Bio 1M Evolutionary Processes (Complete) PDF

Bio 1M: Evolutionary processes (complete) Evolution by natural selection ˆ POLL What is the missing from the story I told last chapter? – Heritable variation in traits – Selection (i.e., differential reproductive success) based on these traits ˆ Answer: Where does heritable variation in traits come...

Bio 1M: Evolutionary processes (complete) Evolution by natural selection ˆ POLL What is the missing from the story I told last chapter? – Heritable variation in traits – Selection (i.e., differential reproductive success) based on these traits ˆ Answer: Where does heritable variation in traits come from? Some genetics ˆ Our basic traits are determined by genes ˆ A location where a gene can occur is called a locus (pl. loci) ˆ A particular version of a gene is called an allele ˆ Complex organisms usually have two alleles at each locus – These can be the same, or different Loci ˆ Complex organisms usually have two alleles at each locus – These can be the same, or different ˆ An organism with different alleles at a particular locus is referred to as heterozygous (adj., n. form heterozygote) ˆ An organism with two copies of the same allele at a particular locus is referred to as homozygous (adj., n. form homozygote) Evolution ˆ Heritable changes in species traits over time ˆ Driven by changes in allele frequencies ˆ POLL What processes cause evolution? – Answer postponed: 1 Analyzing genotype frequencies 1 Genotypes and phenotypes ˆ A genotype is the collection of an individual’s genes ˆ A phenotype is the collection of an individual’s physiological and physical traits – What we can observe about an individual – Phenotype is largely (but by no means entirely) determined by genotype Example: peppered moths ˆ Kettlewell’s experiment https://en.wikipedia.org/wiki/Kettlewell%27s_experiment ˆ Two different alleles possible at the wing color gene: A1 and A2 . – Individuals with A1 A1 genotype have light-winged phenotype – Individuals with A2 A2 genotype have dark-winged phenotype . – Individuals with A1 A2 genotype ??? ˆ If individuals with genotype XY have the same phenotype (on average) as those with XX, we say that X is a dominant allele and Y is a recessive allele. – We will call this simple dominance – This is rarely exactly true, but often close enough to true. Allele interactions ˆ When neither allele dominates, a variety of complicated things can happen. ˆ People also tell complicated stories about naming these things. We’re also not going to worry about that: – Co-dominance – Incomplete dominance – We will use complex dominance for anything that’s not very close to simple dominance ˆ Table 20.1 Analyzing genotype frequencies ˆ We analyze genotype frequencies as follows: – Make simple assumptions about how frequencies work – Calculate expected frequencies under our assumptions – Measure observed frequencies in the population – Look for evidence of systematic (not random) difference between expected and observed frequencies 2 Making simple assumptions ˆ Expected frequencies are usually calculated by assuming that alleles assort randomly and independently, like flipping two coins, or rolling two dice Activity: Coin flipping ˆ I flip two fair coins (ie., each coin will land heads with probability 1/2). ˆ What is the probability of: – Two heads – Two tails? – One of each? ˆ Answer: 1/4, 1/4, 1/2. Activity: Professional coin flipping ˆ A professional gambler can flip a coin so that it lands heads 70% of the time. She flips two coins. ˆ What is the probability of: – Two heads – Two tails? – One of each? ˆ Answer: 0.49, 0.09, 0.42 Hardy-Weinberg distribution ˆ The Hardy-Weinberg distribution is the distribution expected if alleles work like coins (random and independent). ˆ If p is frequency of allele A1 and q is frequency of allele A2 , then: – Frequency of genotype A1 A1 is p2 . – Frequency of genotype A2 A2 is q 2 . – Frequency of genotype A1 A2 is 2pq. ˆ Why the 2? – Answer: Because you could get A1 from Mom and A2 from Dad, or A1 from Dad and A2 from Mom . . . two ways to do it 3 Example: calculating allele frequencies ˆ I collect 20 peppered moths from a particular place, and find that 4 have genotype A1 A1 , 8 have genotype A1 A2 , and 8 have genotype A2 A2 . ˆ What is the observed frequency of each allele? ˆ What is the expected frequency of each genotype under the Hardy-Weinberg assumptions? ˆ Is this population in Hardy-Weinberg equilibrium? – Answer: We see more homozygotes than expected * Answer: We can always summarize as more or less homozygotes * Answer: if allele frequency is right – Answer: But is this reliable evidence? That’s a question for statistics. What do we mean by expected? ˆ If we flip a fair coin 100 times, what is the expected number of heads? – What if we flip it 25 times? ˆ We don’t expect to get exactly the expected value. ˆ The ‘expected value’ is an average of what is expected under our assumptions – The idea is a conceptual average over what would happen if we did the same experiment many times How do you know a coin is perfectly fair? ˆ You can never be sure that a coin is perfectly fair, you can only evaluate your evidence that it’s more or less close to fair. ˆ Similarly, we never have evidence that a population is exactly in Hardy-Weinberg equilibrium ˆ We can only evaluate our evidence that it is far from (or close to) equilibrium ˆ What’s another way to think about the evidence? – Answer: How clear is it that we really have more (or less) homozygotes than expected? 4 Hardy-Weinberg equilibrium ˆ When do we expect genotype frequencies to behave like coins? ˆ Alleles selected at random from the previous generation: – Answer: Random mating within a closed population – Answer: No differences in fitness between genotypes – Answer: No mutation, no drift (see below) ˆ If these assumptions hold exactly, we expect Hardy-Weinberg equilibrium – Hardy-Weinberg distribution, with no change in allele frequencies from generation to generation. ˆ This never happens Differences from equilibrium ˆ If we observe large differences from the Hardy-Weinberg equilibrium, this is usually a sign that mating is not random, or that natural selection is operating ˆ The analysis tells us that something is going on, but not what ˆ Hardy-Weinberg is a null model: it tells us what to expect if complicating effects are absent ˆ Without a null model, we couldn’t ask how do observations differ from expectations Example: Human blood groups ˆ MN blood groups in different human populations are very close to Hardy-Weinberg equilibrium – https://tinyurl.com/MN-morning-2023 – https://tinyurl.com/MN-afternoon-2023 – No evidence for non-random mating, or for fitness differences. – This does not mean it’s not happening, but probably means that it’s small – Especially when we observe the same thing many times 5 Activity: Human blood groups at the global level ˆ POLL At the global level, how will MN blood groups compare to HW expectations? – Answer postponed: ˆ POLL What did we find? – Answer: More homozygotes ˆ POLL Why? – Answer: Mostly because mating is not random – Answer: These data are telling us different (reasonable) stories at different scales Example: Human HLA genes ˆ HLA genes are used by the immune system to recognize disease-causing organisms ˆ Researchers hypothesized that heterozygous individuals may recognize more bacteria and viruses ˆ Data shows that more people are heterozygous for HLA genes than would be expected under the Hardy-Weinberg assumption Heterozygous HLA genes ˆ POLL Why might more people be heterozygous for HLA genes than predicted by Hardy-Weinberg? – Answer: Heterozygous people might be more likely to survive – Answer: Heterozygous people may have more offspring * Answer: Effects of this one are more complicated * Answer: Heterozygotes don’t necessarily have heterozygous offspring – Answer: People might be more attracted to people with different HLA types * Answer: Maybe evolved this way because of reasons above 2 Types of natural selection 2.1 Trait level Directional selection ˆ Directional selection tends to move a population in a particular direction – Giraffe necks – Human brains 6 Multi-directional selection ˆ Directional selection can change through time with the environment – Swallows may get larger during extreme cold spells, smaller again during normal weather * But we need to know whether the changes we saw were heritable – Finch beaks get thicker when food is scarce, and smaller when food is abundant ˆ Why might small-beaked finches have advantages? – Answer: May be faster at processing small seeds – Answer: Can use the resources for something else * Answer: Faster growth, more fat storage Stabilizing selection ˆ Stabilizing selection tends to keep the population where it is – Answer: Usually because population is already adapted Connections between selection types ˆ What happens if the target of directional selection stays the same for a long time? – Answer: The population arrives at the target, and directional selection becomes stabilizing selection ˆ Examples? – Answer: Giraffe necks – Answer: Human brains – Answer: Almost everything we see * Answer: Things often develop by directional selection, but at any given time, most of what we see is under stabilizing selection * Answer: Because most organisms are highly adapted Disruptive selection ˆ Disruptive selection favors phenotypes different from the average value – Black-bellied seedcrackers have different types with different bill sizes. * Big bills may be good for big seeds and small for small * There may not be a lot of medium seeds in many forests – Animals that get eaten a lot (prey) may want to look different from their peers so that the predators that eat them don’t find them as easily ˆ Disruptive selection can lead to speciation – the formation of new species. ˆ Comment: See also F20.9 7 Frequency dependence ˆ Disruptive selection is closely related to frequency dependence ˆ Frequency dependence is the idea that some trait types do relatively better if they are rare. 2.2 Allele level Positive/negative selection ˆ An allele that has greater fitness than others in a particular context is called advantageous – It will tend to increase due to positive (natural) selection ˆ An allele that has less fitness than others in a particular context is called deleterious – It will tend to decrease due to negative (natural) selection ˆ The context can change when the environment changes, or . . . – Answer: When other alleles change Balancing selection ˆ Balancing selection tends to maintain allele diversity – When there is no single best allele ˆ Disruptive selection at the trait level will always cause some balancing selection – Answer: If natural selection is pushing in different directions, there must be some different alleles involved – Comment: Not 100% true, see seedcrackers Example below ˆ Balancing selection can also be caused by heterozygote advantage: when heterozygotes have higher fitness – Answer: The only way to get a heterozygote is by having different alleles combine Example: The sickle cell phenotype ˆ Blood cells that can lose their shape and squash malaria parasites! – People heterozygous for this trait get less sick with malaria – People homozygous for this trait have too much instability and severe anemia ˆ This is an example of: – Answer: heterozygote advantage 8 Example: seedcrackers ˆ What would happen if almost all of the seedcrackers had large bills? – Answer: More small seeds available, small bills become an advantage, an example of . . . * Answer: frequency dependence * Answer: disruptive selection ˆ What happens when large-billed and small-billed individuals breed? – Answer: They could have low-fitness offspring – Answer: Can lead to selection for less heritability – Answer: or selection on mate choice Alleles and traits ˆ Most traits that we measure depend on many alleles from many different loci ˆ We learn a lot from simple traits that depend on a single locus – Simple to study – Simple to explain ˆ Changes at one locus can affect the selection environment at another locus 3 Other evolutionary mechanisms 3.1 Genetic drift ˆ Genetic drift is change in allele frequencies due to random sampling: – Some individuals have more offspring than others due to chance events – Offspring receive certain parental alleles, and not others ˆ These factors will lead to an accumulation of random changes in allele frequencies ˆ Drift is a likely reason why different human populations have different MN allele frequencies Thought experiment ˆ Imagine flipping a fair coin 100 times – Repeat ˆ Now imagine choosing 100 alleles at random (with replacement) from a population of 50 A and 50 B alleles – Repeat, using new population as a starting point 9 Small populations ˆ Drift is much stronger in small populations than in large ones (law of averages). ˆ Even if a population is big now, it may have been small in the past – Founder effects occur when a new population is started by a small number of individuals – Bottlenecks occur when a population becomes small, then large again * ... or, when a beneficial genetic mutation takes over a population * Answer: variation will be lost at that locus because the new gene is better * Answer: but it can also be lost at other loci at random, because the whole future population is descended from individuals with the new mutation Fixation and loss ˆ An allele may drift to a frequency of 0 (it’s lost) or of 1 (it’s fixed) ˆ Advantageous alleles are often (not always) fixed – Answer: Positive selection ˆ Disadvantageous alleles are usually (not always) lost – Answer: Negative selection ˆ Alleles with neutral differences (no selective difference) will be fixed or lost at random – This is also true for alleles with small effects! ˆ Drift tends to reduce genetic variation 3.2 Gene flow ˆ Gene flow is the movement of alleles from one population to another – This happens when individuals move from one population to another and breed ˆ How we think about gene flow depends on how we choose to define a ‘population’ ˆ Gene flow can be an obstacle to speciation; it helps keep populations similar 10 3.3 Mutation ˆ Mutations are heritable errors in copying DNA ˆ Mutations are rare; by themselves they don’t cause much evolution ˆ Mutations are extremely important to evolution, however: – Answer: Mutations provide the variation on which natural selection acts – Answer: Mutation is the only source of new alleles Types of mutations ˆ Mutations can occur at many scales: – a single DNA base might change – chunks of DNA can be added or subtracted – whole genes (or whole chromosomes) can be duplicated ˆ New genetic sequence can come from: – copying errors – other organisms! lateral gene transfer Mutations are random ˆ Most mutations are deleterious – bad for fitness ˆ Very rarely mutations are beneficial – good for fitness – Such mutations are favored by natural selection Complex organisms ˆ Can complex organisms arise through random mutations? – A central question of biology – Large-scale evolution takes a long time – Beneficial changes can accumulate gradually – Much evidence of intermediate forms ˆ Evolution of the eye video https://www.pbslearningmedia.org/resource/tdc02. sci.life.evo.nilssoneye/evolution-of-the-eye/ 11 What about sex? ˆ Sex does not directly change allele frequencies ˆ It does act to bring alleles together (and to split them apart), this is called recombination ˆ Sex is not a source of new alleles – Comment: Depending on how we define alleles – But it is a source of new combinations ˆ There is still active debate on the advantages and disadvantages of sex in evolution 4 Mating patterns 4.1 Inbreeding ˆ Inbreeding refers to mating between close relatives ˆ Since relatives will tend to share similar alleles, inbred populations will tend to differ from Hardy-Weinberg equilibrium in what way? – Answer: More homozygous loci Inbreeding depression ˆ In many populations, it is observed that inbred individuals have lower fitness: – They are more likely to be homozygous for rare genetic defects – They are less likely to be heterozygous for immune-system genes ˆ Inbreeding depression is a serious concern for conservation – As populations get smaller, inbreeding becomes more common ˆ Wildlife studies show that panthers with both parents from Florida (small population) do not survive well ˆ Human demographic studies show strikingly lower survival for children of first cousins 4.2 Sexual selection ˆ Sexual selection is a form of natural selection ˆ Occurs when there is heritable variation in traits related to success in obtaining mates 12 Example: Pukeko ˆ Studied by Quinn lab here at Mac ˆ Hypothesis: Bright crests make males more attractive to females Activity: Pukeko experiments ˆ POLL How would you test this hypothesis? – Answer: Give some males bigger or brighter crests * Answer: Paint, cardboard, dietary supplement – Answer: Test whether they are preferred by females Pukeko analysis ˆ Why not simply find and use birds with naturally better crests? – Answer: The crests may be better because they differ in other ways (bigger, healthier, etc.) – Answer: We always want to make groups as similar as we can ˆ What is a concern with the methods proposed? What could you do about it? – Answer: Whatever we do to improve the crests may have other effects – Answer: Try to compensate and make treatment and control as similar as possible Why the males? ˆ Males often have striking traits that females lack, used in courtship, or in battles for mates – Sexual dimorphism refers to trait differences between males and females ˆ Why do males more often have these traits than females? – Investment in reproduction – Variation in reproductive success Investment in reproduction ˆ In many species, females invest much more in each offspring than males do – Eggs are expensive, sperm are cheap – Females are often more involved in caring for offspring ˆ If females invest a lot in each offspring, they can maximize fitness by being choosy about mates ˆ If males invest little in each offspring, they can maximize fitness by mating as much as possible 13 Testing the theory ˆ POLL How might we test the theory that males compete more sexually because females invest more in offspring? – Answer: Are there any species where these roles seem to be reversed? * Answer: Yes, in some species of pipefish (related to seahorses) the males spend more time and energy caring for young them females – Answer: In these species, do females compete for males? * Answer: Yes, females are larger than males, and develop bright colors at courtship time Variation in reproductive success ˆ Males often have greater variation in reproductive success than females do ˆ This is a side-effect of the fact that females usually invest a lot in each offspring – Reduces potential total number of offspring – Makes females desirable to males ˆ Greater variation in reproductive success means that winning contests is more important to male than female fitness Example: elephant seals ˆ Male elephant seals compete for control of breeding beaches ˆ Huge variation in reproductive success ˆ Huge size difference between males and females (strong sexual dimorphism) Conclusions ˆ Mutation (mistakes!) is the source of new variation ˆ Natural selection drives adaptation: selects variation that allows organisms to thrive in diverse settings ˆ Sex facilitates new combinations, but sexual selection can work against adaptation to the environment ˆ Genetic drift and gene flow are also non-adaptive drivers of evolution ˆ The organisms we see are the result of all of these processes: – adaptive, non-adaptive, previously adaptive © 2017–2023, Jonathan Dushoff and the 1M teaching team. 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