations evolve (good for one or 2 loci) typically, many traits are determined by the combined influences of alleles at many loci often don’t know the exact identities of the loci involved. Changing now bc we can do whole genome sequencing quantitative genetics: tools for analyzing the evolution of multilocus traits Many loci = hundreds or thousands to date, we have focused on examples that are discrete in origin (banded vs. unbanded) qualitative traits: can assign individuals to a one of two or three categories by phenotype or a simple genetic test however, most traits show continuous variation Historically we only focused on qualitative traits (like banded vs unbanded) NS usually works on quantitative traits quantitative traits: characters with continuously distributed phenotypes Phenotypes we see in the wild are usually quantitative Determined by the combined effects of: (1) genotype at many different loci (2) the environment Some trait that’s important for fitness (like body size), size might be important for survival and reproduction. What percentage of the variants can be explained by environment, genetics or genetic by environment interactions G E And G by E How do I explain the variance I see in the wild with genetics, the environment or how those two interact Mendelian genetics & quantitative genetics debate whether Mendel’s model of genetics could be applied to quantitative traits Edward West (1916) - longflower tobacco length of the corolla (tube) location 2 pure-breeding strains (short & long) Mendel was focused on one locus w a few alleles Varinet form of agene Hypothesized mendel's model could be applied to quantitative traits but didn’t know how Long flower tobacco, studied length of corolla as a trait he wanted to explain using quant gen Easier to grow and cross plants compared to other organisms Had 2 pure breeding strains. One pop was short and one had long corollas Could mendel's models explain this variation Mendelian genetics & quantitative genetics crossed individuals from these parental strains to produce F1 hybrids then, let F1 hybrids self-fertilize to produce an F2 generation What do we expect? Hybrids bc they took a short and long then crossed them to get F1 Produced F2 Simplest Mendel model single locus, 2 alleles (codominant) Aa x Aa would get three phenotypes: aa (short), Aa (med), AA (lg) first cross = AA x aa result: all offspring a Aa (medium flowers) F1 self-fertilize: aa(1/4), Aa (1/2), AA (1/4) = F2 too simple; corolla length highly variable Too simple, doesn’t explain the variance saw in the plants Couldn’t say some were small, short and intermediate There was continuous variation from very small to very big Simplest Mendel model (1 locus, 2 alleles) - One locus - Fails to explain variance - - Mendel model with 2 loci (4 alleles) A, a & B, b (capital letter = longer corolla) 5 phenotypes: genotypes of: 0, 1, 2, 3, 4 cross aabb x AABB= AaBb (all medium F1) F1s self-fertilize: offspring are short to long 1/16, 4/16, 6/16, 4/16, 1/16 (4 x 4 Punnett) still has discrete sizes 2 locus model still has discrete categories Still fails to explain variance Simplest Mendel model (2 loci,4 alleles) - 5 phenotypes - Still don’t explain variance Mendel model with 6 loci (24 alleles) yields 13 phenotypes (0 to 12 capital letters aabbccddeeff x AABBCCDDEEFF all F1s will be AaBbCcDdEeFf (medium size) F2: from short to long (64 x 64 Punnett square) 1/4096, 12/4096, 66/4096, 220/4096, …(n=13) phenotypes grade into each other (need ruler) Larger range of phenotypes Started predicting phenotypes that were really close to each other, more of an accurate representation of what was seen in the wild Started capturing variation seen in wild Mendel's model still works but you need to have many loci and many alleles!!! Immune system has variance in MHC genes. Fitness relevant traits tend to be coded for by many loci with many alleles Variability in wild can be seen with examples of many loci w many alleles Edward West’s Dataset - Continuous variation in both small and large plants - Not just one size or large and one size of small Problems? all plants with one genotype should be exactly the same not the case; phenotypic variation among individuals with the same genotype WHY? Answer: each plant in West’s experiment was exposed to a unique environment You can explain all the variation in a trait, got an answer, and do it again in a diff greenhouse and get different results Why? The environment! Weather, pH, sunlight, etc Environment & quantitative genetics environment differences in quantitative phenotypes e.g. Yarrow plants genetically identical reared at different elevations recall: environment & genes The environment and quant gen are linked Yarrow plants Same seeds in different locations (elevation) Gave different results Environment matters in quant gen Same gene give different outcome in varying environment: plasticity (phenotypic plasticity) Plasticity can be stronger or weaker Quantitative trait loci (QTL) QTL: loci that influence quantitative traits 2 common methods: 1. QTL mapping 2. Investigation of candidate loci Loci that influence quantitative traits There are many loci that do not effect phenotype QTL is only interested in the ones that do effect phenotype 1. Taking 2 extreme variants (light and dark fur) get F1 hybrids, make F2 and look at particular loci that impact those traits - Need more lines of breeding 2. Look at a phenotype (immune response) and hit all animals w same pathogen challenge (inert virus) and look at immune response and link it back to different loci - Need huge amount of individuals READ PAGES 334-343: Portions of the genome that influence quantitative traits are called quantitative trait loci, or QTLs. A given QTL may contain one or more genes QTL Mapping: - QTL mapping is the 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 trait. - example from research by H. D. Bradshaw, Jr. and colleagues (1998) on two species of monkeyflowers, Mimulus cardinalis and Mimulus lewisii - Mimulus cardinalis and M. lewisii are sister species. They have overlapping ranges in the Sierra Nevada of California. They hybridize readily in the lab and produce fertile offspring. Yet hybrids have never been found in the field - The reason is that the two monkeyflowers attract different pollinators. Mimulus cardinalis is pollinated by hummingbirds; M. lewisii is pollinated by bees - The questions are: What genes are responsible for the radical makeover of M. cardinalis’s flower? How many of them are there? How strong are their effects? QTL mapping offers a way to find out. - We can detect the presence and location of loci influencing a quantitative trait by crossing parents from populations with fixed differences. Among the grandoffspring, we look for associations between phenotype and genotype at marker loci. steps: - crossed M. lewisii and M. cardinalis to make F1 hybrids - then crossed the F1s to make 465 F2 individuals. - The F2s show a diversity of floral phenotypes - The parental forms, M. lewisii and M. cardinalis, were essentially homozygous at all loci influencing floral appearance -. As a result, the F1s were all heterozygous. - The F2s are the product of genetic recombination among the F1 heterozygotes - At any given locus, a given F2 may be a homozygote for the M. lewisii allele, a heterozygote, or a homozygote for the allele - scored all 465 F2 plants for each of a dozen floral characters that differ between the two species - determined the genotype of each F2 plant at 66 marker loci randomly distributed across the monkeyflower genome - A marker locus is a known site in the genome where the nucleotide sequence varies among chromosomes and where a simple genetic test will identify different alleles. - Bradshaw and colleagues chose marker loci at which M. cardinalis are all homozygous for one allele and M. lewisii are all homozygous for another. - This meant that the F1 plants were all heterozygous, and that the F2s could be homozygous for the M. lewisii allele, heterozygous, or homozygous for the M. cardinalis allele. - To map QTLs in the Mimulus genome, the researchers examined the F2 population for statistical associations between genotype at marker loci and phenotype. If phenotype was associated with genotype at a particular marker locus, they could interpret the association as evidence that a QTL influencing the trait of interest is located near the marker. - To see the logic of QTL mapping, imagine a marker locus at which the lewisii allele is ML and the cardinalis allele is MC. - Imagine also a quantitative trait locus that influences one of the monkeyflower floral traits.. We will call the lewisii allele QL and the cardinalis allele QC. LINKED: - Consider first a case in which the QTL and the marker locus are physically linked—that is, close together on the same chromosome. - The M. lewisii parent had genotype MLQL/MLQL and the M. cardinalis parental plant genotype MCQC/MCQC, where MCQC indicates a two-locus genotype on a single chromosome - The F1 plants all had genotype MLQL/MCQC. - In rare cases crossing over will occur between the QTL and the marker locus, but except for these, the F2 population will consist of plants with three genotypes: MLQL/MLQL, MLQL/MCQC, and MCQC/MCQC - Plants homozygous for the lewisii marker allele will tend toward the lewisii phenotype, heterozygotes will have intermediate phenotypes, and plants homozgyous for the cardinalis marker allele will tend toward the cardinalis phenotype (top right). - In other words, the marker locus and the QTL are in linkage disequilibrium - Of the four possible chromosome genotypes, only two are present. - This linkage disequilibrium reveals itself in a nonrandom association between the genotype at the marker locus and the phenotype influenced by the QTL. UNLINKED: - Consider now a case in which the QTL and the marker locus are unlinked - The M. lewisii parent had genotype ML/MLQL/QL and the M. cardinalis parental plant genotype MC/MCQC/QC - The F1s all had genotype ML/MC QL/QC - Because the QTL and the marker are unlinked, the F2 population will include plants with nine genotypes: ML/ML QL/QL, ML/ML QL/QC, ML/MC QL/QL, and so on - Among the F2s, there will be no association between genotype at the marker and phenotype for the trait influenced by the QTL - By looking for associations with multiple marker loci, researchers can estimate the number of QTLs, their locations, and the strength of their influence on phenotype - In practice, at most of the marker loci that Bradshaw and colleagues used, one allele was dominant and the other recessive. As a result, it was possible to distinguish only two genotypes: homozygous recessive versus other -. For each of the dozen floral traits the researchers scored, they found between one and six QTLs that influence flower phenotype. - To confirm that the QTLs that Bradshaw and colleagues identified were, indeed, the loci subject to selection during the diversification of the two species, Douglas Schemske and Bradshaw (1999) reared a large series of F2 individuals in the greenhouse and recorded the amount of purple pigment, yellow pigment, and nectar in their flowers, along with overall flower size. - Then they planted the individuals in a natural habitat where both species of monkeyflowers naturally coexist, and recorded which pollinators visited which flowers. Their data revealed a strong trend. - Bees prefer large flowers and avoid flowers with a high concentration of yellow pigments. Hummingbirds, in contrast, tended to visit the most nectar-rich flowers and those with the highest amounts of purple pigment. - By collecting tissues from each F2 individual planted in the field and determining which QTL markers they contained, the researchers were able to calculate that an allele associated with increased concentration of yellow pigments reduc

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