EEB214H1 Final: EEB214 Complete Study Guide for Midterm and Finals
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Department
Ecology & Evolutionary Biology
Course
EEB214H1
Professor
Jennifer Carpenter
Semester
Winter

Description
EEB214 Study Guide Why evolution is worth learning about? • Evolution education has been hotly debated in the US for years • Butler Act in 1925 in Tennessee • They wanted to challenge this law so Scopes, a young teacher taught evolution o Got sued for teaching it and breaking the law o the laws were upheld in many states and evolution wasn’t taught for 20-30 years • The space race reignited the debates over evolution o Sputnik: the first artificial satellite to be put into Earth’s orbit (1957) o evolution was added back to the books • with the failure of the last anti-evolution laws in the 80s the creationism movement was reborn o intelligent design ▪ argues that certain aspects of life are too complex to have evolved • One of the core ideas in intelligent design theory was putting out weaknesses or things that don’t make sense [look for weaknesses in evolutionary theory] • This fights start if evolution is really sound or something that makes more sense • the general public just don’t understand evolution [in Canada and US] but among almost all scientists, we have many data backing it up • Diseases evolve every day and we must acknowledge that in order to treat them o pesticides and parasites and how they affect us in evolving o some of the things we do like bacteria and viruses can cause bacteria to evolve o anti-biotics don’t work for all diseases but doctors sometimes just give it out and that can cause problems o but anti biotics don’t work on everyone • Tuberculosis – consumption o over use of anti-biotics causes them to not work on others • Today 100,000 Americans die of infectious diseases than compared to them years ago which could have been treated then • Diseases evolve every day, and we must acknowledge that in order to treat them o stop it or slow it down is important to do using evolution knowledge • Over use of antibiotics has caused selection for resistance in bacteria • evolution can help us plan how to most effectively use the drugs we do have • Evolution can help us feed the world o all plants have evolve differently than their ancestors [e.g., wild corn] ▪ something has happened to make them evolve o what genes have been important and we can use that pattern to change other crops ▪ use the sweetness in corn and use it in wheat and modify it the same way o selection goes in different ways on the same plant • Probably different selection on sexes [height, hip, width] • What are some reasons men have nipples? o They were selected for [aka useful] in the past, but not anymore o they are currently useful and being maintained by selection o they are neutrally evolving in men [and are just kept around because women need them, and men share many genes with women] ▪ cause they never went away o our ancestors happened to have nipples so we still do o look at DNA organs of what things are doing and how things have changed overtime Darwin’s Idea Charles Darwin (1809-1882) in England • John Edmonston, a free slave from the West Indies, tutored Darwin on how to prepare bird skins o he got into naturalism in Scotland while wandering around and observing plants and animals o learned to preserve birds through John • his family told him to become a priest • went to Cambridge to start studying • while at seminary Darwin began collecting beetles o there was much diversity in this area, unified species o they all look so different from each other o Why was there so much variation in nature? • Darwin was influenced by many people at Cambridge o joined a naturalist club • William Paley o philosopher in his program o used the same reasoning that everything was designed • Adam Sedgwick – geologist • William Whewell – geologist • John Henslow – botanist • They helped talked to Darwin about life • Why these changes occur overtime • Darwin red his grandfathers during, another physician o found trans mutation o species can change from the past to a new one o this wasn’t his idea though • Darwin went on his famous trip on the HMS Beagle from 1831-1836 o he was talking to Henslow to go on the trip o Darwin was not hired as a naturalist on the boat, but there to have dinner etc. o after the naturalist resign, Darwin took over • Fitzroy gave Darwin a copy of Lyell’s book o the force that shape geology today, [things that make mountains] are the same forces that are acted in the past o how these natural forces came to be, and how long they’ve been around • Darwin started thinking more about his grandfather’s idea of Transmutation—that new species can be generated from existing species o how those natural forces could be the driving force behind transmutation • 1838, Darwin read Robert Malthus’s essay, On the Principle of Populations o Malthus described life in human population as ‘a struggle for existence’ o human population grow faster than they can produce food o when this happens, food runs short, famines happen and people die o Darwin knew that traits could vary, and that variation was heritable o he also talked to animal breeders and asking them how to pick which animals to breed o knows that traits are inheritable o this variation in nature can be passed on through generations • Darwin combined two ideas o Heritable differences lead to different rates of survival and reproduction o these two going together might have the trait that makes them survive o overtime, population change and you might have those traits that make you survive • Evolution by natural selection is when individuals differ from one another, and some of differences affect an individual’s ability to survive and reproduce, and so they will leave more descendants, and ultimately increase in frequency in the population, causing the population to change overtime o no survival of the fittest o survival and reproduction of which individual can pass on their next generation • For evolution to happen three things need to be true: o variation o reproduction: heritable ▪ make sure the offspring looks like the parent ▪ heritability o differences in survival and reproduction ▪ some individuals have to survive longer than others ▪ has to be variations in the traits, and fitness [how many offspring] • a population of things will change overtime if you have these three things • Example: pigeons variation o brown pigeons vs. gray pigeons o if gray pigeons get killed, then next generation, the brown pigeons will expand • evolution is about the population as a whole changing, not individual change • If this continues, these gray pigeons will die out and next generation will only have brown pigeons • evolution is exploiting the problem with how evolution is acting Evidence #1—Artificial Selection • humans activity selecting which organism gets to breed and passing onto the next generation • humans are INTENDING to create some specific trait • By selecting for different traits humans have created different vegetables • Big leaves, red leaves, many small flowers o cauliflower are both flowers but all the same plants o he used a lot of evidence from crops • Darwin spent a lot of time talking to pigeon fanciers o these people as a hobby grow pigeons, look for weird ones with interesting traits and make more to look weird o by breeding normal pigeons, it can become weird o breeding can only be physical traits • In Darwin’s time an individual with a new phenotype was called a “sport” o called a mutation today o bright blue lobsters o forms appear suddenly [out of the blue] o If those traits are acted on in the environment, it can happen in nature too • When humans intentionally select for a certain traits we call it Artificial Selection o humans breed dogs from wild wolves o in the last 10,000 years • Starring in 1959 Russian scientists have tried to domesticate foxes o Lyudmila Trut –geneticist ▪ take wild foxes to make puppy like foxes o In the first generation some of the foxes were more timid than others o they would approach the foxes, if fox was timid, they got have babies and nasty ones were killed to make fur o They want the nice fox to survive [variation] o They found the tameness in the fox was heritable • After 30 years, the foxes act much more like dogs than wild animals • we can reproduce the event that happened in the past and evolution can cause these changes, not necessarily cause out of the blue • there can be non-heritable traits • environment can affect them • Darwin had evidence from farm animals, pigeons, crops etc., to show these sports could appear and could be heritable even though he didn’t know how it could work Evidence #2—Fossils • Animals or plants die, usually near water • they sink to the bottom, and are rapidly covered with sediments • these sediments then crystalize, taking the shape of the dead organism • these things have to be not disturb long enough for this to happen • hard to get a jellyfish because they’re so soft so it’ll be disturbed • with harder things [exoskeleton], they can last longer • Once we find the fossils, we have to put them back together since they get crushed o in order to understand what the animal is • 0.1%-1% of species on earth get fossilize • the reason why we find huge fossils is because the smaller ones get destroyed before they can be find • That examples why fossils are rare, and frequently only show part of an organism • because fossilization is so hard and rare, we may have huge gap of time where we have no data, no fossil • we have gaps in the fossil records because there were no fossils • What would evidence for evolution look like in the fossil record? o The stuff near the top are more recent o 250mya: mammals o 350mya: amphibians o 400mya: lobbed-finned fish o 600mya: multicellular organisms o 3.5bya: first simple, single celled organisms • Animals that are more closely related to each other should be in nearby levels • Globorotalia menardii was a single called marine protozoa –over a span over 8 million years, these animals reduce the number of chambers in their shells o with similar number of chambers were closely related o recent stuff has fewer chambers compared to newer ones • Trilobites also show change over time • Common in the pre-Cambrian o scientist looked at shales from whales o they counted the number of ribs o researchers show changes in the number of segments in 8 separate lineages over 3 million years o to see if things progressive in ways that makes sense • Transitional fossils of organisms can help us understand how evolution has progressed o Eusthenopteron [385 million years ago] o Acanthostega [365 million years ago] • If we have an estimate of how old a species will be, it makes it easier to find fossils • Ellemere Island contains rocks from the mid-Devonian period of 350-370 million years ago o tiktaalik, which has many features in between fish and reptiles o traits that is in between fish and amphibians o always gaps in the fossil records, as we get more data • Fossils can also show us that some species have not changed in appearance over time o Latimeria chalumnae ▪ looked exactly like their fossils ▪ they’re in the same environment too so nothing changed ▪ “living fossil” ▪ if anything that’s not causing to change traits will not change • One of the most famous transitional fossils is archaeopteryx o fossil between dinosaur and bird o birds are actually dinosaurs [related] o found in 1860, a year after Darwin’s book • Since then, we have discovered many other fossils linking birds and dinosaurs o They had feathers before they were able to fly o it may not be feathers for ability to fly • Now paleontologists agree that birds are dinosaurs Evidence from Vestiges • goose bumps • How can we explain goose bumps? o ancestors o they are vestigial traits—a trait that no longer preforms the function o or they are slowly disappearing • Ostrich wings, another vestigial trait have been co-opted for a new purpose o They have a new function o the ostrich uses its wing to escape predators o uses it for intimidation [making itself look bigger] • Darwin was one of the first one to note that a trait, such as wing, that has been render useless by changing habitats can be coopted for a new use • Why did the trait lose its function? • Why hasn’t the trait disappeared completely? • What do the birds have in common? o all the flightless birds live on islands o the escape the predators and won’t use the wings o some of them were born with smaller wings because they didn’t have to fly away from predators ▪ lost the function of the wings • Wings haven’t completely gone because some of them use to escape predators, while others have been co-opted and this new function maintains them o mating display Gemmules • Darwin suggested that the environment can modify our traits and our gemmules • Does blending inheritance fit with all of what you know about how traits are inherited? o a trait can appear that the parent doesn’t have anymore o you aren’t this blend of your parent for all traits ▪ e.g., red hair o traits can be physical and behavioural o If natural selection is picking extreme value [tallest person have highest fitness], their offspring can’t ever be like them. Things are going to shift • How can traits re-appear after multiple generations? [e.g., hair colour] • regression towards the mean: shifts towards the middle • Huge issue in 1950s and 60s, how can selection do it? • 2 major criticism of how it works • Francis Galton put the idea of gemmules to the test o he took blood from a black rabbit and injected it into white rabbit o we would expect a mix of black and white rabbits but what he saw was he got all white bunnies o the blood always looked like his actual parents and not the blood donor ▪ could not mix blood types ▪ gemmules passing through the blood doesn’t work • Darwin never stated the gemmules were pass through the blood, but it was passed through the body somehow Gregor Mendel • Austrian monk • he did not believe in blending inheritance and he looked to math to test another hypothesis • he grew pea plants [binary traits –shape of peas] • he took some peas that only made round peas and ones that only wrinkly ones • and then took pollen from round peas and put it on wrinkly peas and vice versa the peas ended up being only smooth • genotype effects the phenotype • phenotype is not just physical traits but also behavioural traits • we can use Punnett Squares to think about Mendels two laws and how they will affect the outcomes of a particular cross • all possible combinations are going to be smooth babies • they are segregation independently • we have these two factors every individual carry and one of the two factors is independently passed on to every offspring • alleles : which is the different forms a particular genes can take {w or s} and every individual has two alleles • the allele that masks another allele is said to be dominant • while the other that gets hidden is recessive • if an allele is dominant it effects the phenotype more than the other allele • the only way to get another of the recessive you need to have two phenotypes of the allele • we know that many traits in humans that are now known to be controlled by one gene in a mendelian fashion • every individual has two alleles but other population have more than two • but we discovered that the vast majority of traits are controlled by many genes • its multiple genes that control these traits • humans have around twenty thousand genes • how genes are combined or how alleles are put together to create complexity Genetics • Humans have fewer genes o 20,000 to 25,000 genes, a drop from 30,000-40,000 in 2001 o Flies and worms have fewer genes than humans o the complexity of organism doesn’t mean you have more genes but the number of genes do vary o these are the things selection, evolution is acting o some people thinks protein is the hereditary molecule o if we have lots of different kinds of proteins the better compared to DNA, DNA is too simple to hold data • Using viruses Hersey and Chase showed that DNA was the hereditary molecule o what goes inside the bacteria makes copy of itself, and that explodes to new viruses o Was it the DNA or protein? o They made two kinds of these viruses o T2 Phage: Sulfur has no radioactive DNA o when the protein is radioactive, none of the protein is going in the cell, only DNA was o the stuff of how to make cell was DNA not protein o DNA was the thing passing on instructions of how to make organisms • The next year work by Watson, Crick and Franklin explained the structure of DNA • DNA in cells is a double stranded molecule and it’s made in 4 bases that make up DNA: GTCA • They made radioactive bacteria and when they look inside, none of the protein got inside so it wasn’t protein that was the hereditary molecule • GC, TA, CG, AT • if you unzip it, you can build the other half to make new ones • DNA is the template for making copies of itself o There are proteins that builds new strains and they always know which base it is • DNA is the hereditary molecule, but how does it store the information? Because there wasn’t enough complexity before to store life • DNA is the instruction manual for making all the proteins in an organism • DNARNAProtein • Are all DNA instructions for making protein? o in bacteria, you have a protein then protein etc. lined up o but in other organisms it’s not the case o Humans: 90% does not make protein • So in many organisms the section of DNA that makes proteins is very small. We call these parts that make proteins genes o Promoter=where the DNA starts o Terminator = ends the protein • In eukaryotes genes are a bit more complicated o They have exon = protein coding part that makes into RNA o between the exon = intron  stuff that gets cut out of RNA, not part of the protein o introns are cut off from some other proteins in the cell o all the exons are spliced and glued together into one strand – mRNA o you don’t get all the exons into the RNA ▪ called alternative slicing ▪ single genes can give multiple proteins ▪ only bits of the genes can be used to make protein ▪ mRNA is translated by Ribosome and uses building blocks to put together and that folds itself into whatever protein o How does this step work? from RNA to protein ▪ The Ribosomes can read the RNA 3 letter at a time (codons) to determine the next piece o There are 20 amino acids that proteins are made from ▪ 64 codons ▪ while our genotypes are different, our phenotypes will be the same because our proteins are identical o some of the triplets here are redundant o If we compare selection/diversity acting on the last position, we expect selection to ignore these sites to other sites that are important, how many differences between those two sites can tell us how selection is on average ▪ Synonymous site if you change the two letters of the codons and don’t affect the site • splicing: leaving the yellow protein codon: exons • Multicellular organisms go through meiosis to pass on genetic material o occurs when you’re making sex cells o all of our cells have two copies [mom white, dad red] o the copies are two separate double helix • The first phase of meiosis: these things are copied and they form a cross over o four copies of every one and recombination can happen when crossing over o Homologous chromosomes ▪ recombination is important for mixing DNA and getting different phenotypes ▪ the cell divides twice and splits all their copies into their own cells ▪ Meiosis II becomes sperm or eggs Hardy-Weinberg Equilibrium • In the early 1900s, there was a great debate between the “biometricians” and “mendelians” about how inheritance worked • Mendel’s work was rediscovered and William Bateson and Karl Pearson who was a Biometrician and didn’t use Mendel’s data • Mendel’s data worked well if you have yellow peas or green peas • Udny Yule—one of their arguments centered on the idea of recessive alleles o This recessive trait [humans have all hands the same] would slowly go away because dominant would take over • Punnett described this problem to his friend Hardy o Punnett mentioned Yules example of the hands and normal hands would slowly go away if recessive trait is dominant o Hardy said use math to figure it out, nothing to do with being recessive o he said p2+2pq+q2=1 ▪ Describes genotype of every generation ▪ pp = frequency of AA ▪ 2pq = frequency of Aa and aA • pq+qp • two ways of being a heterozygote ▪ qq = frequency of aa ▪ each of these terms is talking about one of the genotypes ▪ 100% of the population is one of these three possibilities, everyone has to have some combination of those two o This equation tells us the expected frequency of each genotype based on the allele frequency ▪ p= 0 .5 ▪ p2 = 0.25 [homozygotes] ▪ 2pq = 0.5 [heterozygote] ▪ q2 = 0.25 ▪ a quarter of our population should be homo, half is hetero and the other is homo ▪ Mendel’s 3:1 ratio out of this • Smooth = 0.25 + 0.5 = 0.75 • Wrinkly = 0.25 • 0.75:0.25= 3:1 o p+q=1 ▪ There are two alleles, big and small ▪ p = frequency of allele A ▪ q = frequency of allele a ▪ the sum of these has to be 1, because we assume there are two alleles ▪ same alleles = homozygote and two small = heterozygote • Example: • p = 0.25 • AA frequency =0.0625 • Aa frequency = 0.375 • aa frequency = 0.5625 • 90% of our population is heterozygote • If a populations genotype frequencies matches those we get from this equation, then we say the population is in Hardy-Weinberg equilibrium • But if the genotype frequencies do not match we say it is not the equilibrium • Evolution is the change in allele frequencies across generations o if allele frequencies don’t change, no evolution is happening because the offspring has the exact same parameters as the parents o if a population is in HWE then it’s allele frequencies will not change over generations o evolution is only occurring when you are not in HWE • If we have genotype that match the expected, then we’re going to get that genotype next time • So what causes a population to leave Hardy-Weinberg Equilibrium? o no selection o random mating [inbreeding] which increase the homozygotes o genetic drift ▪ large population size o no mutation o no migration [gene flow] • if selection is removing some genotype you may see fewer of it than you expect o we would expect to see huge heterozygotes o selection is favouring one type of genotype • mutation and migration will randomly add genotypes that don’t match expectations o shifting allele frequencies • This population could happen if mating non-random [they always mate with their colour] o we have 0 heterozygote • In small populations random effects can lead to changes in allele frequency o example: more white sheep than blue o impact on small population, random changes on allele frequencies can have a huge impact • The effects of drift were first observed in the lab in the 1950s • Red eyes x white eyes = orange lines • cross homozygotes with orange eyes o 2 red, 5 orange, 2 whites o 107 vile for 20 generation • the data is spread out more in every generation and as further in time, allele changes and no idea with allele population • a lot of white and red eyes • overtime, an allele will get randomly lost and there’s no way to get it back • e.g., white eye population, future generation will only have white eyes • random drifts can cause a population to change • different environment, we can get different outcomes • populations with only 1 allele are “fixed” for that allele • Populations that are smaller, are more affected by genetic drift • larger populations, things stay closer to previous generation, no big jumps compared to small generations o larger populations are subject to less drift than smaller ones, randomness doesn’t effect it much • Genetic drift is the evolutionary force that causes randomness • it is why evolution is not repeatable • small differences in sampling can have huge effects on how a population • larger populations are less subject to random in allele frequency • populations can go through bottlenecks where only a few individuals pass on genes o Catastrophic effect o in the bottleneck, something happened to the population so only a few dogs live [red and blue] o next generation, we only have red and blue dogs o allele frequencies changed o going through bottleneck, increase rare allele frequencies • Bottleneck effects can explain the high prevalence of diseases in some human populations • Huntington’s disease o genetic disorder caused by one gene o e.g., in Africa, the blacks are rare but White and mixed have more Huntington o Dutch and white have higher Huntington’s ▪ because they were colonized because one of the colonist happened to have that allele • Pingelap o population of people who are colour blind and light sensitive o but good vision at night o 10% of the population on the island sees in black and white o huge bottleneck on the island ▪ tsunami hit and killed everyone except 20 and one had this colour blind disease ▪ everyone descendant from him has a higher chance of having it [drift] • In nature, population size can determine if a group will go extinct • So why could population size, and bottle necks in particular affect survival so much? o Why would these random changes in allele frequency affect phenotypes in the population? o Most of these phenotypes, the disease is recessive but in bottleneck frequency, the recessive allele mates with another recessive allele o only happens in small populations [in bottleneck affect] • Population size is an important factor in conservation biology o in small populations a deleterious allele might fix o AA, Aa Aa, aa o bad alleles will start fixing in the population [if it has a disease] and you might lose all that population o 500-5000 biologists say is the vast size ▪ they try to increase population sizes by connecting habitats ▪ separated, so each one are tiny population where drift happens ▪ but biologists make them connected • The bearded vulture is native to the mountains in Europe, Africa and Asia o campaign to get rid of these things because they ate bones o killed in 1900s o few left in zoos in 1970s ▪ these were breed ▪ it’s effective population size is very low ▪ one’s in the wild doesn’t have genes as the one’s in the zoo has ▪ (Ne) is like the effective number of recording individuals in a population • a measure of how strong drift is = effects population size • if smaller population, drift is powerful • effective population size of human: 7 billion • only 10,000 humans breeding in the population • more flies passing on genes than humans • one way of keeping the diversity around is reintroducing • trade birds between zoos to make it more diverse [spreading them around] and making sure they don’t lose alleles every new generation • not losing alleles = Hardy Weinberg equilibrium Selection • Selection is the change in allele frequency caused by organisms with certain alleles surviving or reproducing more than those with other alleles o so certain alleles will do better • Example of cabbage: to make other vegetables and pigeons • Fitness: how good an allele is o An individual’s fitness is it’s genetic contribution to the next generation o How to measure them: mating, raw number of offspring, how many seeds or pollen a plant made o Measuring fitness is hard ▪ count “babies” ▪ example: each pigeon has different number of offspring so they have different allele ▪ but doesn’t always work because the pigeons [2 generations later] those baby pigeons might not reproduce ▪ inclusive fitness o we need to scale the number: scaling them by the maximum fitness in the population o take all fitness numbers and divide by the maximum number [use Wsymbol for fitness] o we often measure relative fitness, that is fitness compared to the best individual in the population o sometimes we’ll also scale by the average fitness • We can compare the fitness of different genotypes to make a simple model of selection • difference in fitness can show how bad the allele is • Since we’re using relative fitness the best genotype will always have a fitness = 1 • 1-s  s = difference in fitness between the two homozygotes • 1 – hs  h is the dominance coefficient, and determine which allele is recessive and by how much o the h is determined by the dominance of the alleles • 1 = measure homozygote • When h is 0, what does the heterozygote look like? o then h = 0 o The heterozygote has the same fitness as the AA homozygote, so the A allele is completely dominant o the heterozygote has the same fitness as the aa homozygote, so the allele is completely dominant • Another example: flower colour from the bees but the heterozygote is pink...they’re a mix of the homozygotes • h  how far between the two homozygotes you are • If h is 0.5 the heterozygote that means about the fitness of heterozygotes? o WAA = 1 o WAa = 1.0.8s o Waa = 1-s o if we have something between half and one it’s closer to the small allele • 3 different kinds of selection: o Directional selection is when one allele is favored, having more of that allele is better ▪ the population is moving towards a particular allele/phenotype ▪ Dawson testes how fast a recessive lethal is eliminated from a population ▪ WAA = 1 ▪ WAa = 1 ▪ Waa = 0 ▪ flower beetles: recessive allele doesn’t show up unless there’s two of it, but if they’re two of it, it’ll kill the recessive allele [esp. if the allele is 0] ▪ if we know how bad the allele is, we can tell quickly when that allele will go away, if selection happens ▪ we can make decision based on a selective effect of the basic allele o Disruptive selection is when both homozygotes have the same fitness, but the heterozygote is bad ▪ WAA = 1 ▪ Waa = 0.5 ▪ Waa = 1 o It’s based on where you start, when selection kicks in under disruptive selection ▪ Gross showed that different mating strategies in salmon are evolving under disruptive selection ▪ example: hook nose and the jack ▪ hook nose is really big and the jack is small ▪ hook nose hatch, grow up and swim back up stream to breed and die after 3-4 years ▪ the jacks don’t do that, they hatch in the ponds and live for a year , breed and die but they never leave the pond ▪ when mating, there’s two strategies: females will lay eggs and male mates ▪ smaller fishes get closer to females if sneaky ▪ big fish will get closer to female if they stay and fight off other males ▪ two different phenotypes pushed away from the middle ▪ smaller are more likely to survive because they stay in the pond and not ocean ▪ the big one’s more likely to die and if they do get to mate if they have a payoff o Balancing selection occurs when both alleles are maintained in the population ▪ within these conditions, we don’t lose any alleles after many generations [starting from 0.5] ▪ you get the most heterozygote when the frequency is at 0.5  population have highest fitness ▪ WAA = 0.5 ▪ WAa = 1 ▪ Waa = 0.5 ▪ drift might get rid of one of the alleles ▪ even though two of alleles Is bad, one of the alleles might be good ▪ This is call heterozygote advantage o When an allele’s fitness depends on how common it is, we call it frequency dependent selection ▪ Gigord showed that in populations where the yellow morph was more common its fitness was lower ▪ more common allele… might disappear overtime when it’s common Mutation • Example of selection in nature, Darwin’s finches • Drs. Rosemary and Peter grant –biologists who studied about the birds o Tagged them and watch what they do • Finches varied in many traits o differences on size, and their beaks • in 1977 there was a severe drought on the islands o tons of death in plants and animals o throughout the drought, changes in phenotypes on the animals o example: seed banks ▪ they take a sample of dirty, and measure the size and shape of seeds ▪ during the course of time, the number of seeds dropped ▪ by the end of the draught, only half or third as much seeds ▪ at the same time, there was also a huge drop in finch population • Seeds with different phenotypes lasted longer o most of the seeds in the beginning was soft, easy to get into and easy to eat by birds o height of the drought, the seeds became hard to eat o after it rained again, the seed bank recovered it was soft again o They want to know maybe birds who were good at getting into the hard seed are the ones who survived • The beak shape of the finches in the population changed over the course of the drought o 1976: Before selection: 751 birds o 1978: After selection: 90 survivors/birds ▪ much less variation ▪ birds on the island have 1mm more beak depth • 3 things for evolution: selection, hereditability, variation o we don’t know if the birds that survive will have certain beak babies • The beak shape was heritable o evolution can and did happen in those population o population changed phenotype in 1-2 year span Mutation • Mutation is a permanent change to the genetic material of an organism o any change in the DNA sequence • Mutation happens primarily in two ways o during DNA replication ▪ building a new strand of DNA and the enzyme can stick in the wrong letter ▪ one in a billion times it makes a mistake o exposure to weird environments ▪ radiation or smoking cigarette ▪ chemicals in your body can break, and the body tries to fix It ▪ pairing that makes the DNA shape funny and then protein goes through takes a letter out and replace it with the correct on ▪ sometimes, if there’s a whole, enzymes can add random stuff until they go together ▪ gene conversion: separate allele from mom and dad, but if dad gets home, then moms will get copied over ▪ without mutation, we wouldn’t be able to change or respond to differences in the environment ▪ mutation is the selective force that causes mutation ▪ mutation is the only one that adds alleles • One of the most common types of mutations is a change in a single base of DNA (a point mutation) o one letter of the DNA has changed o one letter can have huge impact on actual phenotypes • Not all point mutations in genes will have a phenotype effect • Synonymous/silent mutation: UUA  UUG: leu • replacement mutations: UUU  UUC: phe • One example of a point mutation in humans is Sickle Cell Anemia o caused by a single change in the DNA o TA: Glutamic acid  AT: Valine [mutant] ▪ causes Sickle Cell • C;C = good sprinter, C;T, T;T=long distances o changing allele isn’t necessarily bad, just a different phenotype • Another kind of mutation is a deletion o chunk of DNA goes away, causes the chromosome to be smaller o deletions are fairly short o in common, deletions are 3 bases ▪ ribosome comes in ▪ if you delete 3 it doesn’t have a big of an impact on protein ▪ but if you delete any other number, you change other letters which completely changes everything • Cystic fibrosis is often caused by the deletion of a single codon o one amino acid is taken out of a key protein o the disease is recessive o you only need one copy of these to not have this disease o only when you get homozygotes, it happens • A duplication mutation causes a piece of DNA to be copied an extra time o insertions: opposite of deletion o Translocation: a chunk of chromosomes cut off and placed somewhere else in the Geno Duplications • Duplications are used in paternity tests, or crime lab DNA tests o the protein may stop and come back, and not overtime, it copies an extra o huge variation in these repeats because mutation rate is high o paternity tests uses this • Whole duplicated genes are important for the evolution of new proteins o it gives you new stuff for selection to make new genes o destroy and never adds o Duplication: start off with 1 gene with 4 functions ▪ mutation happens and this gene is copied o Divergence: selection could keep both of them around if it’s good to have more copies o or it functionalize the genes ▪ specialize the genes ▪ it ignores some part that’s not important for some function o subfunctionalization: splits it to two genes that does it better o Neofunctionalization: mutation moves all over the place ▪ new amino acid moves around o Degeneration/gene loss: second copy of the gene goes away ▪ left with a non-coding DNA • A translocation or insertion happen when DNA moves around in the genome o end up with two chromosomes that are a combination of two older chromosomes • Down’s Syndrome (Trisomy 21) is caused by a translocation of chromosome 21 o 3 copies of chromosome 21 ▪ happens during miosis and instead of splitting off going into separate egg, two of them stay together • Translocation: Chromosome 21 is attached to some other chromosome : 14 o too many copies of 21 leads to down syndrome • How often do mutations happen? o measure through a mutation accumulation experiment ▪ Grow an organism and compare to its ancestor ▪ getting rid of mutation o every generation, they only take on individual ▪ makes drift strong and selection is weak ▪ and selection can’t act on these things if there’s only one genotype ▪ keeping population small, drift become strong ▪ sequence certain genos, line them up and count number of mutations o These authors found a point mutation rate of 9.7*10-8 site per generation ▪ they only saw 20 mutations ▪ every single letter of the DNA, has 1 in a billion chance of mutating ▪ 9.7*10-8* 14,000 = 0.014 mutations per individual (worm) ▪ 1 of every thousand worms will have mutation o They found an insertion/deletion rate of 3.2*10-4 in one repetitive region ▪ sites in geno are repetitive mutate more • Another way of measuring mutation rate is by comparing parents to offspring o comparing family trees o They showed that humans have a mutation rate of 1.2*10-8 per site per generation o 1.2*10-8 3*109 = 36 mutations per individual ▪ how much mutation kids have that their parents did not have • They also looked at how the father’s age affects mutation rate o for every year older dad is, you’re going to have 2 more mutations o older dads do pass on more mutations to their kids o higher rates of schizophrenic and autistic who have older fathers ▪ those mutations are more likely to cause mental illness • So how often are mutations bad for fitness? o by looking at the value of s = strength of selection o new mutations cause mutation in protein sequence o not looking at random mutation o 35% of mutations that change protein don’t have effect on mutation o other 45% are bad o most mutations/over half of them in this data are bad to some extent ▪ any random change will mess it up ▪ most of the time, a change isn’t going to be beneficial ▪ and will do something bad and increases Migration • Mutation is constantly adding new alleles to populations, migration basically does the same o adding alleles: increasing allele frequency o Migration adds new alleles to population, but it’s not random o if the migration continues, it will homogenize ▪ makes population look more like each other Genes and the environment and Epigenetics • Some diseases phenotypes only show up when inherited certain ways o a deletion on chromosome causes Prader-Willi o really small hands and feet, high rates of childhood obesity o hungry all the time  general chubby and whiny • Same disease causes Angelman syndrome o different phenotypes than Prader-Willi o mental and developmental problems o don’t sleep well, seizures o laugh a lot, don’t cry and don’t ask for food  general skinny • The disease that this deletion causes depends on which parent passed it to their offspring o Paternally inheritance of deletion causes Prader-Willi ▪ if delete from chromosome from dad o Maternally inheritance of deletion causes Angelman • Somehow the DNA knows which parent it came from • One kind of “tag” that can exist on DNA s called methylation o one bonus carbon shoved onto a side of DNA • Previously we thought all tags were removed before genes were passed on to offspring o Now we know that not all tags are removed, some stay o which how Prader-Willi and Angelman syndrome occurs o Mom will put methylation on some parts and dad on others • These “tags” can be added to DNA by the environment throughout life  Beckwith Wiedermann Syndrome o Born through invitro fertilization o commonly get early childhood cancers o same DNA their mom and dad did but were not grown normally • E.g., Egg donors o Remove nucleus from egg cell add somatic cell from adult donor grow in culture to produce an early embryo o DNA can be exactly the same but different phenotypes depending what genes turn on and off • Lots of environmental factors can affect phenotype and methyl tags o Does mother smoking affect which genes are turned on in her offspring? ▪ leads to several hundred genes turned on and off that usually wouldn’t on another environment ▪ the genes is changing how the babies genes are working ▪ the genes can affect the baby for the rest of its life • e.g., affecting growth because some genes are turned off ▪ could be the environment is detected by the geno as the body doesn’t want to grow ▪ e.g., identical twins may react to the environment differently • Can an environment early in life affect offspring’s phenotype? o compared kids who dads smoke before age 11 then compared to later o Father’s sons BMI were affected but not daughters o not just smoking that’s bad, but starting to smoke under 10 can affect sons weight Epigenetics o the study of heritable differences that are not caused by differences in DNA sequence • e.g., egg donors in mice alters methylation tags o Their offspring also carry these changes, even if they were born normally o change in methylation that’s heritable in the next generation o if the rat mother licks babies a lot, her kid can o behavioural difference with how much a baby rat is licked when it’s growing up is heritable • A study in Sweden has shown that these same effects happen in humans o e.g., if grandparents in famine had health impacts in later generations o Data for this study came from studying church records ▪ examined 99 individuals born in Overkalix parish of Norrdbotton in 1905 ▪ used historical records to trace parents and grandparents ▪ analyzed agricultural records to determine how much food had been available to the parents and grandparents when they were young ▪ better for your grandparents to starve from ages 8-14 so your grandchildren will live longer • slow growth period/puberty • this period when boys start making the sperm • when you make sperm during a famine, there’s some gene in there that’s being turned on or off differently during the years when there is a famine • Grandsons of Overkalix boys who had eaten well died an average of 6 years earlier than the grandsons of those who had endured a poor harvest • Girls is different because puberty happens at different times o When is it good for granddaughters when grandmothers starve? ▪ Starving early on is bad for girls but not for boys ▪ females mate their eggs before they’re born vs. boys make it through life • It matters when the gammons are being made o No information from grandfathers to granddaughters or grandmothers on grandsons • This study in combination with the smoking, tell us that there are critical periods in development o certain environment happen at a certain age will impact the environment later o Age 10 critical age for sperm development in guys • If you starve the kid, do their grandchildren live longer? o if a young boy lived through famine year from 8-12, his grandchildren will live longer o grandmothers conferring longer lifespan to granddaughters if when they were young lived through a famine year • Not just what environment you’re in but when you’re in that environment, much better to start smoking late • Why might these epigenetic effects make sense in the light of evolution? o Looked in 700 people between 1943 and 1947 in Amsterdam o 3 categories: people born before famine, during and people conceived after the famine o examined blood glucose and insulin levels • Environmental stresses in a parent may harm the health of subsequent generations o child in utero during famine were unusually small and in later life more prone to diabetes and obesity o other studies have shown that nutritionally stressed foetuses and infants have increased risk of obesity, diabetes • Something about the environment that is turning on genes: example: food, and genes to make you be able to last in the environment by saving food • but if grandfather was starved as a kid, the genes leads to mismatch with environment because your body thinks you’ll be in famine when you aren’t o If there is adequate food, then maybe this combination of genes becomes inappropriate • Maybe these “tags” are turning genes on that will help us prepare for hard times • Mothers might also want to signal something about her health to offspring, to make birth easier o if you mother starved during development, her hips will likely be smaller o if she could communicate that to her offspring so it didn’t grow big, then she would be less likely to die in child birth • If these “thrifty” phenotypes cause diseases why haven’t they been wiped out by selection? o there hasn’t been access of food before and had a famine o these diseases are around now because people didn’t have the diseases because they didn’t have a lot of food before when they were young o some of the alleles act late in life, so having diabetes at 60, won’t have as big of an impact now o selection can effectively remove traits that were bred because selection cannot remove them because they can’t detect how many offspring you’ve had • Could epigenetics explain the global obesity problem? o our bodies aren’t used to the environment we’re in now o over 40% government spends in health care is towards diabetes Adaptation • Adaptation is the process whereby a population becomes better able to live or reproduce in its habitat • Major differences between plants native to the GTA and plants native to a desert? o all plants in deserts have some kinds of spines somewhere o deserts: waxy coding around them o Why are they advantageous? ▪ Why do cacti have spines? • to keep herbivores away • waxing coding: less evaporation o Taller plants = sunlight o Desert plants over flower after rain and GTA bloom every year o Desert plants are more conservative o Many desert plants do not have bark because: ▪ historical—very few woody plants were in the area when it became a desert so it has no history of being woody plants [accident of history] ▪ ancestors have those traits • Animals have adapted to deserts in many similar ways to plants o lizards in deserts have spines o frogs and mucus sacs [can stay in the sacs for years] o camel: hump to store lots of water in the desert ▪ ways of sucking up a ton of water when it rains and they can hold onto the water until they need it • Plants can have different root systems: lots of little roots, one big root above ground, or a few big ones deep into the ground o Why might these two root systems be adaptive? o Desert plants have more shallow roots because when it rains they spread their roots out so they can catch it before it evaporates ▪ to use the water they get efficiently • Selection can cause very closely related species to have very different phenotypes in different environments o Jack rabbit vs. Hare ▪ Jack rabbit has bigger ears but the artic hare has thicker fur to conserve heat ▪ colour to camouflage and when the snow melts, the hare turns brown ▪ hare have bigger, broad feet to distribute their weight over a large area [don’t sink into the snow] ▪ Hare has bigger claws to dig through hard snow ▪ jack rabbit might store more food • Why do animals in deserts have huge ears? o a swamp cooler o pump warm blood into ears to cool off : use it as a heat dispersal thing • Selection can cause very closely related species to have very different phenotypes in different environment • Cool blooded animals like lizards don’t have it • Evolution finds the most efficient way to solve a problem given the resources it has [such as making the ears] o evolution can be repeatable if two species are face with the same problems that needs to be solve, will come to the same solution • Cactus—Americans • Euphorb—Africa o Both wildly different species even if they look similar o Cactus are closer to carnations and Euphorb’s are closer to violets o Both live in the same climates [facing the same heat] • When two groups independently evolve the same trait we call that convergent evolution o they end up in the same place because selection is trying to find a solution [trying to find the cheapest way to save water while having making seeds] • Some plants have good chemicals that it won’t be eaten [marijuana, mint] • Why are spines in deserts: cheap, one time investment, dry hard seeds, don’t require much water • Plants have 3 main kinds of tissues: leaves, stems, roots o cactus spines are modify leaves but euphorb’s are modify stems o overtime, those alleles are selected because it helps the plants survive and leaves more offspring • Convergent evolution o two different species/population get the same solution but evolved separately o example: flight, and lack of flight o Flightlessness in ratites has evolved convergently ▪ environmental reasons good to lose flight: predator escape ▪ but a lot of birds live on islands without predators ▪ overtime, the birds stayed on the ground and one’s didn’t make wings had higher fitness o beneficial to lose flight, because flying is expensive o even though losing of a trait, they’re evolving of another trait: not flying o Example: Cichlids in African lakes have evolved the same phenotypes repeatedly ▪ evolve rapidly: one of the quickest evolving groups we know of ▪ different colour morphs evolve in shallow or deep ones ▪ red one’s are in the deep water, and shallow has blue lights so we see blue lake ▪ related species end up splitting ▪ also, patterns look we see on the fish in the different lakes ▪ some groups have fish have vertical stripes, others evolve horizontal stripes • look similar but different phenotypes • Flightlessness in ratites has evolved convergently • That is why ostriches evolve big because there weren’t a lot of predators around • Cichlids in Africa evolve in the same patterns in different parts of the lake • Another kind of convergent evolution is mimicry o some organisms will evolve to look like other unrelated organisms ▪ Butterflies look similar to each other but all different species and cannot interbreed with each other • Mullerian mimicry o When two harmful species look alike for shared protection o they all help each other [they’re all poisonous], shows a signal to the predators ▪ look like each other for shared protection • Batesian mimicry o one species is not harmful, and is trying to trick predators o Animals that are evolving to look like wasp to get protection so predators avoid them ▪ looks poisonous but isn’t poisonous itself ▪ e.g., Moth and Beetle • How do we know a given trait is an adaptation? o Adaptation is any trait that has a positive effect on fitness o We need to test it ▪ Zebra spider ▪ the flu makes it look like it’s a spider so predators won’t eat it ▪ wings have stripes that make look like spider and they wave them around • The researchers made 5 kinds of flies o they tested this by: waving of the wings and the stripes ▪ took some flies, cut their wings off and glued it back on ▪ Also had a normal house fly which does not wave the wings o Hypothesis: ▪ Markings help deter spiders ▪ Waving helps deter spiders ▪ Neither affects spiders ▪ They only work together o They take 5 groups of flies, introduce a spider next to them and count how often a fly gets attacked o They measured the number of fly attacks on each group o End results: both marking and waving has to work together [to help protect from being eaten from jumping spiders] o Before we test, we cannot tell what the traits are for o fitness and trait = adaptation Niche • All organisms fill a niche, some are more specific than others • Niche = function of a species within a community o What it does in the environment and how it survives [how it fits into the environment and how it adapts to the environment] ▪ Koalas • A simple model of a niche’s is a food web o producers at the bottom which is making most of the energy in the environment [captures sunlight] o eaten by some primary consumers ▪ Tertiary consumers, secondary consumers, primary consumers, producers and decomposers o Niche can have overlap with other species which can determine the traits you have o What an organism is eating is a big part of niche • But niches can be very specific, and it’s not just about what food species eat o Warblers in tree: different species live in the same tree but different parts of a tree ▪ one’s at the top might experience predation [eagles, owls] ▪ the one’s at the bottom would worry about cats or anything living at the bottom of the tree ▪ specialities of how they defend themselves ▪ imagine something happens and one of the warblers from the middle (that eat beetles) of the tree goes extinct • what happens: tons of beetles • maybe the middle ones were eating all of the beetles before the other two could get near there • now that they’re gone, the others can start eating beetles too and move into the middle of the tree • some of them good at catching beetles might start specializing on the beetles and overtime, we’ll see a new species arrive • split into two population • Something will fill the empty niche • Niche partitioning: different parts of species in different areas are split into different species o different environments, species work and try to exploit these areas • Test these on islands o able to see all species, and easy ecosystems o We need to look only at oceanic, not continental islands ▪ Japan = continental ▪ Oceanic islands = volcanos and no new organisms there yet • important because no niches are filled in volcanic island yet [we want to look at new species, diversification] • Species on oceanic islands are all species with long dispersal distances o species that can get to the island first are those that can disperse very far [seeds that float into island, birds, instincts [flying animals] o Species will diversify on the islands to fill empty niches • This helps explain the diversity of finches in the Galapagos island o All descendent from the initial population of few that showed up on the island o Finches specialize on different kinds of food and nesting habitats o when there’s an empty niche, these organisms fill it • These patterns are seen in many species in Hawaii • The Honeycreepers have diversified on Hawaiian lobeliods, a plant family that has hugely diversified on the island o birds are increasing of diversity because of flowers and vice versa because they’re making of interactions which cause niches • Fruit flies also diversified on Hawaii o look wildly different from each other o Hawaiian island has over half of fruit flies on island even though it’s tiny • Islands often have most of the diversity of given group o even though they started from the same birds, there’s diversity in the islands o also diversity in beak length o Evolution manage to specialize them in a short timeframe so they can get different phenotypes o A lot of finches on mainland are in the same niche as their ancestors were for a long time • In the Caribbean islands live Anoles, which have a few different morphs or niches they will o they look different from each other [size, colour] o specialize to the niches o They look similar because it could be that one lizards get on different islands and specialize on something else • Are anoles of the same type more closely related, or are those on the same islands more closely related? o if they’re more closely related to the same morph, we expect them to grow by morph o if we see them diversify, we expect them to be related by island o one lizard gets these islands and diversify because the niches were empty o they didn’t do it on home island because there were other niches filling the duty • Species evolve to fill a certain niche, but when new niches become available they will diversify to fill those new niches Speciation 1 • Darwin’s first work was titled “the origins of species” but it was ironic because it’s not about what makes population split to make new organisms • What is it that keeps two groups apart and what makes 2 groups distinct? • Each organism had a type/perfect model and each species was a copy of that • What is species? Are species arbitrary? o A species isn’t a thing, we’re opposing on nature that isn’t real o Ernst Mayr: studies speciation ▪ Tested this: if different groups of people actually assigned different species to the same group ▪ e.g., Dutch (Papua) New Guinea – locals recognize 136 different birds, while ornithologist recognize 137 ▪ they went and decided how many species they saw on this island o our definition of species needs to distinguish between ▪ animals, plants, micros, and fossils ▪ work across the entire breath of live • The morphological species concept: o Two individuals with similar morphological features are the same o individuals that have different morphological are different species o e.g., works with fossils, certain plants (not Euphorb and Cactus) o morphological: physical characteristics o E.coli, Pseudomonas [does not work in a lot of micros], animals o a lot of sexual dimorphism there’s a problem because we cannot tell them apart o a lot of variation of what organisms look like in any given population = morphological species concept • The biological species concept:
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