 Well, welcome to a Monday. So this is the sixth lecture for the evolution part of Bio1B. Are there any questions from the last lectures? Nothing? Everybody enjoyed the Cal UCLA game? It was OK? Yeah, it was a good game. All right, so my plan today is to finish up briefly with migration. So we talked about the four different forces that change allele frequencies in a population, mutation, natural selection, genetic drift. I want to talk briefly about migration, and then we'll talk about some examples of selection, not only experimental evolution, that is to say evolution in the laboratory and then an example of evolution in the wild. So just to finish up on migration, this is not a very complicated idea, but the idea now is that we have two populations from the species. Remember, each species has at least one population. But we imagine a species that has two populations. There's population one and population two. And migration is just movement of individuals from one population to the next. So in this case, you're going to have movement of individuals from this population of that or that population of this. And so migration can change allele frequencies for the obvious reason that if there's a mutation that appears in this population and an individual that bears that mutation moves from this population of that population then the allele frequencies have obviously changed. Now the main thing you should realize about migration is it's a force that homogenizes the frequencies in different populations. It makes the frequencies of alleles more similar to each other. So if you have lots of migration between two populations, the allele frequencies in the two populations can become very similar. If you cut off migration, that is to say, you just all of a sudden don't allow migration between two populations, what can happen? Well, the allele frequencies over time will become more and more different. And that makes sense. If you have a mutation that appears in this population, there's no way for this mutation to get into this population unless it occurs independently over here. And similarly, you're allowing genetic drift. Even if you start the two populations off with the same allele frequencies and then you turn off migration, then genetic drift will occur differently in the two populations. Maybe an allele will become fixed in this population and lost in this population. When we get to speciation, you'll see that migration and specifically turning off migration. So speaking of, think about having little knobs. You turn up natural selection, turn down natural selection, turn up migration, turn down migration. If you turn off migration, rather, you actually will make the two populations over time will become more and more different. And eventually, they can become new species. Now there are examples of migration. One that I'll just give you involves domesticated rice. And there was a variant of rice that was tested in a plot called Liberty Rice. It was what was this strain? It was LL601. That was a strain name. This particular strain of rice was resistant to a herbicide. The herbicide was called Liberty herbicide. So this was called Liberty strain of rice because it was resistant to this herbicide. And it was grown in a few test plots from 1998 to 2001. And it was never approved for human consumption, so that was the end of it. They terminated the experiment. But it turns out that through migration, some of these Liberty Rice genes got into domesticated rice that was approved for human consumption and it was actually exported across the world, around the world. And so this started to creep up a few years after this test plot was done. And people became very concerned about it. That you actually had this particular strain that actually invaded the domesticated rice. And so it actually was such a concern that Japan for one month actually debanned the rice imports from the US. So from that perspective, migration actually had an economic cost to the farmers who exported rice. So it's just one example of migration. Of course, you might hear about lots of concerns that people have currently about basically migration. That is to say, we might have genetically engineered crops, for instance, and the concern is that the genes from these genetically engineered crops might invade wild populations. For instance, if you make specific crops resistant to herbicides, the concern is that maybe those genes will get into the wild populations of weeds, and before you know it, will have weeds that are also resistant to their herbicides. Now that hasn't really occurred very much, and people kind of debate the importance of this force. But it is a potential concern that you should be aware of. OK, so that's all I really wanted to say about. Yes? Where is the question? Oh, yes? Oh, sure. I don't know if I can actually turn it up or I can reposition it. Is that better? OK, so maybe it was too close to my throat. There's another I sort of forgot to mention. I don't want to say complaints, but concerns about the quality of the slide images for the recording. So a lot of people obviously don't show up to the morning lectures, and they watch the lectures on the web. And I'm sorry about that. That's the one downside, I guess, of not being here in person is that the quality of the images in the webcast aren't as crisp as they are here. Of course, those people can download the PDFs, and they have a very good version of it. So there's nothing really I can do about it. OK, so that's all I wanted to say about population genetics. That was it. That's the end of the math part of evolution. Now, like I said, I want to go into examples of selection. And the two examples I want to give are experimental evolution and then natural selection in the wild. There's lots of examples of experimental evolution. So here's an example which you're probably familiar with if you ever eat corn. So this is a domesticated corn. This is the type of corn you find in the supermarket. Of course, corn has not always been like that. What is the wild relative of corn? It's a plant called tiosinte. And it has very tiny kernels and very pathetic cobs. And over time, and people have a pretty good record of what corn looked like in the past, because you'll often find ancient corn in archaeological digs. So you can actually document what it looked like in the past. But anyways, what you're seeing here is this is what the female part of the corn plant looks like. This is the male tassel. This is what the male part looks like. And this is what's happened over time between just selecting for larger kernel size and larger cobs of corn is done to tiosinte. And there's actually a really interesting experiment, a very long-term experiment that's been performed since 1896 in Illinois. It's an agricultural station in Illinois. So this is the number of generations, over 100 generations of selection for oil content in corn. And so this is what the oil content was in the late 1890s. Over time, people have selected the corn to have higher oil content. That is to say you let the corn reproduce that has the highest oil content in your field. And you can see here they've got these high selected lines where you've gone from about 5% to over 20% oil content in the kernels. And then at certain times, they actually reverse the experiment. So here somewhere around the 1940s, they said let's try and divide the plots and let's start to reverse the selections in the opposite directions. We'll keep selecting for high oil content, but we'll take this other plot of land and have all the corn on that land will start to select for low oil content. And this is what you see. And they've also had a low oil content plot as well over time. So for almost any domesticated species that we're interested in, we can select for traits as long as there's some variation. We can select for traits and get almost anything we want. Give us enough time, give humans enough time and they can select for traits, domesticated crops that will have almost any feature you want. So before I get to the viral example, let me talk about an example that I really love that comes from Michael Rose's lab at UC Irvine. And what Michael Rose does is he studies senescence. So I kind of debate whether even to talk to you guys about senescence, because all your life, all you've known is getting bigger and stronger and better, so to speak, right? You're about 18, 19, 20. And basically up to about 18, 19 or 20, things are good. I remember those days. You get stronger and bigger, you look better looking than you are, you'll ever be in your life again. But from here on out, let me assure you it's downhill, okay? Every year your memory gets worse. Like if I work out, it takes me forever to recover and I'm miserable. It's just, it's worse. And from my perspective, it only gets worse from here on out, right? Cause eventually, you senesce and you, things just fall apart and you die, okay? So it's a very, but this is something we all have to face. And there is an interesting question. Why? Why do we senesce? Wouldn't it be better to be 80 years old and have lots of children? Wouldn't natural selection favor that, okay? And so there is this question of what is the evolutionary explanation for aging or senescence? And the example goes like this. Let me, we have to sort of imagine a perfect population or a population of individuals that don't age, if you can imagine that. So that is to say somebody who's 80 looks just as good as somebody who's 20 is just as fit, just as strong, okay? So there's no difference in their fitness or essentially their physiological age. They don't age. But just because you don't age doesn't mean you don't die. So let's imagine you're like a deer, right? That doesn't age. Well, you still can be run down by mountain lion and eaten, right? That doesn't mean you don't die. Or if humans didn't age, doesn't mean we didn't get run over by a bus or get in a car accident and die, right? There's, just because you don't age doesn't mean you don't die. So keep that distinction in mind. So let's imagine a population of organisms where each year there's a probability of 95.95 that they survive. Okay, 5% of each cohort, say you know, you have a bunch of individuals that are born and every year 5% of them are picked off and they die. Maybe the mountain lions eat 5% of that cohort every year. With me? So what is the probability that you make it to 10 years? I believe I put that down. It's about 0.77. So about 77% of the cohort, that imaginary cohort of non-age organisms will still be alive for 10 years from now. That means over a quarter of them have still died, right? And then what's the chance of them making it 50 years? It's 7%. Only 7% are alive after 50 years. There's still not those 50-year-old animals or plants, whatever they are. Look, just as fit as the one-year-old ones, right? But there's only 7% of that cohort left. And then you can ask, well, what's the probability that you make it to 100 years? It's about 0.005 or about half a percent in this imaginary population. Only half a percent are still alive after 100 years in this ideal non-age. And those half-percent of 100-year-old animals look great, right? But they only represent a small fraction of the cohort that was alive 100 years ago. So this is the scenario we're picking up, I'm trying to describe. So what this means is that if you have a beneficial mutation that acts early in life, there's more individuals on which that beneficial mutation can act. If this beneficial mutation only affects 80-year-old individuals, then only a small fraction of the population can experience that beneficial mutation. And it won't be as strongly selected. So it also means that if you have a beneficial mutation that acts early in life, but has a detrimental effect later in life, that mutation can spread. Because there's more individuals on which it can act and the detrimental effects will be experienced by just a few individuals. So that's the model. That's the theory, okay? So what did Michael Rose do? Well, he said, well, let's test this theory. What, basically the explanation for why organisms age and why you kind of evolution of ageing is because of this model I just described. I should mention too that obviously, senescence or aging evolves, right? Because if you look at humans, we live what, 70 to 80 years? Look at our closest relatives, the chimps. Even in conditions as benign as the ones we live in, they only live 50 or 60 years. Okay, and if you go further out, and you look at a house mouse, right? They're closely related to us and in an evolutionary sense, they're kind of closely related to us. They only live maybe three years, right? So between mice and humans, humans live 80, mice live three. There's been a lot of, you know, obviously aging is something that evolves. So Michael Rose said, well, maybe we can make Drosophila, flies, fruit flies, evolve in terms of aging in the lab. And you should know that the usual, the Drosophila melanogaster, the workhorse for modern genetics, they only live about three or four weeks, right? And flies, they don't suffer from things like, insects typically don't get cancers like mammals do, but they do show signs of senescence, you know, their wings become tattered, they're less active, they're less productive in terms of the reproductive ability. They age like any other organism. So what he did is he said, let's make these late-acting mutations that normally natural selection doesn't care about. Let's make those late-acting mutations important. So how do you do that? Well, he only let the flies reproduce when they got old. So you can think of this as sort of the career woman experiment, but only in flies, right? So at first, he wouldn't let the flies mate until they're two or three weeks old. So you can easily, with flies, you can, you know, they're larving, they kind of dig around in the bottom of the vial, getting food, and then when they metamorphose into flies, you can easily separate the males and the females. You can have a female flask, and you have a male flask of flies. It's then quite easy to say, you know, they can only date, so to speak, when they get to three weeks old, right? So only the oldest flies are reproducing, and then you can raise the bar. So it'd be, instead of three weeks, make it four weeks. Instead of four weeks, make it five weeks, the age at which they're allowed to reproduce. After a while, he had flies that were living 10 days longer on average. Okay, so that'd be kind of equivalent to humans living a lot, 120 years instead of 80, 90 years. Then he continued the experiments even further, and eventually he got flies that were living about six months. He called these the strain of flies, the strain of flies that he selected for it, his so-called Methuselah strain, for obvious reasons. They're very old flies. So there is, you can't actually select for aging, and you can actually, aging is like any other trait, you can actually make it evolve in the lab, okay? But once again, what he did in the lab was make these late-acting deleterious mutations important, so to speak. Normally, natural selection doesn't see these late-acting mutations, because so few individuals are around to experience them, but he made them important, okay? Are there any questions about that? It's a great experiment, and if you're really interested in it, you can go to his website, and you can download his papers. They're quite interesting papers. You can also imagine that he's gotten a lot of funding for this work, often looking at which mutations were responsible for the old age in his strain of flies, with the idea being that whatever mutations are responsible for increased longevity in his fly strains might also be important for, say, us. So there are ramifications for these types of studies for human health. Okay, so now I wanna go to another example of natural selection, but only this time in the lab, once again, but using viruses, and the experiment was performed by these two people. This is Jim Bull, who's at the University of Texas, and this is Holly Wickman, who's at University of Idaho in Moscow. And they were working on these critters, and these critters, what are they? This is a scanning electron micrograph of a virus called Phi X174. So it's Phi X174. And this is just, it's a virus that infects E. coli. This is the bacterium that you can find in your gut. You can raise E. coli quite easily in the lab. In fact, it's a standard strain of bacterium that people often raise in labs for molecular biology type work. And basically, if you had a flask, say, of E. coli that was happily growing at body temperature, 37 degrees Celsius, and you threw in one of these guys, before you know it, the strain would become kind of clear. Basically, you throw in one of these guys that gets into an E. coli and about 200 pop out killing that bacterium, and they infect other bacteria and so forth. And before you know it, a large fraction of the culture of E. coli will be dead, and they have lots of Phi X174. The Phi X174 genome is a double-stranded DNA, and it's circular. So viruses like any other critter have genomes. This is a very small genome. So our genome is about 3 billion ACGs and Ts. This one has a genome that's 5,383 ACGs and Ts. So it's quite small. In fact, this was the first organism to have its genome sequenced, I think, in like 1977. It's the very first organism to have its entire genome sequenced. And the number, or the letters here represent the genes. And so the genes are given actually just letters for their name. So you can talk about the G protein or the H protein or the A protein. And there's a couple of genes here where you see B overlaps with A, star overlapping with A. This is one of these cases where you actually have multiple coding regions in the same piece of DNA, which is unusual. But you don't have to worry about that. You don't have to worry about remembering any of the genes here. What they did is normally, like I said, the E. coli grows well at 37 degrees Celsius. And the bacteria, the Phi X174 is also well adapted for 37 degrees Celsius because that's the temperature at which its host lives, right? So if you're a Phi X174 and you can reproduce rapidly at 37 degrees Celsius, you're golden, right? You're okay. What they did is they raised the temperature of which they incubated the E. coli from 37 degrees Celsius to 43 degrees Celsius. Now what happens? The Phi X174 initially aren't as good. So what you see here is you have this zero line. This is the fitness of the phage. When I say phage, I mean virus. So people call these viruses that infect the E. coli bacteriophage, right, for bacterial viruses. So I've just realized that I'm saying both words here. So bacteriophage or bacterial virus. Initially, their fitness would be here at the zero line, but when you first start off this experiment, you crank the temperature up to 43 degrees Celsius, the phage aren't happy. They don't reproduce as well and they're less fit. That is to say, they produce fewer offspring. Fewer viral particles come out of the bacterium at the 43 degrees, then it does at 37 degrees. But if you continually passage the viruses at 43 degrees Celsius, they get better and better. So what do I mean by passage? It means you have a flask of E. coli, you put in a virus, the virus explodes. Before you know it, you have started off with one viral particle, one 5x174, and before you know it, you have trillions and trillions of them, okay, like over the course of a couple hours. Then you take a small number of the guys from this flask and you put them into a new flask of freshly growing, naive E. coli. That is to say E. coli with no bacteriophage. And you put a few of these guys in here and what happens, they grow up in the lysis one. And then you take a couple of these guys from this flask and you put them into another flask of E. coli. This is what's called passage. You're just taking a few of the viruses from this flask and putting them into a new flask of fresh E. coli that are growing at 43 degrees. So what you're doing is you're favoring mutations that allow the virus to grow well at high temperature. And what you're seeing, this is just a measure of how well the viruses grow. You can see that both in the Texas, they did the experiment twice, once in Texas, once in Idaho. The Texas drained over a few days very rapidly, did much better at 43 degrees and so did the Idaho strain. The Idaho strain for some reasons didn't do quite as well as the Texas strain, but they both increased dramatically in how well they could grow at 43 degrees. So their fitness increased in both cases. Now the neat thing about viruses is, especially a virus like Bix174 that has a small genome, is that you can actually sequence the genome and find out what mutations were responsible for the adaptive response. Which mutations allowed the virus to do well at high temperature? And these are all the changes they saw in the Texas experiment and also in the Idaho experiment. And so what you see here is each, so all of those 5,383 nucleotides in the genome are numbered from one to 5,383. And so what you're seeing here is the position of the change and what type of change it was from. Okay, so this would mean it was from an amino acid T to I. T, tyrosine maybe, I, I forget, isolucine or something like that. I don't have all the 20 amino acid codes remembered, okay, memorized. But this is probably from alanine to valine, for instance. But these are the positions at which you had, had the mutations. Here was a case where you had a deletion in the Texas analysis. And you hear you had a deletion in the Idaho experiment as well. Note that in many of these cases, you see the same exact mutation occurring independently in the Texas experiment and also in the Idaho experiment. So for instance, here's an experiment where, here's a site where we have a change from H to Y, amino acid H to Y at position 4110. And that occurred in both of them. This deletion looks as if it also occurred in the same way in both of these experiments. Now, there's two ways you'd explain this, the fact that you get the same results. One is that there's some sort of wild contamination problem. That doesn't seem likely because the experiments were formed in quite different sites, right? Contamination meaning maybe some of the Texas viruses somehow got into the flasks in Idaho when they're doing this experiment. That's that we can dismiss because they're very careful to do the experiments in widely separated areas. So what that means is these mutations were selected independently in the two different experiments, right? Natural selection or selection in these experiments acted in the same way and favored the same mutations when they occurred. And so here's just the final thing they could do is they could look at the frequencies of these mutations and how they changed over the course of the experiment. So for instance, here's one of the mutations and you can see that kind of like the little computer simulations I showed you where when you had these favored mutations they would sort of go up in frequency and then they'd plateau. We can see the same sort of behavior here but what you're seeing is that these mutations spread through the population and fix incredibly rapidly. They're very large population sizes and these mutations are very favored. That is to say the individuals that bear these mutations have a huge fitness advantage over the individuals that don't. Okay, so that's all I wanted to say about experimental evolution. I gave you an example with the course of corn which isn't so surprising. The senescence experiment that Michael Rose did and then an example with viruses and people are doing these types of experiments all the time in the lab. Often they're not evolutionary biologists interested in testing questions in population genetics say but they're working in companies and they're trying to evolve proteins that say bind something more tightly. So these are for whatever reasons. Maybe a customer wants something that will bind a particular protein for whatever reason and they can actually evolve these things in the lab. So they use evolution or selection in molecular biology labs all over the world. But let's give you some examples from the wild and I'll tell you one of my favorite examples one I'm not gonna show you or describe but one involves a couple, the Rosemary and Peter Grant who are at Princeton University and they've gone back to a particular island in the Galapagos and studied a population of Finch for well, since the 1970s. They go every year, it's a small island and basically what they can do is they can document every single bird on the island. There's not that many of them and how natural selection has favored different beak shapes depending on the seed availability in that year and there's a really good book that I would recommend I actually even recommended it to my mom I thought it was such a good book. It's called the beak of the Finch it's by a fellow named Jonathan Weiner. It's a good readable explanation of these experiments so if you're interested you can check it out of the library and read it. It's not obviously something I would require that you know but just if you're interested. I wanted to give an example not from Princeton but from Cal and so I decided to give you an example of an experiment that was done recently by this woman right here, Hopi Hoekstra. So she was a Bio 1B student she was an integrative biology major here at University of Texas University of California I'm thinking I'm Texas University of California she was on the volleyball team in 1991. There she is. She was in a sorority here. There's a picture of the sorority I took on a game day coming down from the steps from the stadium. Here she is at a party. There she is right there and you should notice there's very discreetly hiding something in their hands I have no idea what it is but I'm sure she's gonna love it that I'm showing those photos of her rather and there here she is in the field so she studies, she's a mnemologist and she studies mice basically in the field and the work she's doing now is actually out in the Gulf of Mexico and she's studying mice that occur in the sand dunes. What I'm gonna describe is the work she did as what's called a postdoc it's what you do after you got your PhD often people have a couple of years where they get to do nothing but research before they get to the job like me where they have all sorts of other responsibilities and she studies cryptic coloration in mice so the cryptic coloration example you've probably gotten in high school is an example with the moths on trees in England this is an experiment or an observation that people made that with industrialization you had trees that became much more sooty and experienced from coal from this they're burning a lot of coal at the time and the wild these moths they're ancient phenotype their primitive phenotype is to be white so they actually match these trees what they're finding is that these melanic forms were actually spreading and increasing in frequency the story isn't quite as little bit more complicated than what I'm saying but not much more complicated I think there's actually another I think there's actually a white moth here and a black moth here but I think that's the black moth maybe I can actually find them they're very cryptic but what she's studying is cryptic coloration in mice and so there's a lot so if you think about the must-must, the must-domesticus the mouse they use in labs all over the world a lot is known about their coat colors and the genes responsible for different coat color polymorphisms so for instance here's a little mouse it has a little it's a piebald mouse and you can actually see the piebald mutation in humans there's a basketball player with the piebald mutation there's the mouse with the piebald mutation this is people know the mutation it's responsible for this right so it's a mutation into endothelian receptor B it's the piebald mutation that's the house mouse she was actually studying here's some more other mutations that you're probably aware of in lots of animals are albinos they have a mutation of tyrosinase mutation this is typically a deleterious mutation because they don't have any melanin so here's an example of albinism in humans and here's some examples this is a gorilla that has this mutation the koala, the zebra and so forth there's an albinos squirrel that's pretty cool and then of course there's the albino mouse very cute little mouse so she was studying adaptive or cryptic coloration in these rock pocket mice that occur in the Southwest the American Southwest and I know, is anybody here from Arizona? Must be a few people I'm not from Arizona but I'll keep my hand down so I guess it's a California university but if you go, if you drive along the southern part of Arizona along say highway eight what you'll see is typically what you see is lots and lots of this hours and hours of this but occasionally when things get very exciting you'll go across these fairly recent lava flows where the rock is more basaltic, darker in color so occasionally you come across these basalt flows so this is an example from the pinnacate lava flow where you see this much darker substrate and what you see in these darker rocks is same species of rock pocket mice but you see this melanic form a darker form and then the typical form you see all over the rest of Arizona has this more light pelage, lighter coat and she was interested in the genes that underlie this and whether or not this coat coloration was of adaptive significance so this is just giving you an example of the different places where she studied her different study sites this is the pinnacates I just showed you located here in Arizona and what she's showing you here is on the lava flow that means this is lava flow, that's not lava flow here's the kensin lava flow, lava flow, not lava flow that is to say the ground just surrounding the lava flows on the lava flows you find lots of these dark mice and right next to the lava flows you find lots of the light mice that's what it means that's what this figure means and that's true for these other lava flows as well here's the kensin all the mice she found on the lava flows were dark and all the mice she found just adjacent to the lava flow were white and that's the true for these others as well oh and then down here is an estimate of the age of these lava flows and for reasons I'll describe later you can actually very precisely date lava flows using what's called radiometric age dating so the age of these lava flows is well established and here's some of the mice in the lab so you can actually see the differences from each of these different lava flows this is the type of mouse you find on the lava flow this is the mouse coloration you'll find just adjacent to the lava flow and the pinnacades and so forth this is what, if you go upstairs and to go through the drawers of the museum here you find lots of examples of mice that look like this kind of flattened out with tags on them not very happy so what she did is she took what's called an association state so she looked at these mice and she noticed and I should say too that this work was done not only with Hopi Hoxtra but with this fellow Michael Nockman who's at the University of Arizona so it's a Nockman Hoxtra what she did is she looked at the hairs on these pinnacati mice the lava flow mice and noticed that the hairs look reminiscent of a mutation that you find in the mice that the house mouse the mouse that everybody studies and labs all over the world and she thought well maybe the same mutations or mutations in the same genes are responsible for the dark coloration in these rock pocket mice as the ones that cause dark coloration in laboratory mice that was the thought so you have 30,000 genes that you can think of out there in the genome she tried to limit which ones to really study a lot by using what's called the candidate gene approach so concentrate your attention based on what you know in a related species and the basic idea is this in these association studies you have some mutation that's responsible for the phenotype and so in this case the mutation in the gene that's responsible for the phenotype is indicated by a star each one of these lines represents a chromosome so these chromosomes might come from would come from different individuals these different mice say now you may not actually have sequenced or actually know what the mutation is you may never actually see the star but what you can get is places nearby that are polymorphic that is to say nucleotide sites, the SNP sites I told you about earlier where you know that there's variation and the idea is that when this mutation appears it's gonna occur on some chromosome and that it's gonna at least initially be associated with specific sets of nucleotide polymorphisms nearby so if you can actually assay the sites you actually assay the vertical lines here you can measure the phenotype and the idea is if you see a phenotype that's associated with certain SNPs that it must also be associated with some gene that's nearby some mutation that's nearby so this is what she did and so she actually looked at a mutation in what's called the MC1R gene it's one of these genes that she knew from the house that the laboratory mouse might be responsible for this this MC1R protein sits on the membrane of the cell it's called the transmembrane G-coupled receptor and what happens is things like MSH will bind to the outside and when it binds to the outside of this it causes C-amp expression to be expressed or increased inside the cell and you get what's called a U-melanin being produced you get dark hair so if you look out, actually lots of people have lots of U-melanin in this class now if agudy is another protein that can bind to this protein, this MC1R and when it binds it shuts it down so when agudy is present it represses the activity of this MC1R gene you don't get a lot of C-amp and you get Phe-melanin being produced so I look out there and I see a few people with very light hair that have lots of Phe-melanin and you get light hair so this is a mouse that has lots of Phe-melanin being produced this U-melanin rather or Phe-melanin, this is an individual that has lots of U-melanin being produced dark hairs so this is the actual data from our paper and what we're seeing here is this is the two different copies of the gene from each mouse this is one particular mouse you can see, remember it has two copies this is the gene one from mom, one from dad so what you're seeing is copy one, copy two for this dark mouse and then you have this other dark mouse where you're seeing copy one, copy two and so forth these are all the dark mice and then here's all the light mice here's for instance, well let's go to the very bottom it's easier to see this line here represents the DNA sequence from mom or dad from one chromosome and here's the sequence from the other chromosome from this particular mouse and wherever you see a dot this is a shorthand notation that people use in these types of figures to mean that it's whatever is here is the same as at the top so it's gonna be a C wherever you see a dot this is the reference sequence at the top so wherever you see a dot it means you put in the reference sequence nucleotide at that position is that clear, is it clear how to read this and you see anything remarkable about this graph or about this figure I mean she sort of draws your attention to it by boxing it in but note this all these dark individuals have a T at this position a T at this position a T at this position and a C at that position in the gene, right and they have at least one copy of that right so up here all these individuals let's see all these individuals at the top from here on up they're all homozygous for having all four of those mutations that is to say both chromosomes have those four mutations these individuals from here down to here that are heterozygous, right and all the individuals down here are homozygous for not having those four mutations and so she used a subscript little D for having not having those four mutations big D for having those mutations so these are all the big D, big D individuals these are the big D, little D and these are the little D, little D what she's pointing out here is that there's a perfect association between the color of the coat of the mouse and these four mutations now the, so the inference is that these four mutations are responsible in the MC1R gene are responsible for the dark coloration you see in the mice now the best experiment she could do which she hasn't been able to manage to do for technical reasons is you take a white mouse and you basically through transgenic methods that you can learn about in advanced molecular biology courses you actually stick that gene into a mouse and see if it becomes a dark colored mouse that's the experiment that most molecular biologists would consider as definitive but this case the evidence is so overwhelming those four mutations are responsible for the coat coloration that's probably not necessary to even do the experiment so this is just to summarize what we have we have those four mutations if you're, if you've got it if you have at least one copy of those four mutations on at least one of the chromosomes you have dark coloration and this is just showing you where those mutations occurred in the MC1R gene two of them occurred on the part of the transmembrane protein that faces outside of the cell that's these up here and two of them occur on the part that faces inside the cell these are the, each one of these circles represents an amino acid that's coded for by the, by the MC1R DNA sequence so this is, this is the situation you have we're just showing you pictures of here I'm showing you a picture of the mice on their natural habit background here's a mouse that's mismatched it's actually a dark mouse on a white background here's a white mouse on a dark background and here's a dark mouse on a dark background on the lava flow so the thought of course is that if you're a predator you can actually see the mismatched individuals much more easily than you can see these individuals but of course when you make a statement like that it seems obvious but you have to remember that's well we're speaking right I look at that and I say it looks very obvious to me that these guys would be the ones that would be easy to find and pick off but you know I don't actually I'm not a predator on mice okay and so it turns out that maybe our intuition is wrong about this so you need to do experiments to actually determine whether the mismatched mice have an advantage so you might imagine I'm a bit of a Trek fan so this is one of the episodes where Kirk has to battle Spock and it's called the amic time it's the episode if you're interested in so what you need to do is some sort of tournament type of study right and so what this is a very difficult experiment to do now but it has been performed about 60 years ago by this fellow Dice and he basically studied alpidation and deer mice they're mice that are similar or closer related to the pocket mice that Dr. Hoekstra and Nockman studied and what he did was this just took a barn and on the floor he made two different arenas he put some dark colored rock on one and he put some light colored sand and rock on the other and he put dark and white mice out onto the deer mice out into these two different arenas and let them sort of scurry around that's what mice do and then he put some barn owls in the barn right and just let the barn owls do what they do which is they eat mice and so the barn owls would sort of swoop down and eat the mice and they just counted which mice were eaten and which survived and what they found in this experiment is that the deer mice that were mismatched to their substrate were much more frequently picked off by the owls you know owls have notoriously good eyesight but even they find it easier to find a mismatched mouse than a mouse that matches the substrate and then Dr. Hoekstra has done similar studies more recently where she was very difficult to get the permission to do experiments like that nowadays I guess people don't like to see the little mice being eaten by barn owls but you can take what she did she took made little clay models of mice so she has an entire lab graduate students in postdocs they have these fun little parties where they make little clay mice and they don't fire the mice okay so it's not like you make the clay mice and fire them you keep them so they're still soft clay and you paint them so you get to paint too it's like a craft thing so they paint the mice they paint them to look as much like they can like the dark colored or the light colored mice and then they go out in the field and in the evening they'll sort of stick these little mice all over the place and the next day they come in or a couple of days later they look around they pick up their little clay mice and they look for evidence of predation so if you see like a bite mark on them that's going to be preserved in the clay or scratch marks like some owl came by and then realize it's just clay it's half you know but they look for evidence of predation and they find in these experiments just like you'd expect the mice that mismatch their background in which they sort of place the clay mice or have show evidence of predation at a much higher rate than the mice that match the background okay just a little bit more on this so she's also studied the distribution of these MC1R alleles the case where you call the big D and little D alleles in what are called transects what you do is you make a line and you just walk along that line and you collect mice whenever you see them okay you trap them actually so you put traps along the transect and so this is the transect there's the lava flow so basically in this transect you have some parts where you have the regular light colored sand of the desert and then this is the dark colored part so this is a substrate color along the transect and as you'd expect the frequency of the MC1R gene allel those big D alleles sky rockets goes almost to one over the lava flows and then decreases on either side of it so this is you can actually if you want and it's useful to think about there being two populations you have the population of mice living on the lava flows and the population of mice not living on the lava flows and here's another example where you have migration of individuals from the lava flows out into the desert and from the desert into the lava flows as far as they can tell the mice don't know any better they don't know if they're mismatched or not okay they're mice they're not super smart and so you have natural migration of the mice that go out here but of course when the dark mice come out in the light sands they probably get eaten up pretty quickly and it's the same for the light mice that find themselves on the rocks and this is just a show that it's not what you do is this is the frequency of the MC1R big D allele over that transect once again noting that on the dark rocks the frequency of that big D allele is very high but it's very low in the white sands but here's another gene so you can say well what is that true for every single gene in the genome do they all show this pattern? because if they all show this pattern then clearly natural selection isn't acting on the MC1R gene and so this is some other gene that does nothing to do with coat coloration and you can see that it doesn't show any pattern going across that transect that its frequency is about the same on the light substrate as it is on the dark substrate so natural selection is clearly targeting just the MC1R gene okay and this is the last slide this is just to point out there's all sorts of interesting things you can do with coat coloration and mice and this is the type of work that Dr. Hoekstra's been doing more recently I should mention that she's now at Harvard that she's got faculty at Harvard and she's been turning her attention to mice that live in Nebraska on sand dunes and mice that live on the beaches along the Gulf of Mexico so I don't know if you know about the Gulf of Mexico but you go along these beaches and they have like pristine almost sugary in color of white sands along these strand beaches and then if you go inland if you go into like Florida just the mainland you see the normal dark dirt like we have everywhere the mice that live on these beaches on the white sand have very light colors coat colors like this guy right here this cute little guy here and here whereas the mice that live inland have more dark normal mousy type coat colors and she's been studying the mutations that are responsible for these light colored mice in the sands so that's it